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  • A Multi-tissue Transcriptome Analysis of Human Metabolites Guides Interpretability of Associations Based on Multi-SNP Models for Gene Expression
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2020-01-23
    Anne Ndungu; Anthony Payne; Jason M. Torres; Martijn van de Bunt; Mark I. McCarthy

    There is particular interest in transcriptome-wide association studies (TWAS) gene-level tests based on multi-SNP predictive models of gene expression—for identifying causal genes at loci associated with complex traits. However, interpretation of TWAS associations may be complicated by divergent effects of model SNPs on phenotype and gene expression. We developed an iterative modeling scheme for obtaining multi-SNP models of gene expression and applied this framework to generate expression models for 43 human tissues from the Genotype-Tissue Expression (GTEx) Project. We characterized the performance of single- and multi-SNP models for identifying causal genes in GWAS data for 46 circulating metabolites. We show that: (A) multi-SNP models captured more variation in expression than did the top cis-eQTL (median 2-fold improvement); (B) predicted expression based on multi-SNP models was associated (false discovery rate < 0.01) with metabolite levels for 826 unique gene-metabolite pairs, but, after stepwise conditional analyses, 90% were dominated by a single eQTL SNP; (C) among the 35% of associations where a SNP in the expression model was a significant cis-eQTL and metabolomic-QTL (met-QTL), 92% demonstrated colocalization between these signals, but interpretation was often complicated by incomplete overlap of QTLs in multi-SNP models; and (D) using a “truth” set of causal genes at 61 met-QTLs, the sensitivity was high (67%), but the positive predictive value was low, as only 8% of TWAS associations (19% when restricted to colocalized associations at met-QTLs) involved true causal genes. These results guide the interpretation of TWAS and highlight the need for corroborative data to provide confident assignment of causality.

  • TTC12 Loss-of-Function Mutations Cause Primary Ciliary Dyskinesia and Unveil Distinct Dynein Assembly Mechanisms in Motile Cilia Versus Flagella
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2020-01-23
    Lucie Thomas; Khaled Bouhouche; Marjorie Whitfield; Guillaume Thouvenin; Andre Coste; Bruno Louis; Claire Szymanski; Emilie Bequignon; Jean-François Papon; Manon Castelli; Michel Lemullois; Xavier Dhalluin; Valérie Drouin-Garraud; Guy Montantin; Sylvie Tissier; Philippe Duquesnoy; Bruno Copin; Florence Dastot; Marie Legendre

    Cilia and flagella are evolutionarily conserved organelles whose motility relies on the outer and inner dynein arm complexes (ODAs and IDAs). Defects in ODAs and IDAs result in primary ciliary dyskinesia (PCD), a disease characterized by recurrent airway infections and male infertility. PCD mutations in assembly factors have been shown to cause a combined ODA-IDA defect, affecting both cilia and flagella. We identified four loss-of-function mutations in TTC12, which encodes a cytoplasmic protein, in four independent families in which affected individuals displayed a peculiar PCD phenotype characterized by the absence of ODAs and IDAs in sperm flagella, contrasting with the absence of only IDAs in respiratory cilia. Analyses of both primary cells from individuals carrying TTC12 mutations and human differentiated airway cells invalidated for TTC12 by a CRISPR-Cas9 approach revealed an IDA defect restricted to a subset of single-headed IDAs that are different in flagella and cilia, whereas TTC12 depletion in the ciliate Paramecium tetraurelia recapitulated the sperm phenotype. Overall, our study, which identifies TTC12 as a gene involved in PCD, unveils distinct dynein assembly mechanisms in human motile cilia versus flagella.

  • Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2020-01-09
    David B. Beck; Ana Petracovici; Chongsheng He; Hannah W. Moore; Raymond J. Louie; Muhammad Ansar; Sofia Douzgou; Sivagamy Sithambaram; Trudie Cottrell; Regie Lyn P. Santos-Cortez; Eloise J. Prijoles; Renee Bend; Boris Keren; Cyril Mignot; Marie-Christine Nougues; Katrin Õunap; Tiia Reimand; Sander Pajusalu; Jill A. Fahrner

    Germline pathogenic variants in chromatin-modifying enzymes are a common cause of pediatric developmental disorders. These enzymes catalyze reactions that regulate epigenetic inheritance via histone post-translational modifications and DNA methylation. Cytosine methylation (5-methylcytosine [5mC]) of DNA is the quintessential epigenetic mark, yet no human Mendelian disorder of DNA demethylation has yet been delineated. Here, we describe in detail a Mendelian disorder caused by the disruption of DNA demethylation. TET3 is a methylcytosine dioxygenase that initiates DNA demethylation during early zygote formation, embryogenesis, and neuronal differentiation and is intolerant to haploinsufficiency in mice and humans. We identify and characterize 11 cases of human TET3 deficiency in eight families with the common phenotypic features of intellectual disability and/or global developmental delay; hypotonia; autistic traits; movement disorders; growth abnormalities; and facial dysmorphism. Mono-allelic frameshift and nonsense variants in TET3 occur throughout the coding region. Mono-allelic and bi-allelic missense variants localize to conserved residues; all but one such variant occur within the catalytic domain, and most display hypomorphic function in an assay of catalytic activity. TET3 deficiency and other Mendelian disorders of the epigenetic machinery show substantial phenotypic overlap, including features of intellectual disability and abnormal growth, underscoring shared disease mechanisms.

  • A Robust Method Uncovers Significant Context-Specific Heritability in Diverse Complex Traits
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2020-01-02
    Andy Dahl; Khiem Nguyen; Na Cai; Michael J. Gandal; Jonathan Flint; Noah Zaitlen

    Gene-environment interactions (GxE) can be fundamental in applications ranging from functional genomics to precision medicine and is a conjectured source of substantial heritability. However, unbiased methods to profile GxE genome-wide are nascent and, as we show, cannot accommodate general environment variables, modest sample sizes, heterogeneous noise, and binary traits. To address this gap, we propose a simple, unifying mixed model for gene-environment interaction (GxEMM). In simulations and theory, we show that GxEMM can dramatically improve estimates and eliminate false positives when the assumptions of existing methods fail. We apply GxEMM to a range of human and model organism datasets and find broad evidence of context-specific genetic effects, including GxSex, GxAdversity, and GxDisease interactions across thousands of clinical and molecular phenotypes. Overall, GxEMM is broadly applicable for testing and quantifying polygenic interactions, which can be useful for explaining heritability and invaluable for determining biologically relevant environments.

  • Neuron-Derived Neurotrophic Factor Is Mutated in Congenital Hypogonadotropic Hypogonadism
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-12-26
    Andrea Messina; Kristiina Pulli; Sara Santini; James Acierno; Johanna Känsäkoski; Daniele Cassatella; Cheng Xu; Filippo Casoni; Samuel A. Malone; Gaetan Ternier; Daniele Conte; Yisrael Sidis; Johanna Tommiska; Kirsi Vaaralahti; Andrew Dwyer; Yoav Gothilf; Giorgio R. Merlo; Federico Santoni; Nelly Pitteloud

    Congenital hypogonadotropic hypogonadism (CHH) is a rare genetic disorder characterized by infertility and the absence of puberty. Defects in GnRH neuron migration or altered GnRH secretion and/or action lead to a severe gonadotropin-releasing hormone (GnRH) deficiency. Given the close developmental association of GnRH neurons with the olfactory primary axons, CHH is often associated with anosmia or hyposmia, in which case it is defined as Kallmann syndrome (KS). The genetics of CHH are heterogeneous, and >40 genes are involved either alone or in combination. Several CHH-related genes controlling GnRH ontogeny encode proteins containing fibronectin-3 (FN3) domains, which are important for brain and neural development. Therefore, we hypothesized that defects in other FN3-superfamily genes would underlie CHH. Next-generation sequencing was performed for 240 CHH unrelated probands and filtered for rare, protein-truncating variants (PTVs) in FN3-superfamily genes. Compared to gnomAD controls the CHH cohort was statistically enriched for PTVs in neuron-derived neurotrophic factor (NDNF) (p = 1.40 × 10−6). Three heterozygous PTVs (p.Lys62∗, p.Tyr128Thrfs∗55, and p.Trp469∗, all absent from the gnomAD database) and an additional heterozygous missense mutation (p.Thr201Ser) were found in four KS probands. Notably, NDNF is expressed along the GnRH neuron migratory route in both mouse embryos and human fetuses and enhances GnRH neuron migration. Further, knock down of the zebrafish ortholog of NDNF resulted in altered GnRH migration. Finally, mice lacking Ndnf showed delayed GnRH neuron migration and altered olfactory axonal projections to the olfactory bulb; both results are consistent with a role of NDNF in GnRH neuron development. Altogether, our results highlight NDNF as a gene involved in the GnRH neuron migration implicated in KS.

  • Loss-of-Function Variants in PPP1R12A: From Isolated Sex Reversal to Holoprosencephaly Spectrum and Urogenital Malformations
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-12-26
    Joel J. Hughes; Ebba Alkhunaizi; Paul Kruszka; Louise C. Pyle; Dorothy K. Grange; Seth I. Berger; Katelyn K. Payne; Diane Masser-Frye; Tommy Hu; Michelle R. Christie; Nancy J. Clegg; Joshua L. Everson; Ariel F. Martinez; Laurence E. Walsh; Emma Bedoukian; Marilyn C. Jones; Catharine Jean Harris; Korbinian M. Riedhammer; David Chitayat

    In two independent ongoing next-generation sequencing projects for individuals with holoprosencephaly and individuals with disorders of sex development, and through international research collaboration, we identified twelve individuals with de novo loss-of-function (LoF) variants in protein phosphatase 1, regulatory subunit 12a (PPP1R12A), an important developmental gene involved in cell migration, adhesion, and morphogenesis. This gene has not been previously reported in association with human disease, and it has intolerance to LoF as illustrated by a very low observed-to-expected ratio of LoF variants in gnomAD. Of the twelve individuals, midline brain malformations were found in five, urogenital anomalies in nine, and a combination of both phenotypes in two. Other congenital anomalies identified included omphalocele, jejunal, and ileal atresia with aberrant mesenteric blood supply, and syndactyly. Six individuals had stop gain variants, five had a deletion or duplication resulting in a frameshift, and one had a canonical splice acceptor site loss. Murine and human in situ hybridization and immunostaining revealed PPP1R12A expression in the prosencephalic neural folds and protein localization in the lower urinary tract at critical periods for forebrain division and urogenital development. Based on these clinical and molecular findings, we propose the association of PPP1R12A pathogenic variants with a congenital malformations syndrome affecting the embryogenesis of the brain and genitourinary systems and including disorders of sex development.

  • Bi-Allelic UQCRFS1 Variants Are Associated with Mitochondrial Complex III Deficiency, Cardiomyopathy, and Alopecia Totalis
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-12-26
    Mirjana Gusic; Gudrun Schottmann; René G. Feichtinger; Chen Du; Caroline Scholz; Matias Wagner; Johannes A. Mayr; Chae-Young Lee; Vicente A. Yépez; Norbert Lorenz; Susanne Morales-Gonzalez; Daan M. Panneman; Agnès Rötig; Richard J.T. Rodenburg; Saskia B. Wortmann; Holger Prokisch; Markus Schuelke

    Isolated complex III (CIII) deficiencies are among the least frequently diagnosed mitochondrial disorders. Clinical symptoms range from isolated myopathy to severe multi-systemic disorders with early death and disability. To date, we know of pathogenic variants in genes encoding five out of 10 subunits and five out of 13 assembly factors of CIII. Here we describe rare bi-allelic variants in the gene of a catalytic subunit of CIII, UQCRFS1, which encodes the Rieske iron-sulfur protein, in two unrelated individuals. Affected children presented with low CIII activity in fibroblasts, lactic acidosis, fetal bradycardia, hypertrophic cardiomyopathy, and alopecia totalis. Studies in proband-derived fibroblasts showed a deleterious effect of the variants on UQCRFS1 protein abundance, mitochondrial import, CIII assembly, and cellular respiration. Complementation studies via lentiviral transduction and overexpression of wild-type UQCRFS1 restored mitochondrial function and rescued the cellular phenotype, confirming UQCRFS1 variants as causative for CIII deficiency. We demonstrate that mutations in UQCRFS1 can cause mitochondrial disease, and our results thereby expand the clinical and mutational spectrum of CIII deficiencies.

  • Allelic Heterogeneity at the CRP Locus Identified by Whole-Genome Sequencing in Multi-ancestry Cohorts
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-12-26
    Laura M. Raffield; Apoorva K. Iyengar; Biqi Wang; Sheila M. Gaynor; Cassandra N. Spracklen; Xue Zhong; Madeline H. Kowalski; Shabnam Salimi; Linda M. Polfus; Emelia J. Benjamin; Joshua C. Bis; Russell Bowler; Brian E. Cade; Won Jung Choi; Alejandro P. Comellas; Adolfo Correa; Pedro Cruz; Harsha Doddapaneni; Paul L. Auer

    Whole-genome sequencing (WGS) can improve assessment of low-frequency and rare variants, particularly in non-European populations that have been underrepresented in existing genomic studies. The genetic determinants of C-reactive protein (CRP), a biomarker of chronic inflammation, have been extensively studied, with existing genome-wide association studies (GWASs) conducted in >200,000 individuals of European ancestry. In order to discover novel loci associated with CRP levels, we examined a multi-ancestry population (n = 23,279) with WGS (∼38× coverage) from the Trans-Omics for Precision Medicine (TOPMed) program. We found evidence for eight distinct associations at the CRP locus, including two variants that have not been identified previously (rs11265259 and rs181704186), both of which are non-coding and more common in individuals of African ancestry (∼10% and ∼1% minor allele frequency, respectively, and rare or monomorphic in 1000 Genomes populations of East Asian, South Asian, and European ancestry). We show that the minor (G) allele of rs181704186 is associated with lower CRP levels and decreased transcriptional activity and protein binding in vitro, providing a plausible molecular mechanism for this African ancestry-specific signal. The individuals homozygous for rs181704186-G have a mean CRP level of 0.23 mg/L, in contrast to individuals heterozygous for rs181704186 with mean CRP of 2.97 mg/L and major allele homozygotes with mean CRP of 4.11 mg/L. This study demonstrates the utility of WGS in multi-ethnic populations to drive discovery of complex trait associations of large effect and to identify functional alleles in noncoding regulatory regions.

  • Bi-Allelic Mutations in NADSYN1 Cause Multiple Organ Defects and Expand the Genotypic Spectrum of Congenital NAD Deficiency Disorders
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-12-26
    Justin O. Szot; Carla Campagnolo; Ye Cao; Kavitha R. Iyer; Hartmut Cuny; Thomas Drysdale; Josue A. Flores-Daboub; Weimin Bi; Lauren Westerfield; Pengfei Liu; Tse Ngong Leung; Kwong Wai Choy; Gavin Chapman; Rui Xiao; Victoria M. Siu; Sally L. Dunwoodie

    Birth defects occur in up to 3% of all live births and are the leading cause of infant death. Here we present five individuals from four unrelated families, individuals who share similar phenotypes with disease-causal bi-allelic variants in NADSYN1, encoding NAD synthetase 1, the final enzyme of the nicotinamide adenine dinucleotide (NAD) de novo synthesis pathway. Defects range from the isolated absence of both kidneys to multiple malformations of the vertebrae, heart, limbs, and kidney, and no affected individual survived for more than three months postnatally. NAD is an essential coenzyme for numerous cellular processes. Bi-allelic loss-of-function mutations in genes required for the de novo synthesis of NAD were previously identified in individuals with multiple congenital abnormalities affecting the heart, kidney, vertebrae, and limbs. Functional assessments of NADSYN1 missense variants, through a combination of yeast complementation and enzymatic assays, show impaired enzymatic activity and severely reduced NAD levels. Thus, NADSYN1 represents an additional gene required for NAD synthesis during embryogenesis, and NADSYN1 has bi-allelic missense variants that cause NAD deficiency-dependent malformations. Our findings expand the genotypic spectrum of congenital NAD deficiency disorders and further implicate mutation of additional genes involved in de novo NAD synthesis as potential causes of complex birth defects.

  • Complete Sequence of the 22q11.2 Allele in 1,053 Subjects with 22q11.2 Deletion Syndrome Reveals Modifiers of Conotruncal Heart Defects
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-12-20
    Yingjie Zhao; Alexander Diacou; H. Richard Johnston; Fadi I. Musfee; Donna M. McDonald-McGinn; Daniel McGinn; T. Blaine Crowley; Gabriela M. Repetto; Ann Swillen; Jeroen Breckpot; Joris R. Vermeesch; Wendy R. Kates; M. Cristina Digilio; Marta Unolt; Bruno Marino; Maria Pontillo; Marco Armando; Fabio Di Fabio; Bernice E. Morrow

    The 22q11.2 deletion syndrome (22q11.2DS) results from non-allelic homologous recombination between low-copy repeats termed LCR22. About 60%–70% of individuals with the typical 3 megabase (Mb) deletion from LCR22A-D have congenital heart disease, mostly of the conotruncal type (CTD), whereas others have normal cardiac anatomy. In this study, we tested whether variants in the hemizygous LCR22A-D region are associated with risk for CTDs on the basis of the sequence of the 22q11.2 region from 1,053 22q11.2DS individuals. We found a significant association (FDR p < 0.05) of the CTD subset with 62 common variants in a single linkage disequilibrium (LD) block in a 350 kb interval harboring CRKL. A total of 45 of the 62 variants were associated with increased risk for CTDs (odds ratio [OR) ranges: 1.64–4.75). Associations of four variants were replicated in a meta-analysis of three genome-wide association studies of CTDs in affected individuals without 22q11.2DS. One of the replicated variants, rs178252, is located in an open chromatin region and resides in the double-elite enhancer, GH22J020947, that is predicted to regulate CRKL (CRK-like proto-oncogene, cytoplasmic adaptor) expression. Approximately 23% of patients with nested LCR22C-D deletions have CTDs, and inactivation of Crkl in mice causes CTDs, thus implicating this gene as a modifier. Rs178252 and rs6004160 are expression quantitative trait loci (eQTLs) of CRKL. Furthermore, set-based tests identified an enhancer that is predicted to target CRKL and is significantly associated with CTD risk (GH22J020946, sequence kernal association test (SKAT) p = 7.21 × 10−5) in the 22q11.2DS cohort. These findings suggest that variance in CTD penetrance in the 22q11.2DS population can be explained in part by variants affecting CRKL expression.

  • Pathogenic Bi-Allelic Mutations in NDUFAF8 Cause Leigh Syndrome with an Isolated Complex I Deficiency
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-12-19
    Charlotte L. Alston; Mike T. Veling; Juliana Heidler; Lucie S. Taylor; Joseph T. Alaimo; Andrew Y. Sung; Langping He; Sila Hopton; Alexander Broomfield; Julija Pavaine; Jullianne Diaz; Eyby Leon; Philipp Wolf; Robert McFarland; Holger Prokisch; Saskia B. Wortmann; Penelope E. Bonnen; Ilka Wittig; Robert W. Taylor

    Leigh syndrome is one of the most common neurological phenotypes observed in pediatric mitochondrial disease presentations. It is characterized by symmetrical lesions found on neuroimaging in the basal ganglia, thalamus, and brainstem and by a loss of motor skills and delayed developmental milestones. Genetic diagnosis of Leigh syndrome is complicated on account of the vast genetic heterogeneity with >75 candidate disease-associated genes having been reported to date. Candidate genes are still emerging, being identified when “omics” tools (genomics, proteomics, and transcriptomics) are applied to manipulated cell lines and cohorts of clinically characterized individuals who lack a genetic diagnosis. NDUFAF8 is one such protein; it has been found to interact with the well-characterized complex I (CI) assembly factor NDUFAF5 in a large-scale protein-protein interaction screen. Diagnostic next-generation sequencing has identified three unrelated pediatric subjects, each with a clinical diagnosis of Leigh syndrome, who harbor bi-allelic pathogenic variants in NDUFAF8. These variants include a recurrent splicing variant that was initially overlooked due to its deep-intronic location. Subject fibroblasts were found to express a complex I deficiency, and lentiviral transduction with wild-type NDUFAF8-cDNA ameliorated both the assembly defect and the biochemical deficiency. Complexome profiling of subject fibroblasts demonstrated a complex I assembly defect, and the stalled assembly intermediates corroborate the role of NDUFAF8 in early complex I assembly. This report serves to expand the genetic heterogeneity associated with Leigh syndrome and to validate the clinical utility of orphan protein characterization. We also highlight the importance of evaluating intronic sequence when a single, definitively pathogenic variant is identified during diagnostic testing.

  • SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-12-19
    Samantha L.P. Schilit; Shreya Menon; Corinna Friedrich; Tammy Kammin; Ellen Wilch; Carrie Hanscom; Sizun Jiang; Sabine Kliesch; Michael E. Talkowski; Frank Tüttelmann; Amy J. MacQueen; Cynthia C. Morton

    Unexplained infertility affects 2%–3% of reproductive-aged couples. One approach to identifying genes involved in infertility is to study subjects with this clinical phenotype and a de novo balanced chromosomal aberration (BCA). While BCAs may reduce fertility by production of unbalanced gametes, a chromosomal rearrangement may also disrupt or dysregulate genes important in fertility. One such subject, DGAP230, has severe oligozoospermia and 46,XY,t(20;22)(q13.3;q11.2). We identified exclusive overexpression of SYCP2 from the der(20) allele that is hypothesized to result from enhancer adoption. Modeling the dysregulation in budding yeast resulted in disrupted structural integrity of the synaptonemal complex, a common cause of defective spermatogenesis in mammals. Exome sequencing of infertile males revealed three heterozygous SYCP2 frameshift variants in additional subjects with cryptozoospermia and azoospermia. In sum, this investigation illustrates the power of precision cytogenetics for annotation of the infertile genome, suggests that these mechanisms should be considered as an alternative etiology to that of segregation of unbalanced gametes in infertile men harboring a BCA, and provides evidence of SYCP2-mediated male infertility in humans.

  • UK Biobank Whole-Exome Sequence Binary Phenome Analysis with Robust Region-based Rare-Variant Test
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-12-19
    Zhangchen Zhao; Wenjian Bi; Wei Zhou; Peter VandeHaar; Lars G. Fritsche; Seunggeun Lee

    In biobank data analysis, most binary phenotypes have unbalanced case-control ratios, and this can cause inflation of type I error rates. Recently, a saddle point approximation (SPA) based single-variant test has been developed to provide an accurate and scalable method to test for associations of such phenotypes. For gene- or region-based multiple-variant tests, a few methods exist that can adjust for unbalanced case-control ratios; however, these methods are either less accurate when case-control ratios are extremely unbalanced or not scalable for large data analyses. To address these problems, we propose SKAT- and SKAT-O- type region-based tests; in these tests, the single-variant score statistic is calibrated based on SPA and efficient resampling (ER). Through simulation studies, we show that the proposed method provides well-calibrated p values. In contrast, when the case-control ratio is 1:99, the unadjusted approach has greatly inflated type I error rates (90 times that of exome-wide sequencing α = 2.5 × 10−6). Additionally, the proposed method has similar computation time to the unadjusted approaches and is scalable for large sample data. In our application, the UK Biobank whole-exome sequence data analysis of 45,596 unrelated European samples and 791 PheCode phenotypes identified 10 rare-variant associations with p value < 10−7, including the associations between JAK2 and myeloproliferative disease, HOXB13 and cancer of prostate, and F11 and congenital coagulation defects. All analysis summary results are publicly available through a web-based visual server, and this availability can help facilitate the identification of the genetic basis of complex diseases.

  • Gain-of-Function MN1 Truncation Variants Cause a Recognizable Syndrome with Craniofacial and Brain Abnormalities
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-12-12
    Noriko Miyake; Hidehisa Takahashi; Kazuyuki Nakamura; Bertrand Isidor; Yoko Hiraki; Eriko Koshimizu; Masaaki Shiina; Kazunori Sasaki; Hidefumi Suzuki; Ryota Abe; Yayoi Kimura; Tomoko Akiyama; Shin-ichi Tomizawa; Tomonori Hirose; Kohei Hamanaka; Satoko Miyatake; Satomi Mitsuhashi; Takeshi Mizuguchi; Naomichi Matsumoto

    MN1 was originally identified as a tumor-suppressor gene. Knockout mouse studies have suggested that Mn1 is associated with craniofacial development. However, no MN1-related phenotypes have been established in humans. Here, we report on three individuals who have de novo MN1 variants that lead to a protein lacking the carboxyl (C) terminus and who presented with severe developmental delay, craniofacial abnormalities with specific facial features, and structural abnormalities in the brain. An in vitro study revealed that the deletion of the C-terminal region led to increased protein stability, an inhibitory effect on cell proliferation, and enhanced MN1 aggregation in nuclei compared to what occurred in the wild type, suggesting that a gain-of-function mechanism is involved in this disease. Considering that C-terminal deletion increases the fraction of intrinsically disordered regions of MN1, it is possible that altered phase separation could be involved in the mechanism underlying the disease. Our data indicate that MN1 participates in transcriptional regulation of target genes through interaction with the transcription factors PBX1, PKNOX1, and ZBTB24 and that mutant MN1 impairs the binding with ZBTB24 and RING1, which is an E3 ubiquitin ligase. On the basis of our findings, we propose the model that C-terminal deletion interferes with MN1’s interaction molecules related to the ubiquitin-mediated proteasome pathway, including RING1, and increases the amount of the mutant protein; this increase leads to the dysregulation of MN1 target genes by inhibiting rapid MN1 protein turnover.

  • Identification of African-Specific Admixture between Modern and Archaic Humans
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-12-05
    Jeffrey D. Wall, Aakrosh Ratan, Eric Stawiski

    Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.

  • Sex-Based Analysis of De Novo Variants in Neurodevelopmental Disorders
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-27
    Tychele N. Turner, Amy B. Wilfert, Trygve E. Bakken, Raphael A. Bernier, Micah R. Pepper, Zhancheng Zhang, Rebecca I. Torene, Kyle Retterer, Evan E. Eichler

    While genes with an excess of de novo mutations (DNMs) have been identified in children with neurodevelopmental disorders (NDDs), few studies focus on DNM patterns where the sex of affected children is examined separately. We considered ∼8,825 sequenced parent-child trios (n ∼26,475 individuals) and identify 54 genes with a DNM enrichment in males (n = 18), females (n = 17), or overlapping in both the male and female subsets (n = 19). A replication cohort of 18,778 sequenced parent-child trios (n = 56,334 individuals) confirms 25 genes (n = 3 in males, n = 7 in females, n = 15 in both male and female subsets). As expected, we observe significant enrichment on the X chromosome for females but also find autosomal genes with potential sex bias (females, CDK13, ITPR1; males, CHD8, MBD5, SYNGAP1); 6.5% of females harbor a DNM in a female-enriched gene, whereas 2.7% of males have a DNM in a male-enriched gene. Sex-biased genes are enriched in transcriptional processes and chromatin binding, primarily reside in the nucleus of cells, and have brain expression. By downsampling, we find that DNM gene discovery is greatest when studying affected females. Finally, directly comparing de novo allele counts in NDD-affected males and females identifies one replicated genome-wide significant gene (DDX3X) with locus-specific enrichment in females. Our sex-based DNM enrichment analysis identifies candidate NDD genes differentially affecting males and females and indicates that the study of females with NDDs leads to greater gene discovery consistent with the female-protective effect.

  • Validation Studies for Single Circulating Trophoblast Genetic Testing as a Form of Noninvasive Prenatal Diagnosis
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-27
    Liesbeth Vossaert, Qun Wang, Roseen Salman, Anne K. McCombs, Vipulkumar Patel, Chunjing Qu, Michael A. Mancini, Dean P. Edwards, Anna Malovannaya, Pengfei Liu, Chad A. Shaw, Brynn Levy, Ronald J. Wapner, Weimin Bi, Amy M. Breman, Ignatia B. Van den Veyver, Arthur L. Beaudet

    It has long been appreciated that genetic analysis of fetal or trophoblast cells in maternal blood could revolutionize prenatal diagnosis. We implemented a protocol for single circulating trophoblast (SCT) testing using positive selection by magnetic-activated cell sorting and single-cell low-coverage whole-genome sequencing to detect fetal aneuploidies and copy-number variants (CNVs) at ∼1 Mb resolution. In 95 validation cases, we identified on average 0.20 putative trophoblasts/mL, of which 55% were of high quality and scorable for both aneuploidy and CNVs. We emphasize the importance of analyzing individual cells because some cells are apoptotic, in S-phase, or otherwise of poor quality. When two or more high-quality trophoblast cells were available for singleton pregnancies, there was complete concordance between all trophoblasts unless there was evidence of confined placental mosaicism. SCT results were highly concordant with available clinical data from chorionic villus sampling (CVS) or amniocentesis procedures. Although determining the exact sensitivity and specificity will require more data, this study further supports the potential for SCT testing to become a diagnostic prenatal test.

  • Loss of Oxidation Resistance 1, OXR1, Is Associated with an Autosomal-Recessive Neurological Disease with Cerebellar Atrophy and Lysosomal Dysfunction
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-27
    Julia Wang, Justine Rousseau, Emily Kim, Sophie Ehresmann, Yi-Ting Cheng, Lita Duraine, Zhongyuan Zuo, Ye-Jin Park, David Li-Kroeger, Weimin Bi, Lee-Jun Wong, Jill Rosenfeld, Joseph Gleeson, Eissa Faqeih, Fowzan S. Alkuraya, Klaas J. Wierenga, Jiani Chen, Alexandra Afenjar, Philippe M. Campeau

    We report an early-onset autosomal-recessive neurological disease with cerebellar atrophy and lysosomal dysfunction. We identified bi-allelic loss-of-function (LoF) variants in Oxidative Resistance 1 (OXR1) in five individuals from three families; these individuals presented with a history of severe global developmental delay, current intellectual disability, language delay, cerebellar atrophy, and seizures. While OXR1 is known to play a role in oxidative stress resistance, its molecular functions are not well established. OXR1 contains three conserved domains: LysM, GRAM, and TLDc. The gene encodes at least six transcripts, including some that only consist of the C-terminal TLDc domain. We utilized Drosophila to assess the phenotypes associated with loss of mustard (mtd), the fly homolog of OXR1. Strong LoF mutants exhibit late pupal lethality or pupal eclosion defects. Interestingly, although mtd encodes 26 transcripts, severe LoF and null mutations can be rescued by a single short human OXR1 cDNA that only contains the TLDc domain. Similar rescue is observed with the TLDc domain of NCOA7, another human homolog of mtd. Loss of mtd in neurons leads to massive cell loss, early death, and an accumulation of aberrant lysosomal structures, similar to what we observe in fibroblasts of affected individuals. Our data indicate that mtd and OXR1 are required for proper lysosomal function; this is consistent with observations that NCOA7 is required for lysosomal acidification.

  • Integrating Clinical Data and Imputed Transcriptome from GWAS to Uncover Complex Disease Subtypes: Applications in Psychiatry and Cardiology
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-27
    Liangying Yin, Carlos K.L. Chau, Pak-Chung Sham, Hon-Cheong So

    Classifying subjects into clinically and biologically homogeneous subgroups will facilitate the understanding of disease pathophysiology and development of targeted prevention and intervention strategies. Traditionally, disease subtyping is based on clinical characteristics alone, but subtypes identified by such an approach may not conform exactly to the underlying biological mechanisms. Very few studies have integrated genomic profiles (e.g., those from GWASs) with clinical symptoms for disease subtyping. Here we proposed an analytic framework capable of finding complex diseases subgroups by leveraging both GWAS-predicted gene expression levels and clinical data by a multi-view bicluster analysis. This approach connects SNPs to genes via their effects on expression, so the analysis is more biologically relevant and interpretable than a pure SNP-based analysis. Transcriptome of different tissues can also be readily modeled. We also proposed various evaluation metrics for assessing clustering performance. Our framework was able to subtype schizophrenia subjects into diverse subgroups with different prognosis and treatment response. We also applied the framework to the Northern Finland Birth Cohort (NFBC) 1966 dataset and identified high and low cardiometabolic risk subgroups in a gender-stratified analysis. The prediction strength by cross-validation was generally greater than 80%, suggesting good stability of the clustering model. Our results suggest a more data-driven and biologically informed approach to defining metabolic syndrome and subtyping psychiatric disorders. Moreover, we found that the genes “blindly” selected by the algorithm are significantly enriched for known susceptibility genes discovered in GWASs of schizophrenia or cardiovascular diseases. The proposed framework opens up an approach to subject stratification.

  • Homozygous Null TBX4 Mutations Lead to Posterior Amelia with Pelvic and Pulmonary Hypoplasia
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-21
    Ariana Kariminejad, Emmanuelle Szenker-Ravi, Caroline Lekszas, Homa Tajsharghi, Ali-Reza Moslemi, Thomas Naert, Hong Thi Tran, Fatemeh Ahangari, Minoo Rajaei, Mojila Nasseri, Thomas Haaf, Afrooz Azad, Andrea Superti-Furga, Reza Maroofian, Siavash Ghaderi-Sohi, Hossein Najmabadi, Mohammad Reza Abbaszadegan, Kris Vleminckx, Bruno Reversade

    The development of hindlimbs in tetrapod species relies specifically on the transcription factor TBX4. In humans, heterozygous loss-of-function TBX4 mutations cause dominant small patella syndrome (SPS) due to haploinsufficiency. Here, we characterize a striking clinical entity in four fetuses with complete posterior amelia with pelvis and pulmonary hypoplasia (PAPPA). Through exome sequencing, we find that PAPPA syndrome is caused by homozygous TBX4 inactivating mutations during embryogenesis in humans. In two consanguineous couples, we uncover distinct germline TBX4 coding mutations, p.Tyr113∗ and p.Tyr127Asn, that segregated with SPS in heterozygous parents and with posterior amelia with pelvis and pulmonary hypoplasia syndrome (PAPPAS) in one available homozygous fetus. A complete absence of TBX4 transcripts in this proband with biallelic p.Tyr113∗ stop-gain mutations revealed nonsense-mediated decay of the endogenous mRNA. CRISPR/Cas9-mediated TBX4 deletion in Xenopus embryos confirmed its restricted role during leg development. We conclude that SPS and PAPPAS are allelic diseases of TBX4 deficiency and that TBX4 is an essential transcription factor for organogenesis of the lungs, pelvis, and hindlimbs in humans.

  • Making the Most of Clumping and Thresholding for Polygenic Scores
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-21
    Florian Privé, Bjarni J. Vilhjálmsson, Hugues Aschard, Michael G.B. Blum

    Polygenic prediction has the potential to contribute to precision medicine. Clumping and thresholding (C+T) is a widely used method to derive polygenic scores. When using C+T, several p value thresholds are tested to maximize predictive ability of the derived polygenic scores. Along with this p value threshold, we propose to tune three other hyper-parameters for C+T. We implement an efficient way to derive thousands of different C+T scores corresponding to a grid over four hyper-parameters. For example, it takes a few hours to derive 123K different C+T scores for 300K individuals and 1M variants using 16 physical cores. We find that optimizing over these four hyper-parameters improves the predictive performance of C+T in both simulations and real data applications as compared to tuning only the p value threshold. A particularly large increase can be noted when predicting depression status, from an AUC of 0.557 (95% CI: [0.544–0.569]) when tuning only the p value threshold to an AUC of 0.592 (95% CI: [0.580–0.604]) when tuning all four hyper-parameters we propose for C+T. We further propose stacked clumping and thresholding (SCT), a polygenic score that results from stacking all derived C+T scores. Instead of choosing one set of hyper-parameters that maximizes prediction in some training set, SCT learns an optimal linear combination of all C+T scores by using an efficient penalized regression. We apply SCT to eight different case-control diseases in the UK biobank data and find that SCT substantially improves prediction accuracy with an average AUC increase of 0.035 over standard C+T.

  • Genome-Wide Associations Reveal Human-Mouse Genetic Convergence and Modifiers of Myogenesis, CPNE1 and STC2
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-21
    Ana I. Hernandez Cordero, Natalia M. Gonzales, Clarissa C. Parker, Greta Sokolof, David J. Vandenbergh, Riyan Cheng, Mark Abney, Andrew Sko, Alex Douglas, Abraham A. Palmer, Jennifer S. Gregory, Arimantas Lionikas

    Muscle bulk in adult healthy humans is highly variable even after height, age, and sex are accounted for. Low muscle mass, due to fewer and/or smaller constituent muscle fibers, would exacerbate the impact of muscle loss occurring in aging or disease. Genetic variability substantially influences muscle mass differences, but causative genes remain largely unknown. In a genome-wide association study (GWAS) on appendicular lean mass (ALM) in a population of 85,750 middle-aged (aged 38–49 years) individuals from the UK Biobank (UKB), we found 182 loci associated with ALM (p < 5 × 10−8). We replicated associations for 78% of these loci (p < 5 × 10−8) with ALM in a population of 181,862 elderly (aged 60–74 years) individuals from UKB. We also conducted a GWAS on hindlimb skeletal muscle mass of 1,867 mice from an advanced intercross between two inbred strains (LG/J and SM/J); this GWAS identified 23 quantitative trait loci. Thirty-eight positional candidates distributed across five loci overlapped between the two species. In vitro studies of positional candidates confirmed CPNE1 and STC2 as modifiers of myogenesis. Collectively, these findings shed light on the genetics of muscle mass variability in humans and identify targets for the development of interventions for treatment of muscle loss. The overlapping results between humans and the mouse model GWAS point to shared genetic mechanisms across species.

  • Mutations in TTC29, Encoding an Evolutionarily Conserved Axonemal Protein, Result in Asthenozoospermia and Male Infertility
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-14
    Patrick Lorès, Denis Dacheux, Zine-Eddine Kherraf, Jean-Fabrice Nsota Mbango, Charles Coutton, Laurence Stouvenel, Come Ialy-Radio, Amir Amiri-Yekta, Marjorie Whitfield, Alain Schmitt, Caroline Cazin, Maëlle Givelet, Lucile Ferreux, Selima Fourati Ben Mustapha, Lazhar Halouani, Ouafi Marrakchi, Abbas Daneshipour, Elma El Khouri, Aminata Touré

    In humans, structural or functional defects of the sperm flagellum induce asthenozoospermia, which accounts for the main sperm defect encountered in infertile men. Herein we focused on morphological abnormalities of the sperm flagellum (MMAF), a phenotype also termed “short tails,” which constitutes one of the most severe sperm morphological defects resulting in asthenozoospermia. In previous work based on whole-exome sequencing of a cohort of 167 MMAF-affected individuals, we identified bi-allelic loss-of-function mutations in more than 30% of the tested subjects. In this study, we further analyzed this cohort and identified five individuals with homozygous truncating variants in TTC29, a gene preferentially and highly expressed in the testis, and encoding a tetratricopeptide repeat-containing protein related to the intraflagellar transport (IFT). One individual carried a frameshift variant, another one carried a homozygous stop-gain variant, and three carried the same splicing variant affecting a consensus donor site. The deleterious effect of this last variant was confirmed on the corresponding transcript and protein product. In addition, we produced and analyzed TTC29 loss-of-function models in the flagellated protist T. brucei and in M. musculus. Both models confirmed the importance of TTC29 for flagellar beating. We showed that in T. brucei the TPR structural motifs, highly conserved between the studied orthologs, are critical for TTC29 axonemal localization and flagellar beating. Overall our work demonstrates that TTC29 is a conserved axonemal protein required for flagellar structure and beating and that TTC29 mutations are a cause of male sterility due to MMAF.

  • Bi-allelic Mutations in TTC29 Cause Male Subfertility with Asthenoteratospermia in Humans and Mice
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-14
    Chunyu Liu, Xiaojin He, Wangjie Liu, Shenmin Yang, Lingbo Wang, Weiyu Li, Huan Wu, Shuyan Tang, Xiaoqing Ni, Jiaxiong Wang, Yang Gao, Shixiong Tian, Lin Zhang, Jiangshan Cong, Zhihua Zhang, Qing Tan, Jingjing Zhang, Hong Li, Feng Zhang

    As a type of severe asthenoteratospermia, multiple morphological abnormalities of the flagella (MMAF) are characterized by the presence of immotile spermatozoa with severe flagellar malformations. MMAF is a genetically heterogeneous disorder, and the known MMAF-associated genes can only account for approximately 60% of human MMAF cases. Here we conducted whole-exome sequencing and identified bi-allelic truncating mutations of the TTC29 (tetratricopeptide repeat domain 29) gene in three (3.8%) unrelated cases from a cohort of 80 MMAF-affected Han Chinese men. TTC29 is preferentially expressed in the testis, and TTC29 protein contains the tetratricopeptide repeat domains that play an important role in cilia- and flagella-associated functions. All of the men harboring TTC29 mutations presented a typical MMAF phenotype and dramatic disorganization in axonemal and/or other peri-axonemal structures. Immunofluorescence assays of spermatozoa from men harboring TTC29 mutations showed deficiency of TTC29 and remarkably reduced staining of intraflagellar-transport-complex-B-associated proteins (TTC30A and IFT52). We also generated a Ttc29-mutated mouse model through the use of CRISPR-Cas9 technology. Remarkably, Ttc29-mutated male mice also presented reduced sperm motility, abnormal flagellar ultrastructure, and male subfertility. Furthermore, intracytoplasmic sperm injections performed for Ttc29-mutated mice and men harboring TTC29 mutations consistently acquired satisfactory outcomes. Collectively, our experimental observations in humans and mice suggest that bi-allelic mutations in TTC29, as an important genetic pathogeny, can induce MMAF-related asthenoteratospermia. Our study also provided effective guidance for clinical diagnosis and assisted reproduction treatments.

  • A Fast and Accurate Method for Genome-Wide Scale Phenome-Wide G × E Analysis and Its Application to UK Biobank
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-14
    Wenjian Bi, Zhangchen Zhao, Rounak Dey, Lars G. Fritsche, Bhramar Mukherjee, Seunggeun Lee

    The etiology of most complex diseases involves genetic variants, environmental factors, and gene-environment interaction (G × E) effects. Compared with marginal genetic association studies, G × E analysis requires more samples and detailed measure of environmental exposures, and this limits the possible discoveries. Large-scale population-based biobanks with detailed phenotypic and environmental information, such as UK-Biobank, can be ideal resources for identifying G × E effects. However, due to the large computation cost and the presence of case-control imbalance, existing methods often fail. Here we propose a scalable and accurate method, SPAGE (SaddlePoint Approximation implementation of G × E analysis), that is applicable for genome-wide scale phenome-wide G × E studies. SPAGE fits a genotype-independent logistic model only once across the genome-wide analysis in order to reduce computation cost, and SPAGE uses a saddlepoint approximation (SPA) to calibrate the test statistics for analysis of phenotypes with unbalanced case-control ratios. Simulation studies show that SPAGE is 33–79 times faster than the Wald test and 72–439 times faster than the Firth’s test, and SPAGE can control type I error rates at the genome-wide significance level even when case-control ratios are extremely unbalanced. Through the analysis of UK-Biobank data of 344,341 white British European-ancestry samples, we show that SPAGE can efficiently analyze large samples while controlling for unbalanced case-control ratios.

  • TMX2 Is a Crucial Regulator of Cellular Redox State, and Its Dysfunction Causes Severe Brain Developmental Abnormalities
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-14
    Laura V. Vandervore, Rachel Schot, Chiara Milanese, Daphne J. Smits, Esmee Kasteleijn, Andrew E. Fry, Daniela T. Pilz, Stefanie Brock, Esra Börklü-Yücel, Marco Post, Nadia Bahi-Buisson, María José Sánchez-Soler, Marjon van Slegtenhorst, Boris Keren, Alexandra Afenjar, Stephanie A. Coury, Wen-Hann Tan, Renske Oegema, Grazia M.S. Mancini

    The redox state of the neural progenitors regulates physiological processes such as neuronal differentiation and dendritic and axonal growth. The relevance of endoplasmic reticulum (ER)-associated oxidoreductases in these processes is largely unexplored. We describe a severe neurological disorder caused by bi-allelic loss-of-function variants in thioredoxin (TRX)-related transmembrane-2 (TMX2); these variants were detected by exome sequencing in 14 affected individuals from ten unrelated families presenting with congenital microcephaly, cortical polymicrogyria, and other migration disorders. TMX2 encodes one of the five TMX proteins of the protein disulfide isomerase family, hitherto not linked to human developmental brain disease. Our mechanistic studies on protein function show that TMX2 localizes to the ER mitochondria-associated membranes (MAMs), is involved in posttranslational modification and protein folding, and undergoes physical interaction with the MAM-associated and ER folding chaperone calnexin and ER calcium pump SERCA2. These interactions are functionally relevant because TMX2-deficient fibroblasts show decreased mitochondrial respiratory reserve capacity and compensatory increased glycolytic activity. Intriguingly, under basal conditions TMX2 occurs in both reduced and oxidized monomeric form, while it forms a stable dimer under treatment with hydrogen peroxide, recently recognized as a signaling molecule in neural morphogenesis and axonal pathfinding. Exogenous expression of the pathogenic TMX2 variants or of variants with an in vitro mutagenized TRX domain induces a constitutive TMX2 polymerization, mimicking an increased oxidative state. Altogether these data uncover TMX2 as a sensor in the MAM-regulated redox signaling pathway and identify it as a key adaptive regulator of neuronal proliferation, migration, and organization in the developing brain.

  • TRIDENT-2: National Implementation of Genome-Wide Non-Invasive Prenatal Testing as a First-Tier Screening Test in the Netherlands
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-07
    Karuna R.M. van der Meij, Erik A. Sistermans, Merryn V.E. Macville, Servi J.C. Stevens, Caroline J. Bax, Mireille N. Bekker, Caterina M. Bilardo, Elles M.J. Boon, Marjan Boter, Karin E.M. Diderich, Christine E.M. de Die-Smulders, Leonie K. Duin, Brigitte H.W. Faas, Ilse Feenstra, Monique C. Haak, Mariëtte J.V. Hoffer, Nicolette S. den Hollander, Iris H.I.M. Hollink, Marjan M. Weiss

    The Netherlands launched a nationwide implementation study on non-invasive prenatal testing (NIPT) as a first-tier test offered to all pregnant women. This started on April 1, 2017 as the TRIDENT-2 study, licensed by the Dutch Ministry of Health. In the first year, NIPT was performed in 73,239 pregnancies (42% of all pregnancies), 7,239 (4%) chose first-trimester combined testing, and 54% did not participate. The number of trisomies 21 (239, 0.33%), 18 (49, 0.07%), and 13 (55, 0.08%) found in this study is comparable to earlier studies, but the Positive Predictive Values (PPV)—96% for trisomy 21, 98% for trisomy 18, and 53% for trisomy 13—were higher than expected. Findings other than trisomy 21, 18, or 13 were reported on request of the pregnant women; 78% of women chose to have these reported. The number of additional findings was 207 (0.36%); these included other trisomies (101, 0.18%, PPV 6%, many of the remaining 94% of cases are likely confined placental mosaics and possibly clinically significant), structural chromosomal aberrations (95, 0.16%, PPV 32%,) and complex abnormal profiles indicative of maternal malignancies (11, 0.02%, PPV 64%). The implementation of genome-wide NIPT is under debate because the benefits of detecting other fetal chromosomal aberrations must be balanced against the risks of discordant positives, parental anxiety, and a potential increase in (invasive) diagnostic procedures. Our first-year data, including clinical data and laboratory follow-up data, will fuel this debate. Furthermore, we describe how NIPT can successfully be embedded into a national screening program with a single chain for prenatal care including counseling, testing, and follow-up.

  • A Comprehensive Haplotype Targeting Strategy for Allele-Specific HTT Suppression in Huntington Disease
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-07
    Chris Kay, Jennifer A. Collins, Nicholas S. Caron, Luciana de Andrade Agostinho, Hailey Findlay-Black, Lorenzo Casal, Dulika Sumathipala, Vajira H.W. Dissanayake, Mario Cornejo-Olivas, Fiona Baine, Amanda Krause, Jacquie L. Greenberg, Carmen Lúcia Antão Paiva, Ferdinando Squitieri, Michael R. Hayden

    Huntington disease (HD) is a fatal neurodegenerative disorder caused by a gain-of-function mutation in HTT. Suppression of mutant HTT has emerged as a leading therapeutic strategy for HD, with allele-selective approaches targeting HTT SNPs now in clinical trials. Haplotypes associated with the HD mutation (A1, A2, A3a) represent panels of allele-specific gene silencing targets for efficient treatment of individuals with HD of Northern European and indigenous South American ancestry. Here we extend comprehensive haplotype analysis of the HD mutation to key populations of Southern European, South Asian, Middle Eastern, and admixed African ancestry. In each of these populations, the HD mutation occurs predominantly on the A2 HTT haplotype. Analysis of HD haplotypes across all affected population groups enables rational selection of candidate target SNPs for development of allele-selective gene silencing therapeutics worldwide. Targeting SNPs on the A1 and A2 haplotypes in parallel is essential to achieve treatment of the most HD-affected subjects in populations where HD is most prevalent. Current allele-specific approaches will leave a majority of individuals with HD untreated in populations where the HD mutation occurs most frequently on the A2 haplotype. We further demonstrate preclinical development of potent and selective ASOs targeting SNPs on the A2 HTT haplotype, representing an allele-specific treatment strategy for these individuals. On the basis of comprehensive haplotype analysis, we show the maximum proportion of HD-affected subjects that may be treated with three or four allele targets in different populations worldwide, informing current allele-specific HTT silencing strategies.

  • CAKUT and Autonomic Dysfunction Caused by Acetylcholine Receptor Mutations
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-11-07
    Nina Mann, Franziska Kause, Erik K. Henze, Anant Gharpure, Shirlee Shril, Dervla M. Connaughton, Makiko Nakayama, Verena Klämbt, Amar J. Majmundar, Chen-Han W. Wu, Caroline M. Kolvenbach, Rufeng Dai, Jing Chen, Amelie T. van der Ven, Hadas Ityel, Madeleine J. Tooley, Jameela A. Kari, Lucy Bownass, Friedhelm Hildebrandt

    Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause of chronic kidney disease in the first three decades of life, and in utero obstruction to urine flow is a frequent cause of secondary upper urinary tract malformations. Here, using whole-exome sequencing, we identified three different biallelic mutations in CHRNA3, which encodes the α3 subunit of the nicotinic acetylcholine receptor, in five affected individuals from three unrelated families with functional lower urinary tract obstruction and secondary CAKUT. Four individuals from two families have additional dysautonomic features, including impaired pupillary light reflexes. Functional studies in vitro demonstrated that the mutant nicotinic acetylcholine receptors were unable to generate current following stimulation with acetylcholine. Moreover, the truncating mutations p.Thr337Asnfs∗81 and p.Ser340∗ led to impaired plasma membrane localization of CHRNA3. Although the importance of acetylcholine signaling in normal bladder function has been recognized, we demonstrate for the first time that mutations in CHRNA3 can cause bladder dysfunction, urinary tract malformations, and dysautonomia. These data point to a pathophysiologic sequence by which monogenic mutations in genes that regulate bladder innervation may secondarily cause CAKUT.

  • Multivariate Genome-Wide Association Analysis of a Cytokine Network Reveals Variants with Widespread Immune, Haematological, and Cardiometabolic Pleiotropy
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-10-31
    Artika P. Nath, Scott C. Ritchie, Nastasiya F. Grinberg, Howard Ho-Fung Tang, Qin Qin Huang, Shu Mei Teo, Ari V. Ahola-Olli, Peter Würtz, Aki S. Havulinna, Kristiina Santalahti, Niina Pitkänen, Terho Lehtimäki, Mika Kähönen, Leo-Pekka Lyytikäinen, Emma Raitoharju, Ilkka Seppälä, Antti-Pekka Sarin, Samuli Ripatti, Michael Inouye

    Cytokines are essential regulatory components of the immune system, and their aberrant levels have been linked to many disease states. Despite increasing evidence that cytokines operate in concert, many of the physiological interactions between cytokines, and the shared genetic architecture that underlies them, remain unknown. Here, we aimed to identify and characterize genetic variants with pleiotropic effects on cytokines. Using three population-based cohorts (n = 9,263), we performed multivariate genome-wide association studies (GWAS) for a correlation network of 11 circulating cytokines, then combined our results in meta-analysis. We identified a total of eight loci significantly associated with the cytokine network, of which two (PDGFRB and ABO) had not been detected previously. In addition, conditional analyses revealed a further four secondary signals at three known cytokine loci. Integration, through the use of Bayesian colocalization analysis, of publicly available GWAS summary statistics with the cytokine network associations revealed shared causal variants between the eight cytokine loci and other traits; in particular, cytokine network variants at the ABO, SERPINE2, and ZFPM2 loci showed pleiotropic effects on the production of immune-related proteins, on metabolic traits such as lipoprotein and lipid levels, on blood-cell-related traits such as platelet count, and on disease traits such as coronary artery disease and type 2 diabetes.

  • Genome Sequencing Explores Complexity of Chromosomal Abnormalities in Recurrent Miscarriage
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-10-31
    Zirui Dong, Junhao Yan, Fengping Xu, Jianying Yuan, Hui Jiang, Huilin Wang, Haixiao Chen, Lei Zhang, Lingfei Ye, Jinjin Xu, Yuhua Shi, Zhenjun Yang, Ye Cao, Lingyun Chen, Qiaoling Li, Xia Zhao, Jiguang Li, Ao Chen, Zi-Jiang Chen

    Recurrent miscarriage (RM) affects millions of couples globally, and half of them have no demonstrated etiology. Genome sequencing (GS) is an enhanced and novel cytogenetic tool to define the contribution of chromosomal abnormalities in human diseases. In this study we evaluated its utility in RM-affected couples. We performed low-pass GS retrospectively for 1,090 RM-affected couples, all of whom had routine chromosome analysis. A customized sequencing and interpretation pipeline was developed to identify chromosomal rearrangements and deletions/duplications with confirmation by fluorescence in situ hybridization, chromosomal microarray analysis, and PCR studies. Low-pass GS yielded results in 1,077 of 1,090 couples (98.8%) and detected 127 chromosomal abnormalities in 11.7% (126/1,077) of couples; both members of one couple were identified with inversions. Of the 126 couples, 39.7% (50/126) had received former diagnostic results by karyotyping characteristic of normal human male or female karyotypes. Low-pass GS revealed additional chromosomal abnormalities in 50 (4.0%) couples, including eight with balanced translocations and 42 inversions. Follow-up studies of these couples showed a higher miscarriage/fetal-anomaly rate of 5/10 (50%) compared to 21/93 (22.6%) in couples with normal GS, resulting in a relative risk of 2.2 (95% confidence interval, 1.1 to 4.6). In these couples, this protocol significantly increased the diagnostic yield of chromosomal abnormalities per couple (11.7%) in comparison to chromosome analysis (8.0%, chi-square test p = 0.000751). In summary, low-pass GS identified underlying chromosomal aberrations in 1 in 9 RM-affected couples, enabling identification of a subgroup of couples with increased risk of subsequent miscarriage who would benefit from a personalized intervention.

  • Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2016-06-21
    Ching-Ti Liu,Sridharan Raghavan,Nisa Maruthur,Edmond Kato Kabagambe,Jaeyoung Hong,Maggie C Y Ng,Marie-France Hivert,Yingchang Lu,Ping An,Amy R Bentley,Anne M Drolet,Kyle J Gaulton,Xiuqing Guo,Loren L Armstrong,Marguerite R Irvin,Man Li,Leonard Lipovich,Denis V Rybin,Kent D Taylor,Charles Agyemang,Nicholette D Palmer,Brian E Cade,Wei-Min Chen,Marco Dauriz,Joseph A C Delaney,Todd L Edwards,Daniel S Evans,Michele K Evans,Leslie A Lange,Aaron Leong,Jingmin Liu,Yongmei Liu,Uma Nayak,Sanjay R Patel,Bianca C Porneala,Laura J Rasmussen-Torvik,Marieke B Snijder,Sarah C Stallings,Toshiko Tanaka,Lisa R Yanek,Wei Zhao,Diane M Becker,Lawrence F Bielak,Mary L Biggs,Erwin P Bottinger,Donald W Bowden,Guanjie Chen,Adolfo Correa,David J Couper,Dana C Crawford,Mary Cushman,John D Eicher,Myriam Fornage,Nora Franceschini,Yi-Ping Fu,Mark O Goodarzi,Omri Gottesman,Kazuo Hara,Tamara B Harris,Richard A Jensen,Andrew D Johnson,Min A Jhun,Andrew J Karter,Margaux F Keller,Abel N Kho,Jorge R Kizer,Ronald M Krauss,Carl D Langefeld,Xiaohui Li,Jingling Liang,Simin Liu,William L Lowe,Thomas H Mosley,Kari E North,Jennifer A Pacheco,Patricia A Peyser,Alan L Patrick,Kenneth M Rice,Elizabeth Selvin,Mario Sims,Jennifer A Smith,Salman M Tajuddin,Dhananjay Vaidya,Mary P Wren,Jie Yao,Xiaofeng Zhu,Julie T Ziegler,Joseph M Zmuda,Alan B Zonderman,Aeilko H Zwinderman,,,,,,Adebowale Adeyemo,Eric Boerwinkle,Luigi Ferrucci,M Geoffrey Hayes,Sharon L R Kardia,Iva Miljkovic,James S Pankow,Charles N Rotimi,Michele M Sale,Lynne E Wagenknecht,Donna K Arnett,Yii-Der Ida Chen,Michael A Nalls,,Michael A Province,W H Linda Kao,David S Siscovick,Bruce M Psaty,James G Wilson,Ruth J F Loos,Josée Dupuis,Stephen S Rich,Jose C Florez,Jerome I Rotter,Andrew P Morris,James B Meigs

    Knowledge of the genetic basis of the type 2 diabetes (T2D)-related quantitative traits fasting glucose (FG) and insulin (FI) in African ancestry (AA) individuals has been limited. In non-diabetic subjects of AA (n = 20,209) and European ancestry (EA; n = 57,292), we performed trans-ethnic (AA+EA) fine-mapping of 54 established EA FG or FI loci with detailed functional annotation, assessed their relevance in AA individuals, and sought previously undescribed loci through trans-ethnic (AA+EA) meta-analysis. We narrowed credible sets of variants driving association signals for 22/54 EA-associated loci; 18/22 credible sets overlapped with active islet-specific enhancers or transcription factor (TF) binding sites, and 21/22 contained at least one TF motif. Of the 54 EA-associated loci, 23 were shared between EA and AA. Replication with an additional 10,096 AA individuals identified two previously undescribed FI loci, chrX FAM133A (rs213676) and chr5 PELO (rs6450057). Trans-ethnic analyses with regulatory annotation illuminate the genetic architecture of glycemic traits and suggest gene regulation as a target to advance precision medicine for T2D. Our approach to utilize state-of-the-art functional annotation and implement trans-ethnic association analysis for discovery and fine-mapping offers a framework for further follow-up and characterization of GWAS signals of complex trait loci.

  • Fine mapping seronegative and seropositive rheumatoid arthritis to shared and distinct HLA alleles by adjusting for the effects of heterogeneity.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2014-03-25
    Buhm Han,Dorothée Diogo,Steve Eyre,Henrik Kallberg,Alexandra Zhernakova,John Bowes,Leonid Padyukov,Yukinori Okada,Miguel A González-Gay,Solbritt Rantapää-Dahlqvist,Javier Martin,Tom W J Huizinga,Robert M Plenge,Jane Worthington,Peter K Gregersen,Lars Klareskog,Paul I W de Bakker,Soumya Raychaudhuri

    Despite progress in defining human leukocyte antigen (HLA) alleles for anti-citrullinated-protein-autoantibody-positive (ACPA(+)) rheumatoid arthritis (RA), identifying HLA alleles for ACPA-negative (ACPA(-)) RA has been challenging because of clinical heterogeneity within clinical cohorts. We imputed 8,961 classical HLA alleles, amino acids, and SNPs from Immunochip data in a discovery set of 2,406 ACPA(-) RA case and 13,930 control individuals. We developed a statistical approach to identify and adjust for clinical heterogeneity within ACPA(-) RA and observed independent associations for serine and leucine at position 11 in HLA-DRβ1 (p = 1.4 × 10(-13), odds ratio [OR] = 1.30) and for aspartate at position 9 in HLA-B (p = 2.7 × 10(-12), OR = 1.39) within the peptide binding grooves. These amino acid positions induced associations at HLA-DRB1(∗)03 (encoding serine at 11) and HLA-B(∗)08 (encoding aspartate at 9). We validated these findings in an independent set of 427 ACPA(-) case subjects, carefully phenotyped with a highly sensitive ACPA assay, and 1,691 control subjects (HLA-DRβ1 Ser11+Leu11: p = 5.8 × 10(-4), OR = 1.28; HLA-B Asp9: p = 2.6 × 10(-3), OR = 1.34). Although both amino acid sites drove risk of ACPA(+) and ACPA(-) disease, the effects of individual residues at HLA-DRβ1 position 11 were distinct (p < 2.9 × 10(-107)). We also identified an association with ACPA(+) RA at HLA-A position 77 (p = 2.7 × 10(-8), OR = 0.85) in 7,279 ACPA(+) RA case and 15,870 control subjects. These results contribute to mounting evidence that ACPA(+) and ACPA(-) RA are genetically distinct and potentially have separate autoantigens contributing to pathogenesis. We expect that our approach might have broad applications in analyzing clinical conditions with heterogeneity at both major histocompatibility complex (MHC) and non-MHC regions.

  • Loss of BRCC3 deubiquitinating enzyme leads to abnormal angiogenesis and is associated with syndromic moyamoya.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2011-05-21
    Snaigune Miskinyte,Matthew G Butler,Dominique Hervé,Catherine Sarret,Marc Nicolino,Jacob D Petralia,Francoise Bergametti,Minh Arnould,Van N Pham,Aniket V Gore,Konstantinos Spengos,Steven Gazal,France Woimant,Gary K Steinberg,Brant M Weinstein,Elisabeth Tournier-Lasserve

    Moyamoya is a cerebrovascular angiopathy characterized by a progressive stenosis of the terminal part of the intracranial carotid arteries and the compensatory development of abnormal and fragile collateral vessels, also called moyamoya vessels, leading to ischemic and hemorrhagic stroke. Moyamoya angiopathy can either be the sole manifestation of the disease (moyamoya disease) or be associated with various conditions, including neurofibromatosis, Down syndrome, TAAD (autosomal-dominant thoracic aortic aneurysm), and radiotherapy of head tumors (moyamoya syndromes). Its prevalence is ten times higher in Japan than in Europe, and an estimated 6%-12% of moyamoya disease is familial in Japan. The pathophysiological mechanisms of this condition remain obscure. Here, we report on three unrelated families affected with an X-linked moyamoya syndrome characterized by the association of a moyamoya angiopathy, short stature, and a stereotyped facial dysmorphism. Other symptoms include an hypergonadotropic hypogonadism, hypertension, dilated cardiomyopathy, premature coronary heart disease, premature hair graying, and early bilateral acquired cataract. We show that this syndromic moyamoya is caused by Xq28 deletions removing MTCP1/MTCP1NB and BRCC3. We also show that brcc3 morphant zebrafish display angiogenesis defects that are rescued by endothelium-specific expression of brcc3. Altogether, these data strongly suggest that BRCC3, a deubiquitinating enzyme that is part of the cellular BRCA1 and BRISC complexes, is an important player in angiogenesis and that BRCC3 loss-of-function mutations are associated with moyamoya angiopathy.

  • BRD2 (RING3) is a probable major susceptibility gene for common juvenile myoclonic epilepsy.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2003-06-28
    Deb K Pal,Oleg V Evgrafov,Paula Tabares,Fengli Zhang,Martina Durner,David A Greenberg

    Juvenile myoclonic epilepsy (JME) is a common form of generalized epilepsy that starts in adolescence. A major JME susceptibility locus (EJM1) was mapped to chromosomal region 6p21 in three independent linkage studies, and association was reported between JME and a microsatellite marker in the 6p21 region. The critical region for EJM1 is delimited by obligate recombinants at HLA-DQ and HLA-DP. In the present study, we found highly significant linkage disequilibrium (LD) between JME and a core haplotype of five single-nucleotide-polymorphism (SNP) and microsatellite markers in this critical region, with LD peaking in the BRD2 (RING3) gene (odds ratio 6.45; 95% confidence interval 2.36-17.58). DNA sequencing revealed two JME-associated SNP variants in the BRD2 (RING3) promoter region but no other potentially causative coding mutations in 20 probands from families with positive LOD scores. BRD2 (RING3) is a putative nuclear transcriptional regulator from a family of genes that are expressed during development. Our findings strongly suggest that BRD2 (RING3) is EJM1, the first gene identified for a common idiopathic epilepsy. These findings also suggest that abnormalities of neural development may be a cause of common idiopathic epilepsy, and the findings have implications for the generalizability of proposed pathogenetic mechanisms, derived from diseases that show Mendelian transmission, to their complex counterparts.

  • Characterization of recombination in the HLA class II region.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 1997-02-01
    M Cullen,J Noble,H Erlich,K Thorpe,S Beck,W Klitz,J Trowsdale,M Carrington

    Studies of linkage disequilibrium across the HLA class II region have been useful in predicting where recombination is most likely to occur. The strong associations between genes within the 85-kb region from DQB1 to DRB1 are consistent with low frequency of recombination in this segment of DNA. Conversely, a lack of association between alleles of TAP1 and TAP2 (approximately 15 kb) has been observed, suggesting that recombination occurs here with relatively high frequency. Much of the HLA class II region has now been sequenced, providing the tools to undertake detailed analysis of recombination. Twenty-seven families containing one or two recombinant chromosomes within the 500-kb interval between the DPB1 and DRB1 genes were used to determine patterns of recombination across this region. SSCP analysis and microsatellite typing yielded identification of 127 novel polymorphic markers distributed throughout the class II region, allowing refinement of the site of crossover in 30 class II recombinant chromosomes. The three regions where recombination was observed most frequently are as follows: the 45-kb interval between HLA-DNA and RING3 (11 cases), the 50-kb interval between DQB3 and DQB1 (6 cases), and an 8.8-kb segment of the TAP2 gene (3 cases). Six of the 10 remaining recombinants await further characterization, pending identification of additional informative markers, while four recombinants were localized to other intervals (outliers). Analysis of association between markers flanking HLA-DNA to RING3 (45 kb), as well as TAP1 to TAP2 (15 kb), by use of independent CEPH haplotypes indicated little or no linkage disequilibrium, supporting the familial recombination data. A notable sequence motif located within a region associated with increased rates of recombination consisted of a (TGGA)12 tandem repeat within the TAP2 gene.

  • A Genome-wide Association Study of Nonsyndromic Cleft Palate Identifies an Etiologic Missense Variant in GRHL3.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2016-03-29
    Elizabeth J Leslie,Huan Liu,Jenna C Carlson,John R Shaffer,Eleanor Feingold,George Wehby,Cecelia A Laurie,Deepti Jain,Cathy C Laurie,Kimberly F Doheny,Toby McHenry,Judith Resick,Carla Sanchez,Jennifer Jacobs,Beth Emanuele,Alexandre R Vieira,Katherine Neiswanger,Jennifer Standley,Andrew E Czeizel,Frederic Deleyiannis,Kaare Christensen,Ronald G Munger,Rolv T Lie,Allen Wilcox,Paul A Romitti,L Leigh Field,Carmencita D Padilla,Eva Maria C Cutiongco-de la Paz,Andrew C Lidral,Luz Consuelo Valencia-Ramirez,Ana Maria Lopez-Palacio,Dora Rivera Valencia,Mauricio Arcos-Burgos,Eduardo E Castilla,Juan C Mereb,Fernando A Poletta,Iêda M Orioli,Flavia M Carvalho,Jacqueline T Hecht,Susan H Blanton,Carmen J Buxó,Azeez Butali,Peter A Mossey,Wasiu L Adeyemo,Olutayo James,Ramat O Braimah,Babatunde S Aregbesola,Mekonen A Eshete,Milliard Deribew,Mine Koruyucu,Figen Seymen,Lian Ma,Javier Enríquez de Salamanca,Seth M Weinberg,Lina Moreno,Robert A Cornell,Jeffrey C Murray,Mary L Marazita

    Cleft palate (CP) is a common birth defect occurring in 1 in 2,500 live births. Approximately half of infants with CP have a syndromic form, exhibiting other physical and cognitive disabilities. The other half have nonsyndromic CP, and to date, few genes associated with risk for nonsyndromic CP have been characterized. To identify such risk factors, we performed a genome-wide association study of this disorder. We discovered a genome-wide significant association with a missense variant in GRHL3 (p.Thr454Met [c.1361C>T]; rs41268753; p = 4.08 × 10(-9)) and replicated the result in an independent sample of case and control subjects. In both the discovery and replication samples, rs41268753 conferred increased risk for CP (OR = 8.3, 95% CI 4.1-16.8; OR = 2.16, 95% CI 1.43-3.27, respectively). In luciferase transactivation assays, p.Thr454Met had about one-third of the activity of wild-type GRHL3, and in zebrafish embryos, perturbed periderm development. We conclude that this mutation is an etiologic variant for nonsyndromic CP and is one of few functional variants identified to date for nonsyndromic orofacial clefting. This finding advances our understanding of the genetic basis of craniofacial development and might ultimately lead to improvements in recurrence risk prediction, treatment, and prognosis.

  • Wild-type huntingtin reduces the cellular toxicity of mutant huntingtin in vivo.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2001-01-03
    B R Leavitt,J A Guttman,J G Hodgson,G H Kimel,R Singaraja,A W Vogl,M R Hayden

    We have developed yeast artificial chromosome (YAC) transgenic mice expressing normal (YAC18) and mutant (YAC46 or YAC72) human huntingtin (htt), in a developmental- and tissue-specific manner, that is identical to endogenous htt. YAC72 mice develop selective degeneration of medium spiny projection neurons in the lateral striatum, similar to what is observed in Huntington disease. Mutant human htt expressed by YAC transgenes can compensate for the absence of endogenous htt and can rescue the embryonic lethality that characterizes mice homozygous for targeted disruption of the endogenous Hdh gene (-/-). YAC72 mice lacking endogenous htt (YAC72 -/-) manifest a novel phenotype characterized by infertility, testicular atrophy, aspermia, and massive apoptotic cell death in the testes. The testicular cell death in YAC72 -/- mice can be markedly reduced by increasing endogenous htt levels. YAC72 mice with equivalent levels of both wild-type and mutant htt (YAC72 +/+) breed normally and have no evidence of increased testicular cell death. Similar findings are seen in YAC46 -/- mice compared with YAC46 +/+ mice, in which wild-type htt can completely counteract the proapoptotic effects of mutant htt. YAC18 -/- mice display no evidence of increased cellular apoptosis, even in the complete absence of endogenous htt, demonstrating that the massive cellular apoptosis observed in YAC46 -/- mice and YAC72 -/- mice is polyglutamine-mediated toxicity from the mutant transgene. These data provide the first direct in vivo evidence of a role for wild-type htt in decreasing the cellular toxicity of mutant htt.

  • 2-Methyl-3-hydroxybutyryl-CoA dehydrogenase deficiency is caused by mutations in the HADH2 gene.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2003-04-16
    Rob Ofman,Jos P N Ruiter,Marike Feenstra,Marinus Duran,Bwee Tien Poll-The,Johannes Zschocke,Regina Ensenauer,Willy Lehnert,Jörn Oliver Sass,Wolfgang Sperl,Ronald J A Wanders

    2-methyl-3-hydroxybutyryl-CoA dehydrogenase (MHBD) deficiency is a novel inborn error of isoleucine degradation. In this article, we report the elucidation of the molecular basis of MHBD deficiency. To this end, we purified the enzyme from bovine liver. MALDI-TOF mass spectrometry analysis revealed that the purified protein was identical to bovine 3-hydroxyacyl-CoA dehydrogenase type II. The human homolog of this bovine enzyme is a short-chain 3-hydroxyacyl-CoA dehydrogenase, also known as the "endoplasmic reticulum-associated amyloid-beta binding protein" (ERAB). This led to the identification of the X-chromosomal gene involved, which previously had been denoted "HADH2." Sequence analysis of the HADH2 gene from patients with MHBD deficiency revealed the presence of two missense mutations (R130C and L122V). Heterologous expression of the mutant cDNAs in Escherichia coli showed that both mutations almost completely abolish enzyme activity. This confirms that MHBD deficiency is caused by mutations in the HADH2 gene.

  • An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2016-01-11
    Joe R Davis,Laure Fresard,David A Knowles,Mauro Pala,Carlos D Bustamante,Alexis Battle,Stephen B Montgomery

    Methods for multiple-testing correction in local expression quantitative trait locus (cis-eQTL) studies are a trade-off between statistical power and computational efficiency. Bonferroni correction, though computationally trivial, is overly conservative and fails to account for linkage disequilibrium between variants. Permutation-based methods are more powerful, though computationally far more intensive. We present an alternative correction method called eigenMT, which runs over 500 times faster than permutations and has adjusted p values that closely approximate empirical ones. To achieve this speed while also maintaining the accuracy of permutation-based methods, we estimate the effective number of independent variants tested for association with a particular gene, termed Meff, by using the eigenvalue decomposition of the genotype correlation matrix. We employ a regularized estimator of the correlation matrix to ensure Meff is robust and yields adjusted p values that closely approximate p values from permutations. Finally, using a common genotype matrix, we show that eigenMT can be applied with even greater efficiency to studies across tissues or conditions. Our method provides a simpler, more efficient approach to multiple-testing correction than existing methods and fits within existing pipelines for eQTL discovery.

  • Correcting for Sample Contamination in Genotype Calling of DNA Sequence Data.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2015-08-04
    Matthew Flickinger,Goo Jun,Gonçalo R Abecasis,Michael Boehnke,Hyun Min Kang

    DNA sample contamination is a frequent problem in DNA sequencing studies and can result in genotyping errors and reduced power for association testing. We recently described methods to identify within-species DNA sample contamination based on sequencing read data, showed that our methods can reliably detect and estimate contamination levels as low as 1%, and suggested strategies to identify and remove contaminated samples from sequencing studies. Here we propose methods to model contamination during genotype calling as an alternative to removal of contaminated samples from further analyses. We compare our contamination-adjusted calls to calls that ignore contamination and to calls based on uncontaminated data. We demonstrate that, for moderate contamination levels (5%-20%), contamination-adjusted calls eliminate 48%-77% of the genotyping errors. For lower levels of contamination, our contamination correction methods produce genotypes nearly as accurate as those based on uncontaminated data. Our contamination correction methods are useful generally, but are particularly helpful for sample contamination levels from 2% to 20%.

  • Rare-variant association analysis: study designs and statistical tests.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2014-07-06
    Seunggeung Lee,Gonçalo R Abecasis,Michael Boehnke,Xihong Lin

    Despite the extensive discovery of trait- and disease-associated common variants, much of the genetic contribution to complex traits remains unexplained. Rare variants can explain additional disease risk or trait variability. An increasing number of studies are underway to identify trait- and disease-associated rare variants. In this review, we provide an overview of statistical issues in rare-variant association studies with a focus on study designs and statistical tests. We present the design and analysis pipeline of rare-variant studies and review cost-effective sequencing designs and genotyping platforms. We compare various gene- or region-based association tests, including burden tests, variance-component tests, and combined omnibus tests, in terms of their assumptions and performance. Also discussed are the related topics of meta-analysis, population-stratification adjustment, genotype imputation, follow-up studies, and heritability due to rare variants. We provide guidelines for analysis and discuss some of the challenges inherent in these studies and future research directions.

  • General framework for meta-analysis of rare variants in sequencing association studies.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2013-06-19
    Seunggeun Lee,Tanya M Teslovich,Michael Boehnke,Xihong Lin

    We propose a general statistical framework for meta-analysis of gene- or region-based multimarker rare variant association tests in sequencing association studies. In genome-wide association studies, single-marker meta-analysis has been widely used to increase statistical power by combining results via regression coefficients and standard errors from different studies. In analysis of rare variants in sequencing studies, region-based multimarker tests are often used to increase power. We propose meta-analysis methods for commonly used gene- or region-based rare variants tests, such as burden tests and variance component tests. Because estimation of regression coefficients of individual rare variants is often unstable or not feasible, the proposed method avoids this difficulty by calculating score statistics instead that only require fitting the null model for each study and then aggregating these score statistics across studies. Our proposed meta-analysis rare variant association tests are conducted based on study-specific summary statistics, specifically score statistics for each variant and between-variant covariance-type (linkage disequilibrium) relationship statistics for each gene or region. The proposed methods are able to incorporate different levels of heterogeneity of genetic effects across studies and are applicable to meta-analysis of multiple ancestry groups. We show that the proposed methods are essentially as powerful as joint analysis by directly pooling individual level genotype data. We conduct extensive simulations to evaluate the performance of our methods by varying levels of heterogeneity across studies, and we apply the proposed methods to meta-analysis of rare variant effects in a multicohort study of the genetics of blood lipid levels.

  • Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2012-10-30
    Goo Jun,Matthew Flickinger,Kurt N Hetrick,Jane M Romm,Kimberly F Doheny,Gonçalo R Abecasis,Michael Boehnke,Hyun Min Kang

    DNA sample contamination is a serious problem in DNA sequencing studies and may result in systematic genotype misclassification and false positive associations. Although methods exist to detect and filter out cross-species contamination, few methods to detect within-species sample contamination are available. In this paper, we describe methods to identify within-species DNA sample contamination based on (1) a combination of sequencing reads and array-based genotype data, (2) sequence reads alone, and (3) array-based genotype data alone. Analysis of sequencing reads allows contamination detection after sequence data is generated but prior to variant calling; analysis of array-based genotype data allows contamination detection prior to generation of costly sequence data. Through a combination of analysis of in silico and experimentally contaminated samples, we show that our methods can reliably detect and estimate levels of contamination as low as 1%. We evaluate the impact of DNA contamination on genotype accuracy and propose effective strategies to screen for and prevent DNA contamination in sequencing studies.

  • Rare-variant association testing for sequencing data with the sequence kernel association test.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2011-07-09
    Michael C Wu,Seunggeun Lee,Tianxi Cai,Yun Li,Michael Boehnke,Xihong Lin

    Sequencing studies are increasingly being conducted to identify rare variants associated with complex traits. The limited power of classical single-marker association analysis for rare variants poses a central challenge in such studies. We propose the sequence kernel association test (SKAT), a supervised, flexible, computationally efficient regression method to test for association between genetic variants (common and rare) in a region and a continuous or dichotomous trait while easily adjusting for covariates. As a score-based variance-component test, SKAT can quickly calculate p values analytically by fitting the null model containing only the covariates, and so can easily be applied to genome-wide data. Using SKAT to analyze a genome-wide sequencing study of 1000 individuals, by segmenting the whole genome into 30 kb regions, requires only 7 hr on a laptop. Through analysis of simulated data across a wide range of practical scenarios and triglyceride data from the Dallas Heart Study, we show that SKAT can substantially outperform several alternative rare-variant association tests. We also provide analytic power and sample-size calculations to help design candidate-gene, whole-exome, and whole-genome sequence association studies.

  • 更新日期:2019-11-01
  • Two families with familial amyotrophic lateral sclerosis are linked to a novel locus on chromosome 16q.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2003-07-04
    Deborah M Ruddy,Matthew J Parton,Ammar Al-Chalabi,Cathryn M Lewis,Caroline Vance,Bradley N Smith,P Nigel Leigh,John F Powell,Teepu Siddique,Eelco Postumus Meyjes,Frank Baas,Vianney de Jong,Christopher E Shaw

    Amyotrophic lateral sclerosis (ALS) is a fatal adult-onset disease in which motor neurons in the brain and spinal cord degenerate by largely unknown mechanisms. ALS is familial (FALS) in 10% of cases, and the inheritance is usually dominant, with variable penetrance. Mutations in copper/zinc super oxide dismutase (SOD1) are found in 20% of familial and 3% of sporadic ALS cases. Five families with ALS and frontotemporal dementia (ALS-FTD) are linked to 9q21, whereas one family with pure ALS is linked to 18q21. We identified two large European families with ALS without SOD1 mutations or linkage to known FALS loci and conducted a genomewide linkage screen using 400 microsatellite markers. In both families, two-point LOD scores >1 and a haplotype segregating with disease were demonstrated only across regions of chromosome 16. Subsequent fine mapping in family 1 gave a maximum two-point LOD score of 3.62 at D16S3137 and a three-point LOD score of 3.85 for markers D16S415 and D16S3137. Haplotype analysis revealed no recombination > approximately 30 cM, (flanking markers at D16S3075 and D16S3112). The maximum two-point LOD score for family 2 was 1.84 at D16S415, and the three-point LOD score was 2.10 for markers D16S419 and D16S415. Definite recombination occurred in several individuals, which narrowed the shared haplotype in affected individuals to a 10.1-cM region (flanking markers: D16S3396 and D16S3112). The region shared by both families on chromosome 16q12 corresponds to approximately 4.5 Mb on the Marshfield map. Bioinformatic analysis of the region has identified 18 known genes and 70 predicted genes in this region, and sequencing of candidate genes has now begun.

  • Cohen syndrome is caused by mutations in a novel gene, COH1, encoding a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2003-05-06
    Juha Kolehmainen,Graeme C M Black,Anne Saarinen,Kate Chandler,Jill Clayton-Smith,Ann-Liz Träskelin,Rahat Perveen,Satu Kivitie-Kallio,Reijo Norio,Mette Warburg,Jean-Pierre Fryns,Albert de la Chapelle,Anna-Elina Lehesjoki

    Cohen syndrome is an uncommon autosomal recessive disorder whose diagnosis is based on the clinical picture of nonprogressive psychomotor retardation and microcephaly, characteristic facial features, retinal dystrophy, and intermittent neutropenia. We have refined the critical region on chromosome 8q22 by haplotype analysis, and we report the characterization of a novel gene, COH1, that is mutated in patients with Cohen syndrome. The longest transcript (14,093 bp) is widely expressed and is transcribed from 62 exons that span a genomic region of approximately 864 kb. COH1 encodes a putative transmembrane protein of 4,022 amino acids, with a complex domain structure. Homology to the Saccharomyces cerevisiae VPS13 protein suggests a role for COH1 in vesicle-mediated sorting and transport of proteins within the cell.

  • Missense mutations in the homeodomain of HOXD13 are associated with brachydactyly types D and E.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2003-03-22
    David Johnson,Shih-Hsin Kan,Michael Oldridge,Richard C Trembath,Philippe Roche,Robert M Esnouf,Henk Giele,Andrew O M Wilkie

    HOXD13, the most 5' gene of the HOXD cluster, encodes a homeodomain transcription factor with important functions in limb patterning and growth. Heterozygous mutations of human HOXD13, encoding polyalanine expansions or frameshifts, are believed to act by dominant negative or haploinsufficiency mechanisms and are predominantly associated with synpolydactyly phenotypes. Here, we describe two mutations of HOXD13 (923C-->G encoding Ser308Cys and 940A-->C encoding Ile314Leu) that cause missense substitutions within the homeodomain. Both are associated with distinctive limb phenotypes in which brachydactyly of specific metacarpals, metatarsals, and phalangeal bones is the most constant feature, exhibiting overlap with brachydactyly types D and E. We investigated the binding of synthetic mutant proteins to double-stranded DNA targets in vitro. No consistent differences were found for the Ser308Cys mutation compared with the wild type, but the Ile314Leu mutation (which resides at the 47th position of the homeodomain) exhibited increased affinity for a target containing the core recognition sequence 5'-TTAC-3' but decreased affinity for a 5'-TTAT-3' target. Molecular modeling of the Ile314Leu mutation indicates that this mixed gain and loss of affinity may be accounted for by the relative positions of methyl groups in the amino acid side chain and target base.

  • Genetic evidence for interaction of the 5q31 cytokine locus and the CARD15 gene in Crohn disease.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2003-03-06
    Muddassar M Mirza,Sheila A Fisher,Kathy King,Andrew P Cuthbert,Jochen Hampe,Jeremy Sanderson,John Mansfield,Peter Donaldson,Andrew J S Macpherson,Alastair Forbes,Stefan Schreiber,Cathryn M Lewis,Christopher G Mathew

    A common haplotype spanning 250 kb in the cytokine gene cluster on chromosome 5q31 has recently been reported to be strongly associated with Crohn disease (CD) in Canadian families. We have replicated this finding by both the transmission-disequilibrium test (TDT) (P=.016) and in a case-control association study (P=.008) in a large European cohort of patients with CD, although the increase in disease risk was small (odds ratio 1.49 for homozygotes, 95% CI 1.11-2.0). No association was detected in families or individuals with ulcerative colitis (UC). Stratification of offspring with CD in the TDT sample by mutation status in the CD susceptibility gene CARD15 showed that the association with the 5q31 risk haplotype was present only in offspring with at least one of the known CARD15 disease susceptibility alleles (P=.044). The 5q31 risk haplotype frequency was 53.1% in unrelated individuals with CD who had one or two CARD15 mutations versus 43.7% in control subjects (P=.0001) but was not significantly elevated in individuals with CD who had no CARD15 mutations (45.4%, P=.41). Kaplan-Meier survival analysis of age at disease onset showed a significantly earlier onset in homozygotes for the 5q31 risk haplotype (P=.0019). These findings suggest that genetic variants at the 5q31 (IBD5) locus may hasten the onset of Crohn disease and cooperate with CARD15 in disease causation.

  • A genomewide scan identifies two novel loci involved in specific language impairment.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2002-01-16

    Approximately 4% of English-speaking children are affected by specific language impairment (SLI), a disorder in the development of language skills despite adequate opportunity and normal intelligence. Several studies have indicated the importance of genetic factors in SLI; a positive family history confers an increased risk of development, and concordance in monozygotic twins consistently exceeds that in dizygotic twins. However, like many behavioral traits, SLI is assumed to be genetically complex, with several loci contributing to the overall risk. We have compiled 98 families drawn from epidemiological and clinical populations, all with probands whose standard language scores fall > or =1.5 SD below the mean for their age. Systematic genomewide quantitative-trait-locus analysis of three language-related measures (i.e., the Clinical Evaluation of Language Fundamentals-Revised [CELF-R] receptive and expressive scales and the nonword repetition [NWR] test) yielded two regions, one on chromosome 16 and one on 19, that both had maximum LOD scores of 3.55. Simulations suggest that, of these two multipoint results, the NWR linkage to chromosome 16q is the most significant, with empirical P values reaching 10(-5), under both Haseman-Elston (HE) analysis (LOD score 3.55; P=.00003) and variance-components (VC) analysis (LOD score 2.57; P=.00008). Single-point analyses provided further support for involvement of this locus, with three markers, under the peak of linkage, yielding LOD scores >1.9. The 19q locus was linked to the CELF-R expressive-language score and exceeds the threshold for suggestive linkage under all types of analysis performed-multipoint HE analysis (LOD score 3.55; empirical P=.00004) and VC (LOD score 2.84; empirical P=.00027) and single-point HE analysis (LOD score 2.49) and VC (LOD score 2.22). Furthermore, both the clinical and epidemiological samples showed independent evidence of linkage on both chromosome 16q and chromosome 19q, indicating that these may represent universally important loci in SLI and, thus, general risk factors for language impairment.

  • A genomewide scan for type 1-diabetes susceptibility in Scandinavian families: identification of new loci with evidence of interactions.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2001-10-13
    J Nerup,F Pociot,

    Type 1 diabetes mellitus (TIDM) has a multifactorial etiology, with major genetic-susceptibility determinants located in the HLA and insulin-gene (INS) regions. Linkage data implicating other disease-susceptibility loci are conflicting. This is likely due to (1) the limited power for detection of contributions of additional susceptibility loci, given the limited number of informative families available for study, (2) factors such as genetic heterogeneity between populations, and (3) potential gene-gene and gene-environment interactions. To circumvent some of these problems, we have conducted a genomewide linkage analysis for T1DM-susceptibility loci in 408 multiplex families from Scandinavia, a population expected to be homogeneous for genetic and environmental factors. In addition to verifying the HLA and INS susceptibility loci, the study provides confirmation of IDDM15 on chromosome 6q21. Suggestive evidence of additional susceptibility loci was found on chromosomes 2p, 5q, and 16p. For some loci, the support for linkage increased substantially when families were stratified on the basis of HLA or INS genotypes, with statistically significant heterogeneity between the stratified subgroups. Our data support both the existence of non-HLA genes of significance for T1DM and interaction between HLA and non-HLA loci in the determination of the T1DM phenotype.

  • A genomewide scan for loci predisposing to type 2 diabetes in a U.K. population (the Diabetes UK Warren 2 Repository): analysis of 573 pedigrees provides independent replication of a susceptibility locus on chromosome 1q.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2001-08-03
    S Wiltshire,A T Hattersley,G A Hitman,M Walker,J C Levy,M Sampson,S O'Rahilly,T M Frayling,J I Bell,G M Lathrop,A Bennett,R Dhillon,C Fletcher,C J Groves,E Jones,P Prestwich,N Simecek,P V Rao,M Wishart,G F Bottazzo,R Foxon,S Howell,D Smedley,L R Cardon,S Menzel,M I McCarthy

    Improved molecular understanding of the pathogenesis of type 2 diabetes is essential if current therapeutic and preventative options are to be extended. To identify diabetes-susceptibility genes, we have completed a primary (418-marker, 9-cM) autosomal-genome scan of 743 sib pairs (573 pedigrees) with type 2 diabetes who are from the Diabetes UK Warren 2 repository. Nonparametric linkage analysis of the entire data set identified seven regions showing evidence for linkage, with allele-sharing LOD scores > or =1.18 (P< or =.01). The strongest evidence was seen on chromosomes 8p21-22 (near D8S258 [LOD score 2.55]) and 10q23.3 (near D10S1765 [LOD score 1.99]), both coinciding with regions identified in previous scans in European subjects. This was also true of two lesser regions identified, on chromosomes 5q13 (D5S647 [LOD score 1.22] and 5q32 (D5S436 [LOD score 1.22]). Loci on 7p15.3 (LOD score 1.31) and 8q24.2 (LOD score 1.41) are novel. The final region showing evidence for linkage, on chromosome 1q24-25 (near D1S218 [LOD score 1.50]), colocalizes with evidence for linkage to diabetes found in Utah, French, and Pima families and in the GK rat. After dense-map genotyping (mean marker spacing 4.4 cM), evidence for linkage to this region increased to a LOD score of 1.98. Conditional analyses revealed nominally significant interactions between this locus and the regions on chromosomes 10q23.3 (P=.01) and 5q32 (P=.02). These data, derived from one of the largest genome scans undertaken in this condition, confirm that individual susceptibility-gene effects for type 2 diabetes are likely to be modest in size. Taken with genome scans in other populations, they provide both replication of previous evidence indicating the presence of a diabetes-susceptibility locus on chromosome 1q24-25 and support for the existence of additional loci on chromosomes 5, 8, and 10. These data should accelerate positional cloning efforts in these regions of interest.

  • Estimating Scandinavian and Gaelic ancestry in the male settlers of Iceland.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2000-08-10
    A Helgason,S Sigureth ardóttir,J Nicholson,B Sykes,E W Hill,D G Bradley,V Bosnes,J R Gulcher,R Ward,K Stefánsson

    We present findings based on a study of Y-chromosome diallelic and microsatellite variation in 181 Icelanders, 233 Scandinavians, and 283 Gaels from Ireland and Scotland. All but one of the Icelandic Y chromosomes belong to haplogroup 1 (41.4%), haplogroup 2 (34.2%), or haplogroup 3 (23.8%). We present phylogenetic networks of Icelandic Y-chromosome variation, using haplotypes constructed from seven diallelic markers and eight microsatellite markers, and we propose two new clades. We also report, for the first time, the phylogenetic context of the microsatellite marker DYS385 in Europe. A comparison of haplotypes based on six diallelic loci and five microsatellite loci indicates that some Icelandic haplogroup-1 chromosomes are likely to have a Gaelic origin, whereas for most Icelandic haplogroup-2 and -3 chromosomes, a Scandinavian origin is probable. The data suggest that 20%-25% of Icelandic founding males had Gaelic ancestry, with the remainder having Norse ancestry. The closer relationship with the Scandinavian Y-chromosome pool is supported by the results of analyses of genetic distances and lineage sharing. These findings contrast with results based on mtDNA data, which indicate closer matrilineal links with populations of the British Isles. This supports the model, put forward by some historians, that the majority of females in the Icelandic founding population had Gaelic ancestry, whereas the majority of males had Scandinavian ancestry.

  • Localization of the Netherton syndrome gene to chromosome 5q32, by linkage analysis and homozygosity mapping.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2000-03-11
    S Chavanas,C Garner,C Bodemer,M Ali,D H Teillac,J Wilkinson,J L Bonafé,M Paradisi,D P Kelsell,S i Ansai,Y Mitsuhashi,M Larrègue,I M Leigh,J I Harper,A Taïeb,Y d Prost,L R Cardon,A Hovnanian

    Netherton syndrome (NS [MIM 256500]) is a rare and severe autosomal recessive disorder characterized by congenital ichthyosis, a specific hair-shaft defect (trichorrhexis invaginata), and atopic manifestations. Infants with this syndrome often fail to thrive; life-threatening complications result in high postnatal mortality. We report the assignment of the NS gene to chromosome 5q32, by linkage analysis and homozygosity mapping in 20 families affected with NS. Significant evidence for linkage (maximum multipoint LOD score 10.11) between markers D5S2017 and D5S413 was obtained, with no evidence for locus heterogeneity. Analysis of critical recombinants mapped the NS locus between markers D5S463 and D5S2013, within an <3.5-cM genetic interval. The NS locus is telomeric to the cytokine gene cluster in 5q31. The five known genes encoding casein kinase Ialpha, the alpha subunit of retinal rod cGMP phosphodiesterase, the regulator of mitotic-spindle assembly, adrenergic receptor beta2, and the diastrophic dysplasia sulfate-transporter gene, as well as the 38 expressed-sequence tags mapped within the critical region, are not obvious candidates. Our study is the first step toward the positional cloning of the NS gene. This finding promises a better understanding of the molecular mechanisms that control epidermal differentiation and immunity.

  • Lessons Learned from Large-Scale, First-Tier Clinical Exome Sequencing in a Highly Consanguineous Population.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-10-05
    Dorota Monies,Mohammed Abouelhoda,Mirna Assoum,Nabil Moghrabi,Rafiullah Rafiullah,Naif Almontashiri,Mohammed Alowain,Hamad Alzaidan,Moeen Alsayed,Shazia Subhani,Edward Cupler,Maha Faden,Amal Alhashem,Alya Qari,Aziza Chedrawi,Hisham Aldhalaan,Wesam Kurdi,Sameena Khan,Zuhair Rahbeeni,Maha Alotaibi,Ewa Goljan,Hadeel Elbardisy,Mohamed ElKalioby,Zeeshan Shah,Hibah Alruwaili,Amal Jaafar,Ranad Albar,Asma Akilan,Hamsa Tayeb,Asma Tahir,Mohammed Fawzy,Mohammed Nasr,Shaza Makki,Abdullah Alfaifi,Hanna Akleh,Suad Yamani,Dalal Bubshait,Mohammed Mahnashi,Talal Basha,Afaf Alsagheir,Musad Abu Khaled,Khalid Alsaleem,Maisoon Almugbel,Manal Badawi,Fahad Bashiri,Saeed Bohlega,Raashida Sulaiman,Ehab Tous,Syed Ahmed,Talal Algoufi,Hamoud Al-Mousa,Emadia Alaki,Susan Alhumaidi,Hadeel Alghamdi,Malak Alghamdi,Ahmed Sahly,Shapar Nahrir,Ali Al-Ahmari,Hisham Alkuraya,Ali Almehaidib,Mohammed Abanemai,Fahad Alsohaibaini,Bandar Alsaud,Rand Arnaout,Ghada M H Abdel-Salam,Hasan Aldhekri,Suzan AlKhater,Khalid Alqadi,Essam Alsabban,Turki Alshareef,Khalid Awartani,Hanaa Banjar,Nada Alsahan,Ibraheem Abosoudah,Abdullah Alashwal,Wajeeh Aldekhail,Sami Alhajjar,Sulaiman Al-Mayouf,Abdulaziz Alsemari,Walaa Alshuaibi,Saeed Altala,Abdulhadi Altalhi,Salah Baz,Muddathir Hamad,Tariq Abalkhail,Badi Alenazi,Alya Alkaff,Fahad Almohareb,Fuad Al Mutairi,Mona Alsaleh,Abdullah Alsonbul,Somaya Alzelaye,Shakir Bahzad,Abdulaziz Bin Manee,Ola Jarrad,Neama Meriki,Bassem Albeirouti,Amal Alqasmi,Mohammed AlBalwi,Nawal Makhseed,Saeed Hassan,Isam Salih,Mustafa A Salih,Marwan Shaheen,Saadeh Sermin,Shamsad Shahrukh,Shahrukh Hashmi,Ayman Shawli,Ameen Tajuddin,Abdullah Tamim,Ahmed Alnahari,Ibrahim Ghemlas,Maged Hussein,Sami Wali,Hatem Murad,Brian F Meyer,Fowzan S Alkuraya

  • Distinct HLA Associations with Rheumatoid Arthritis Subsets Defined by Serological Subphenotype.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2019-10-05
    Chikashi Terao,Boel Brynedal,Zuomei Chen,Xia Jiang,Helga Westerlind,Monika Hansson,Per-Johan Jakobsson,Karin Lundberg,Karl Skriner,Guy Serre,Johan Rönnelid,Linda Mathsson-Alm,Mikael Brink,Solbritt Rantapää Dahlqvist,Leonid Padyukov,Peter K Gregersen,Anne Barton,Lars Alfredsson,Lars Klareskog,Soumya Raychaudhuri

  • MCM9 mutations are associated with ovarian failure, short stature, and chromosomal instability.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2014-12-07
    Michelle A Wood-Trageser,Fatih Gurbuz,Svetlana A Yatsenko,Elizabeth P Jeffries,L Damla Kotan,Urvashi Surti,Deborah M Ketterer,Jelena Matic,Jacqueline Chipkin,Huaiyang Jiang,Michael A Trakselis,A Kemal Topaloglu,Aleksandar Rajkovic

    Premature ovarian failure (POF) is genetically heterogeneous and manifests as hypergonadotropic hypogonadism either as part of a syndrome or in isolation. We studied two unrelated consanguineous families with daughters exhibiting primary amenorrhea, short stature, and a 46,XX karyotype. A combination of SNP arrays, comparative genomic hybridization arrays, and whole-exome sequencing analyses identified homozygous pathogenic variants in MCM9, a gene implicated in homologous recombination and repair of double-stranded DNA breaks. In one family, the MCM9 c.1732+2T>C variant alters a splice donor site, resulting in abnormal alternative splicing and truncated forms of MCM9 that are unable to be recruited to sites of DNA damage. In the second family, MCM9 c.394C>T (p.Arg132(∗)) results in a predicted loss of functional MCM9. Repair of chromosome breaks was impaired in lymphocytes from affected, but not unaffected, females in both families, consistent with MCM9 function in homologous recombination. Autosomal-recessive variants in MCM9 cause a genomic-instability syndrome associated with hypergonadotropic hypogonadism and short stature. Preferential sensitivity of germline meiosis to MCM9 functional deficiency and compromised DNA repair in the somatic component most likely account for the ovarian failure and short stature.

  • Incorporating Functional Information in Tests of Excess De Novo Mutational Load.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2015-08-04
    Yu Jiang,Yujun Han,Slavé Petrovski,Kouros Owzar,David B Goldstein,Andrew S Allen

    A number of recent studies have investigated the role of de novo mutations in various neurodevelopmental and neuropsychiatric disorders. These studies attempt to implicate causal genes by looking for an excess load of de novo mutations within those genes. Current statistical methods for assessing this excess are based on the implicit assumption that all qualifying mutations in a gene contribute equally to disease. However, it is well established that different mutations can have radically different effects on the ultimate protein product and, as a result, on disease risk. Here, we propose a method, fitDNM, that incorporates functional information in a test of excess de novo mutational load. Specifically, we derive score statistics from a retrospective likelihood that incorporates the probability of a mutation being damaging to gene function. We show that, under the null, the resulting test statistic is distributed as a weighted sum of Poisson random variables and we implement a saddlepoint approximation of this distribution to obtain accurate p values. Using simulation, we have shown that our method outperforms current methods in terms of statistical power while maintaining validity. We have applied this approach to four de novo mutation datasets of neurodevelopmental and neuropsychiatric disorders: autism spectrum disorder, epileptic encephalopathy, schizophrenia, and severe intellectual disability. Our approach also implicates genes that have been implicated by existing methods. Furthermore, our approach provides strong statistical evidence supporting two potentially causal genes: SUV420H1 in autism spectrum disorder and TRIO in a combined analysis of the four neurodevelopmental and neuropsychiatric disorders investigated here.

  • Mutations in FEZF1 cause Kallmann syndrome.
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2014-09-06
    L Damla Kotan,B Ian Hutchins,Yusuf Ozkan,Fatma Demirel,Hudson Stoner,Paul J Cheng,Ihsan Esen,Fatih Gurbuz,Y Kenan Bicakci,Eda Mengen,Bilgin Yuksel,Susan Wray,A Kemal Topaloglu

    Gonadotropin-releasing hormone (GnRH) neurons originate outside the CNS in the olfactory placode and migrate into the CNS, where they become integral components of the hypothalamic-pituitary-gonadal (HPG) axis. Disruption of this migration results in Kallmann syndrome (KS), which is characterized by anosmia and pubertal failure due to hypogonadotropic hypogonadism. Using candidate-gene screening, autozygosity mapping, and whole-exome sequencing in a cohort of 30 individuals with KS, we searched for genes newly associated with KS. We identified homozygous loss-of-function mutations in FEZF1 in two independent consanguineous families each with two affected siblings. The FEZF1 product is known to enable axons of olfactory receptor neurons (ORNs) to penetrate the CNS basal lamina in mice. Because a subset of axons in these tracks is the migratory pathway for GnRH neurons, in FEZF1 deficiency, GnRH neurons also fail to enter the brain. These results indicate that FEZF1 is required for establishment of the central component of the HPG axis in humans.

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上海纽约大学William Glover