locStra is an R-package for the analysis of regional and global population stratification in whole genome sequencing studies, where regional stratification refers to the substructure defined by the loci in a particular region on the genome. Population substructure can be assessed based on the genetic covariance matrix, the genomic relationship matrix, and the unweighted/weighted genetic Jaccard similarity

Telomeres present unique challenges for genomes with linear chromosomes, including the inability of the semi-conservative DNA replication machinery to fully duplicate the ends of linear molecules. This is solved in virtually all eukaryotes by the enzyme telomerase, through the addition of telomeric repeats onto chromosome ends. It is widely assumed that the primary site of action for telomerase is

SNP heritability of a trait is measured by the proportion of total variance explained by the additive effects of genome-wide single nucleotide polymorphisms (SNPs). Linear mixed models are routinely used to estimate SNP heritability for many complex traits. The basic concept behind this approach is to model genetic contribution as a random effect, where the variance of this genetic contribution attributes

CpG islands (CGIs) represent a distinctive and widespread genetic feature of vertebrate genomes, being associated with ~70% of all annotated gene promoters. CGIs have been proposed to control transcription initiation by conferring nearby promoters with unique chromatin properties. In addition, there are thousands of distal or orphan CGIs (oCGIs) whose functional relevance and mechanism of action are

Precise genome editing is a valuable tool to study gene function in model organisms. Prime editing, a precise editing system developed in mammalian cells, does not require double strand breaks or donor DNA and has low off-target effects. Here, we applied prime editing for the model organism Drosophila melanogaster and developed conditions for optimal editing. By expressing prime editing components

Repair of Cas9-induced double-stranded breaks results primarily in formation of small indels, but can also cause potentially harmful large deletions. While mechanisms leading to the creation of small indels are relatively well understood, very little is known about the origins of large deletions. Using a novel library of clonal mouse embryonic stem cells bona fide deficient for 32 DNA repair genes

The development of CRISPR/Cas9 technology has vastly sped up the process of genome editing by introducing a bacterial system that can be exploited for reverse genetics-based research. However, generating homozygous knockout (KO) animals using traditional CRISPR/Cas9-mediated techniques requires three generations of animals. A founder animal with a desired mutation is crossed to produce heterozygous

There is currently only limited understanding of the genetic aetiology of obstructive sleep apnoea (OSA). The aim of our study is to identify genetic loci associated with OSA risk and to test if OSA and its comorbidities share a common genetic background. We conducted the first large-scale genome-wide association study of OSA using FinnGen Study (217,955 individuals) with 16,761 OSA patients identified

Variants identified by genome-wide association studies (GWAS) are often expression quantitative trait loci (eQTLs), suggesting they are proxies or are themselves regulatory. Across many datasets analyses show that variants often affect multiple genes. Lacking data on many tissue types, developmental time points and homogeneous cell types, the extent of this one-to-many relationship is underestimated

The R47H variant in the microglial TREM2 receptor is a strong risk factor for Alzheimer's disease (AD). To characterize processes affected by R47H we performed integrative network analysis of genes expressed in brains of AD patients with R47H, sporadic AD without the variant and patients with polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL), a systemic disease with

Variants in the LIM homeobox transcription factor 1-beta gene (LMX1B) predispose individuals to elevated intraocular pressure (IOP), a key risk factor for glaucoma. However, the effect of LMX1B mutations varies widely between individuals. To better understand mechanisms underlying LMX1B-related phenotypes and individual differences, we backcrossed the Lmx1bV265D (also known as Lmx1bIcst) allele onto

microRNAs (miRNAs) and RNA binding proteins (RBPs) regulate gene expression at the post-transcriptional level, but the extent to which these key regulators of gene expression coordinate and the precise mechanisms of their coordination are not well understood. RNA binding proteins often have recognizable RNA binding domains that correlate with specific protein function. Recently, several RBPs containing

Undiagnosed neurodevelopmental disease is significantly associated with rare variants in cis-regulatory elements (CRE) but demonstrating causality is challenging as target gene consequences may differ from a causative variant affecting the coding region. Here, we address this challenge by applying a procedure to discriminate likely diagnostic regulatory variants from those of neutral/low-penetrant

Background/Aims: Dietary aflatoxin B1 (AFB1) exposure, which induces DNA damage and codon 249 mutation of the TP53 gene, is one of the major risk factors for hepatocellular carcinoma (HCC). Hepatitis B virus (HBV) infection and AFB1 exert synergistic effects to promote carcinogenesis and TP53 R249S mutation in HCC. Methods: A genome-wide association study (GWAS) was conducted on 485 cases of HCC with

Genomes of tens of thousands of SARS-CoV2 isolates have been sequenced across the world and the total number of changes (predominantly single base substitutions) in these isolates exceeds ten thousand. We compared the mutational spectrum in the new SARS-CoV-2 mutation dataset with the previously published mutation spectrum in hypermutated genomes of rubella - another positive single stranded (ss) RNA

Due to their universal presence and high sequence conservation, rRNA sequences are used widely in phylogenetics for inferring evolutionary relationships between microbes and in metagenomics for analyzing the composition of microbial communities. Most microbial genomes encode multiple copies of ribosomal RNA (rRNA) genes to supply cells with sufficient capacity for protein synthesis. These copies typically

CRISPR genome editing has revolutionized genetics in many organisms. In the nematode Caenorhabditis elegans one injection into each of the two gonad arms of an adult hermaphrodite exposes hundreds of meiotic germ cells to editing mixtures, permitting the recovery of multiple indels or small precision edits from each successfully injected animal. Unfortunately, particularly for long insertions, editing

Over 200 murine imprinted genes have currently been identified, many are expressed in the brain, and a subset have been associated with neurological and behavioural phenotypes. These studies have led to the suggestion that imprinted genes show enriched expression in certain key brain functions; however, this has never been formally tested. Here we use fifteen available single-cell RNA sequencing datasets

Genetic variation in VKORC1 is associated with differences in the coagulation of blood and consequentially with sensitivity to the drug warfarin. Variation in VKORC1 has also been linked to parental dementia. However, it is unclear whether the relationship persists for the diagnosis in patients themselves, whether the association holds only for certain forms of dementia, and if those taking warfarin

Genome-wide association studies (GWAS) have found hundreds of single nucleotide polymorphisms (SNPs) associated with increased risk of cancer. However, the amount of heritable risk explained by these variants is limited, thus leaving most of cancer heritability unexplained. Recent studies have shown that genomic regions associated with specific biological functions explain a large proportion of the

Meiosis in female oocytes lack centrosomes, the major microtubule-organizing center, which may make them especially vulnerable to aneuploidy. In the acentrosomal oocytes of Drosophila, meiotic spindle assembly depends on the chromosomal passenger complex (CPC). Aurora B is the catalytic component of the CPC while the remaining subunits regulate its localization. Using an inhibitor of Aurora B activity

Non-random mating among individuals can lead to spatial clustering of genetically similar individuals and population stratification. This deviation from panmixia is commonly observed in natural populations. Consequently, individuals can have parentage in single populations or involving hybridization between differentiated populations. Accounting for this mixture and structure is important when mapping

The development of Cas9/gRNA-mediated gene-drive systems has bolstered the advancement of genetic technologies for controlling vector-borne pathogen transmission. These include population suppression approaches, genetic analogs of insecticidal techniques that reduce the number of vector insects, and population modification (replacement/alteration) approaches, which interfere with competence to transmit

Background and aims: Oncostatin M (OSM) signaling is implicated in atherosclerosis, however the mechanism remains unclear. We investigated the impact of common genetic variants in OSM and its receptors, OSMR and LIFR, on overall plaque vulnerability, plaque phenotype, intraplaque OSMR and LIFR expression, coronary artery calcification burden and cardiovascular disease susceptibility. Methods and results:

Base editing technique and PRIME editing techniques derived from the CRISPR/Cas9 discovery permit to modify selected nucleotides. We initially used the base editing technique to introduce in the APP gene the A673T mutation, which prevents the development of Alzheimer disease. Although the desired cytidine to thymidine mutation was inserted in up to 17% of the APP gene in HEK393T, there were also modifications

Achondroplasia (ACH) is the most common genetic form of dwarfism and belongs to dominant monogenic disorder caused by a gain-of-function point mutation in the transmembrane region of FGFR3. Stem cells and gene-editing technology provide us with effective methods and ideas for research and treatment of ACH. Here we generated non-integrated iPSCs from one ACH girl skin and one ACH boy urine via Sendai

Signalling lipids of the N-acyl ethanolamine (NAE) and ceramide (CER) classes are emerging as novel cardiovascular disease biomarkers. We sought to establish the heritability of plasma NAEs (including the endocannabinoid anandamide) and CERs, and identify common DNA variants influencing the circulating concentrations of the heritable lipid species. Nine NAE and sixteen CER species were analysed in

Cohesin helps mediate sister chromatid cohesion, chromosome condensation, DNA repair and transcription regulation. Cohesin can tether two regions of DNA and also extrude DNA loops. We interrogated cohesin architecture, oligomerization and function in vivo through proximity based labeling of cohesin domains. Our results suggest that the hinge and head domain of cohesin both bind DNA, and that cohesin

Genetic similarity is a measure for the genetic relatedness among individuals. The standard method for computing similarity matrices involves the inner product of observed genetic variant matrices. Such an approach is inaccurate or impossible if genotypes are not available, or not densely sampled, or of poor quality (for example, genetic analysis of extinct species). We provide a new method for computing

Due to the field soil changes, high density planting, and straw-returning methods, wheat common root rot (spot blotch) and Fusarium crown rot (FCR) have become severe threatens to global wheat productions. Only a few wheat genotypes show moderate resistance to these root and crown rot fungal diseases, and the genetic determinants of wheat resistance to these two devastating diseases have been poorly

Crossover frequency often differs substantially between sexes (i.e. heterochiasmy). Although this phenomenon is widespread throughout taxa, the mechanisms that lead to heterochiasmy remain unclear. One pattern that has emerged is that the overall length of the synaptonemal complex likely has a direct influence on the total number of crossovers in each sex. However, this has only been investigated in

Human brain has a complex functional architecture and remains active during resting conditions. Resting-state functional magnetic resonance imaging (rsfMRI) measures brain activity at rest, which is closely linked with cognition and clinical outcomes. The role of genetics in human brain function is largely unknown. Here we utilized rsfMRI of 44,190 multi-ethnic individuals (37,339 in the UK Biobank)

Genetic surveillance of malaria parasites supports malaria control programmes, treatment guidelines and elimination strategies. Surveillance studies often pose questions about malaria parasite ancestry (e.g. how antimalarial resistance has spread) and employ statistical methods that characterise parasite population structure. Many of the methods used to characterise structure are unsupervised machine

The idea that deaf intermarriage increases deafness was forcefully pushed in the late 19th century by Alexander Graham Bell, in proceedings published by the National Academy of Science. Bell's hypothesis was not supported by a 19th century study by Edward Allen Fay, which was funded by Bell's own organization, the Volta Bureau. The Fay study showed through an analysis of 4,471 deaf marriages that the

The contribution of low-frequency variants to the genomic architecture of normal-range facial traits is unknown. Therefore, we studied the influence of 31347 low-frequency coding variants (MAF < 1%) in 8091 genes on multi-dimensional facial shape phenotypes in a European cohort of 2329 healthy individuals. Using three-dimensional facial images, we partitioned the full face into 31 hierarchically arranged

We present a novel method to detect runs of homozygosity (ROH) from low-coverage genotype data typical for ancient human DNA. ROH are the genetic signature of matings between closely related parents, and as such, the frequency and length distribution of these blocks can give insight into recent population history and mating patterns. Existing methods identify ROH by scanning for regions that lack heterozygote

Case-control genetic association study is an efficient tool to search for the deleterious genetic variants predispose to human complex diseases, where the additive mode of inheritance is commonly assumed. However, how the genetic variants influence the occurrence of a certain disease is impossible to know beforehand. We show numerically that the existing procedures using the Hardy-Weinberg equilibrium

Genomic prediction can be advantageous in barley breeding for traits such as yield and malting quality to increase selection accuracy and minimize expensive phenotyping. In this paper, we investigate the possibilities of genomic selection for malting quality traits using a limited training population. The size of the training population is an important factor in determining the prediction accuracy

The advent of animal husbandry and hunting increased human exposure to zoonotic pathogens. To understand how a zoonotic disease influenced human evolution, we studied changes in human expression of anthrax toxin receptor 2 (ANTXR2), which encodes a cell surface protein necessary for Bacillus anthracis virulence toxins to cause anthrax disease. In immune cells, ANTXR2 was 8-fold down-regulated in all

Baculoviruses constitute a large group of invertebrate DNA viruses, predominantly infecting larvae of the insect order Lepidoptera. During a baculovirus infection, the virus spreads throughout the insect body producing a systemic infection in multiple larval tissues. Some behavioral and physiological changes in lepidopteran larvae have been described following a baculovirus infection and those changes

Understanding how regulatory sequences control gene expression is fundamental to explain how phenotypes arise in health and disease. Traditional reporter assays inform about function of individual regulatory elements, typically in isolation. However, regulatory elements must ultimately be understood by perturbing them within their genomic environment and developmental- or tissue-specific contexts.

Importance: Molecular genetic studies of alcohol and nicotine use have identified hundreds of genome-wide risk loci. Few studies have examined the influence of aggregate genetic risk on substance use trajectories over time. Objective: We examined the predictive utility of drinking and smoking polygenic risk scores (PRS) for alcohol and nicotine use from late childhood to early adulthood, substance-specific

Importance: Large consortia of genome wide association studies have yielded more accurate polygenic risk scores (PRS) that aggregate the small effects of many genetic variants to characterize the genetic architecture of disorders and provide a personalized measure of genetic risk. Objective: We examined whether a PRS for smoking measured genetic risk for general behavioral disinhibition by estimating

Genome editing via homology-directed repair (HDR) has made possible precise and deliberate modifications to gene sequences. CRISPR/Cas9-mediated HDR is the simplest means to carry this out. However, technical challenges remain to improve efficiency and broaden applicability to any genetic background of Drosophila melanogaster as well as to other Drosophila species. To address these issues, we developed

Globoid Cell Leukodystrophy (GLD, or Krabbe disease) is a rare lysosomal storage disease caused by inherited deficiency of beta-galactocerebrosidase (GALC). The build-up of galactosylsphingosine (psychosine) and other undegraded galactosylsphingolipids in the nervous system causes severe demyelination and neurodegeneration. The molecular mechanisms of GLD are poorly elucidated in neural cells and whether

Mitotic recombination is the predominant mechanism for repairing double-strand breaks in Saccharomyces cerevisiae. Current recombination models are largely based on studies utilizing the enzyme I-SceI or HO to create a site-specific break, each of which generates broken ends with 3′ overhangs. In this study sequence-diverged ectopic substrates were used to assess whether the frequent Pol δ-mediated

Compared to free-living bacteria, endosymbionts of sap-feeding insects have tiny and rapidly evolving genomes. Increased genetic drift, high mutation rates, and relaxed selection associated with host control of key cellular functions all likely contribute to genome decay. Phylogenetic comparisons have revealed massive variation in endosymbiont evolutionary rate, but such methods make it difficult to

Ultracold preservation is widely used for storage of genetic stocks of Caenorhabditis elegans. Current cryopreservation protocols are vulnerable to refrigeration failures, which can result in the loss of stock viability due to damage during re-freezing. Here we present a method for preserving worms in a dehydrated and frozen form that retains viability after multiple freeze/thaw cycles. After dehydration

Cancer incidence varies by tissue due to differences in environmental risk factor exposure, gene variant inheritance, and lifetime number of stem cell divisions in a tissue. Folate deficiency is associated with increased risk for colorectal cancer (CRC) and acute lymphocytic leukemia. Conversely, high folic acid (FA) intake has been associated with higher CRC risk. However, the mutagenic potential

Aging and longevity are complex processes controlled at different levels, including genetic level. We evaluated the association of seven drug and DNA-repair gene polymorphisms with longevity in an Italian cohort. A sample of 756 subjects aged 18-98 was genotyped for CYP1A1 exon 7 A>G, GSTT1 null, GSTM1 null, GSTP A>G, XRCC1 exon 6 C>T, XRCC1 exon 9 A> G and XPC exon 15 A>C gene polymorphisms. The association

Deafness, the most frequent sensory deficit in humans, is extremely heterogenous with hundreds of genes probably involved. Clinical and genetic analyses of an extended consanguineous family with pre-lingual, moderate-to-profound autosomal recessive sensorineural hearing loss, allowed us to identify CLRN2, encoding a tetraspan protein as a new deafness gene. Homozygosity mapping followed by exome sequencing

Due to their sessile lifestyle, plants have evolved unique mechanisms to deal with environmental challenges. Under stress, plant lipids are important as alternative sources of carbon and energy when sugars or starch are limited. Here, we applied combined heat and darkness and extended darkness to a panel of ~ 300 Arabidopsis accessions to study lipid remodeling under carbon starvation. Natural allelic

While thousands of loci have been associated with human phenotypes, the role of gene-environment (GxE) interactions in determining individual risk of human diseases remains unclear. This is partly due to the severe erosion of statistical power resulting from the massive number of statistical tests required to detect such interactions. Here, we focus on improving the power of GxE tests by developing

Tissue-specific knockout techniques are widely applied in biological studies to probe the tissue-specific roles of specific genes in physiology, development, and disease. CRISPR/Cas9 is a widely used technology to perform fast and efficient genome editing in vitro and in vivo. Here, we report a robust CRISPR-based gateway system for tissue-specific gene inactivation in zebrafish. A transgenic fish

Temporally spaced genetic data allow for more accurate inference of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel likelihood-based method for jointly estimating selection coefficient and allele age from time series data of allele frequencies. Our approach is based on a hidden Markov model where the underlying process

Two drought-tolerant wheat cultivars, ‘TAM 111’ and ‘TAM 112’, have been widely grown in the Southern Great Plains of the U.S. and used as parents in many wheat breeding programs worldwide. This study aimed to reveal genetic control of yield and yield components in the two cultivars under both dryland and irrigated conditions. A mapping population containing 124 F5:7 recombinant inbred lines (RILs)

Biological interactions are prevalent in the functioning organisms. Correspondingly, statistical geneticists developed various models to identify genetic interactions through genotype-phenotype association mapping. The current standard protocols in practice test single variants or single regions (that contain multiple local variants) sequentially along the genome, followed by functional annotations

Interaction analysis is used to investigate the magnitude of an effect which two risk factors have on disease risk, and on each other. To study interactions, both additive and multiplicative models have been used, although their interpretations are not universally understood. In this study, we set out to investigate the resulting interactions of several risk factors relationships in additive or multiplicative

The Cre/lox recombinase system has been widely used for spatiotemporal control of gene expression in animal model systems, however, efficient methods to isolate zebrafish Cre drivers that reliably recapitulate endogenous gene expression patterns are needed. Here, we apply CRISPR/Cas9 targeting to integrate a 2A-Cre recombinase transgene with 48bp homology arms into proneural genes ascl1b, olig2 and

The feeling of hunger or satiety results from integration of the sensory nervous system with other physiological and metabolic cues. This regulates food intake, maintains homeostasis and prevents disease. In C. elegans, chemosensory neurons sense food and relay information to the rest of the animal via hormones to control food-related behaviour and physiology. Here we identify a new component of this