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Screening of disease-related biomarkers related to neuropathic pain (NP) after spinal cord injury (SCI) Hum. Genomics (IF 3.351) Pub Date : 2021-01-25 Jia Zhao; Li Yang; Limin Huang; Zinan Li
Based on the molecular expression level, this paper compares lncRNA and mRNA expressions respectively in peripheral blood samples of the patients after SCI with NP and without NP, and screens disease-related biomarkers related to NP after SCI in peripheral blood samples of patients. The expression spectrum of 25 human peripheral blood samples (12 samples of refractory NP patients after SCI) was downloaded
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Correction to: Hyperinsulinism associated with GLUD1 mutation: allosteric regulation and functional characterization of p.G446V glutamate dehydrogenase Hum. Genomics (IF 3.351) Pub Date : 2021-01-25 Karolina Luczkowska; Caroline Stekelenburg; Frédérique Sloan-Béna; Emmanuelle Ranza; Giacomo Gastaldi; Valérie Schwitzgebel; Pierre Maechler
An amendment to this paper has been published and can be accessed via the original article.
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Comprehensive assessments of germline deletion structural variants reveal the association between prognostic MUC4 and CEP72 deletions and immune response gene expression in colorectal cancer patients Hum. Genomics (IF 3.351) Pub Date : 2021-01-11 Peng-Chan Lin; Hui-O Chen; Chih-Jung Lee; Yu-Min Yeh; Meng-Ru Shen; Jung-Hsien Chiang
Functional disruptions by large germline genomic structural variants in susceptible genes are known risks for cancer. We used deletion structural variants (DSVs) generated from germline whole-genome sequencing (WGS) and DSV immune-related association tumor microenvironment (TME) to predict cancer risk and prognosis. We investigated the contribution of germline DSVs to cancer susceptibility and prognosis
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Alu retrotransposons and COVID-19 susceptibility and morbidity Hum. Genomics (IF 3.351) Pub Date : 2021-01-04 Manci Li; Luca Schifanella; Peter A. Larsen
SARS-CoV-2 has spread rapidly across the world and is negatively impacting the global human population. COVID-19 patients display a wide variety of symptoms and clinical outcomes, including those attributed to genetic ancestry. Alu retrotransposons have played an important role in human evolution, and their variants influence host response to viral infection. Intronic Alus regulate gene expression
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Network machine learning maps phytochemically rich “Hyperfoods” to fight COVID-19 Hum. Genomics (IF 3.351) Pub Date : 2021-01-02 Ivan Laponogov; Guadalupe Gonzalez; Madelen Shepherd; Ahad Qureshi; Dennis Veselkov; Georgia Charkoftaki; Vasilis Vasiliou; Jozef Youssef; Reza Mirnezami; Michael Bronstein; Kirill Veselkov
In this paper, we introduce a network machine learning method to identify potential bioactive anti-COVID-19 molecules in foods based on their capacity to target the SARS-CoV-2-host gene-gene (protein-protein) interactome. Our analyses were performed using a supercomputing DreamLab App platform, harnessing the idle computational power of thousands of smartphones. Machine learning models were initially
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COVID-19 update: the first 6 months of the pandemic Hum. Genomics (IF 3.351) Pub Date : 2020-12-23 Giuseppe Novelli; Michela Biancolella; Ruty Mehrian-Shai; Caroline Erickson; Krystal J. Godri Pollitt; Vasilis Vasiliou; Jessica Watt; Juergen K. V. Reichardt
The COVID-19 pandemic is sweeping the world and will feature prominently in all our lives for months and most likely for years to come. We review here the current state 6 months into the declared pandemic. Specifically, we examine the role of the pathogen, the host and the environment along with the possible role of diabetes. We also firmly believe that the pandemic has shown an extraordinary light
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A rational approach to COVID-19 Hum. Genomics (IF 3.351) Pub Date : 2020-12-22 Ruty Mehrian-Shai
It is crucial to use the wealth of information emerging from the ongoing SARS-CoV-2 pandemic and confront COVID-19 with a rational approach. There are proactive steps to prevent and fight COVID-19. Management of the disease should be according to clinical features and laboratory test markers and personalized therapeutic targets.
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The haplotypes of various TNF related genes associated with scleritis in Chinese Han Hum. Genomics (IF 3.351) Pub Date : 2020-12-07 Yingnan Gao; Liping Du; Fuzhen Li; Jiadong Ding; Geng Li; Qingfeng Cao; Na Li; Guannan Su; Aize Kijlstra; Peizeng Yang
Several studies have stated that TNF-α participates in the pathogenesis of scleritis, but also in several systemic autoimmune diseases and vasculitis, of which some are associated with scleritis. Earlier GWAS and SNP studies have confirmed that multiple SNPs of TNF related genes are associated with many immune-mediated disorders. The purpose of this study was to examine the association of TNF related
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KVarPredDB: a database for predicting pathogenicity of missense sequence variants of keratin genes associated with genodermatoses Hum. Genomics (IF 3.351) Pub Date : 2020-12-07 Yuyi Ying; Lu Lu; Santasree Banerjee; Lizhen Xu; Qiang Zhao; Hao Wu; Ruiqi Li; Xiao Xu; Hua Yu; Dante Neculai; Yongmei Xi; Fan Yang; Jiale Qin; Chen Li
Germline variants of ten keratin genes (K1, K2, K5, K6A, K6B, K9, K10, K14, K16, and K17) have been reported for causing different types of genodermatoses with an autosomal dominant mode of inheritance. Among all the variants of these ten keratin genes, most of them are missense variants. Unlike pathogenic and likely pathogenic variants, understanding the clinical importance of novel missense variants
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Pathogenic variants identified by whole-exome sequencing in 43 patients with epilepsy Hum. Genomics (IF 3.351) Pub Date : 2020-12-07 Linlin Zhang; Jinshuang Gao; Hailiang Liu; Yuan Tian; Xiaoli Zhang; Wei Lei; Ying Li; Yaqing Guo; Haiyang Yu; Erfeng Yuan; Lisi Liang; Shihong Cui; Xiaoan Zhang
Epilepsy is a group of neurological disorders characterized by recurrent epileptic seizures. Epilepsy is affected by many factors, approximately 20–30% of cases are caused by acquired conditions, but in the remaining cases, genetic factors play an important role. Early establishment of a specific diagnosis is important to treat and manage this disease. In this study, we have recruited 43 epileptic
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Microarray analysis identification of key pathways and interaction network of differential gene expressions during osteogenic differentiation Hum. Genomics (IF 3.351) Pub Date : 2020-11-25 Fatemeh Khodabandehloo; Sara Taleahmad; Reza Aflatoonian; Farzad Rajaei; Zahra Zandieh; Marjan Nassiri-Asl; Mohamadreza Baghaban Eslaminejad
Adult bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stem cells that can differentiate into three lineages. They are suitable sources for cell-based therapy and regenerative medicine applications. This study aims to evaluate the hub genes and key pathways of differentially expressed genes (DEGs) related to osteogenesis by bioinformatics analysis in three different days. The DEGs
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Correction to: The social, economic, political, and genetic value of race and ethnicity in 2020 Hum. Genomics (IF 3.351) Pub Date : 2020-11-24 Tesfaye B. Mersha; Andrew F. Beck
An amendment to this paper has been published and can be accessed via the original article.
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Aldh1l2 knockout mouse metabolomics links the loss of the mitochondrial folate enzyme to deregulation of a lipid metabolism observed in rare human disorder Hum. Genomics (IF 3.351) Pub Date : 2020-11-09 Natalia I. Krupenko; Jaspreet Sharma; Peter Pediaditakis; Kristi L. Helke; Madeline S. Hall; Xiuxia Du; Susan Sumner; Sergey A. Krupenko
Mitochondrial folate enzyme ALDH1L2 (aldehyde dehydrogenase 1 family member L2) converts 10-formyltetrahydrofolate to tetrahydrofolate and CO2 simultaneously producing NADPH. We have recently reported that the lack of the enzyme due to compound heterozygous mutations was associated with neuro-ichthyotic syndrome in a male patient. Here, we address the role of ALDH1L2 in cellular metabolism and highlight
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Human genetic factors associated with susceptibility to SARS-CoV-2 infection and COVID-19 disease severity Hum. Genomics (IF 3.351) Pub Date : 2020-10-22 Cleo Anastassopoulou; Zoi Gkizarioti; George P. Patrinos; Athanasios Tsakris
The emergence of the novel coronavirus in Wuhan, Hubei Province, China, in December 2019 marked the synchronization of the world to a peculiar clock that is counting infected cases and deaths instead of hours and minutes. The pandemic, highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has indeed caused considerable morbidity and mortality and drastically changed our
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Mild dyserythropoiesis and β-like globin gene expression imbalance due to the loss of histone chaperone ASF1B Hum. Genomics (IF 3.351) Pub Date : 2020-10-16 Petros Papadopoulos; Athanassia Kafasi; Iris M. De Cuyper; Vilma Barroca; Daniel Lewandowski; Zahra Kadri; Martijn Veldthuis; Jeffrey Berghuis; Nynke Gillemans; Celina María Benavente Cuesta; Frank G. Grosveld; Rob van Zwieten; Sjaak Philipsen; Muriel Vernet; Laura Gutiérrez; George P. Patrinos
The expression of the human β-like globin genes follows a well-orchestrated developmental pattern, undergoing two essential switches, the first one during the first weeks of gestation (ε to γ), and the second one during the perinatal period (γ to β). The γ- to β-globin gene switching mechanism includes suppression of fetal (γ-globin, HbF) and activation of adult (β-globin, HbA) globin gene transcription
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A miR-182 variant and risk of hepatocellular carcinoma in a southern Chinese population Hum. Genomics (IF 3.351) Pub Date : 2020-10-15 Moqin Qiu; Yingchun Liu; Qiuling Lin; Zihan Zhou; Yanji Jiang; Rongrui Huo; Xiumei Liang; Xiangyuan Yu; Ji Cao; Xianguo Zhou; Hongping Yu
MicroRNAs (miRNAs) play important roles in the regulation of gene expression at the posttranscriptional level and are involved in human carcinogenesis. The aim of the current study was to investigate the associations between miR-182 single nucleotide polymorphisms and HCC risk in a southern Chinese population. In this case-control study of 863 HCC patients and 908 cancer-free controls, we performed
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The social, economic, political, and genetic value of race and ethnicity in 2020 Hum. Genomics (IF 3.351) Pub Date : 2020-10-15 Tesfaye B. Mersha; Andrew F. Beck
Disparities across racial and ethnic groups are present for a range of health outcomes. In this opinion piece, we consider the origin of racial and ethnic groupings, a history that highlights the sociopolitical nature of these terms. Indeed, the terms race and ethnicity exist purely as social constructs and must not be used interchangeably with genetic ancestry. There is no scientific evidence that
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Evaluation of a genetic risk score for severity of COVID-19 using human chromosomal-scale length variation Hum. Genomics (IF 3.351) Pub Date : 2020-10-09 Christopher Toh; James P. Brody
The course of COVID-19 varies from asymptomatic to severe in patients. The basis for this range in symptoms is unknown. One possibility is that genetic variation is partly responsible for the highly variable response. We evaluated how well a genetic risk score based on chromosomal-scale length variation and machine learning classification algorithms could predict severity of response to SARS-CoV-2
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Practicing precision medicine with intelligently integrative clinical and multi-omics data analysis Hum. Genomics (IF 3.351) Pub Date : 2020-10-02 Zeeshan Ahmed
Precision medicine aims to empower clinicians to predict the most appropriate course of action for patients with complex diseases like cancer, diabetes, cardiomyopathy, and COVID-19. With a progressive interpretation of the clinical, molecular, and genomic factors at play in diseases, more effective and personalized medical treatments are anticipated for many disorders. Understanding patient’s metabolomics
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Aberration of the modulatory functions of intronic microRNA hsa-miR-933 on its host gene ATF2 results in type II diabetes mellitus and neurodegenerative disease development Hum. Genomics (IF 3.351) Pub Date : 2020-09-29 Abul Bashar Mir Md. Khademul Islam; Eusra Mohammad; Md. Abdullah-Al-Kamran Khan
MicroRNAs are ~ 22-nucleotide-long biological modifiers that act as the post-transcriptional modulator of gene expression. Some of them are identified to be embedded within the introns of protein-coding genes, these miRNAs are called the intronic miRNAs. Previous findings state that these intronic miRNAs are co-expressed with their host genes. This co-expression is necessary to maintain the robustness
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Exploration of CYP21A2 and CYP17A1 polymorphisms and preeclampsia risk among Chinese Han population: a large-scale case-control study based on 5021 subjects Hum. Genomics (IF 3.351) Pub Date : 2020-09-25 Bo Hou; Xuewen Jia; Ziwen Deng; Xin Liu; Huitang Liu; Haichu Yu; Shiguo Liu
Several genome-wide association studies have identified single-nucleotide polymorphisms (SNPs), such as rs4409766, rs1004467, and rs3824755 in CYP17A1 and rs2021783 in CYP21A2, as new hypertension susceptibility genetic variants in the Chinese population. This study aimed to look into the relationship between preeclampsia (PE) and these SNPs in Chinese Han women. Overall, 5021 unrelated pregnant women
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A de novo frameshift pathogenic variant in TBR1 identified in autism without intellectual disability. Hum. Genomics (IF 3.351) Pub Date : 2020-09-18 Laurie-Anne Sapey-Triomphe,Julie Reversat,Gaëtan Lesca,Nicolas Chatron,Marina Bussa,Sylvie Mazoyer,Christina Schmitz,Sandrine Sonié,Patrick Edery
In order to be able to provide accurate genetic counseling to patients with Autism Spectrum Disorder (ASD), it is crucial to identify correlations between heterogeneous phenotypes and genetic alterations. Among the hundreds of de novo pathogenic variants reported in ASD, single-nucleotide variations and small insertions/deletions were reported in TBR1. This gene encodes a transcription factor that
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Long non-coding RNA MIR4300HG polymorphisms are associated with postoperative nausea and vomiting: a genome-wide association study. Hum. Genomics (IF 3.351) Pub Date : 2020-09-14 Shigekazu Sugino,Daisuke Konno,Yosuke Kawai,Masao Nagasaki,Yasuhiro Endo,Tomo Hayase,Misako Yamazaki-Higuchi,Yukihiro Kumeta,Shunsuke Tachibana,Katsuhiko Saito,Jun Suzuki,Kanta Kido,Nahoko Kurosawa,Akiyoshi Namiki,Masanori Yamauchi
Genetic factors such as single-nucleotide polymorphisms (SNPs) play a key role in the development of postoperative nausea and vomiting (PONV). However, previous findings are not widely applicable to different populations because of population-specific genetic variation. We developed a Japanese-specific DNA microarray for high-throughput genotyping. The aim of the current study was to identify SNPs
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Genetic variants of the human host influencing the coronavirus-associated phenotypes (SARS, MERS and COVID-19): rapid systematic review and field synopsis. Hum. Genomics (IF 3.351) Pub Date : 2020-09-11 Emilio Di Maria,Andrea Latini,Paola Borgiani,Giuseppe Novelli
The COVID-19 pandemic has strengthened the interest in the biological mechanisms underlying the complex interplay between infectious agents and the human host. The spectrum of phenotypes associated with the SARS-CoV-2 infection, ranging from the absence of symptoms to severe systemic complications, raised the question as to what extent the variable response to coronaviruses (CoVs) is influenced by
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Analysis of ACE2 genetic variants in 131 Italian SARS-CoV-2-positive patients. Hum. Genomics (IF 3.351) Pub Date : 2020-09-11 Antonio Novelli,Michela Biancolella,Paola Borgiani,Dario Cocciadiferro,Vito Luigi Colona,Maria Rosaria D'Apice,Paola Rogliani,Salvatore Zaffina,Francesca Leonardis,Andrea Campana,Massimiliano Raponi,Massimo Andreoni,Sandro Grelli,Giuseppe Novelli
Coronaviruses (CoV) are a large family of viruses that are common in humans and many animal species. Animal coronaviruses rarely infect humans with the exceptions of the Middle East respiratory syndrome ( MERS-CoV ), the severe acute respiratory syndrome corona virus (SARS-CoV), and now SARS-CoV-2, which is the cause of the ongoing pandemic of coronavirus disease 2019 (COVID-19). Several studies suggested
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Delineation of molecular findings by whole-exome sequencing for suspected cases of paediatric-onset mitochondrial diseases in the Southern Chinese population. Hum. Genomics (IF 3.351) Pub Date : 2020-09-10 Mandy H Y Tsang,Anna K Y Kwong,Kate L S Chan,Jasmine L F Fung,Mullin H C Yu,Christopher C Y Mak,Kit-San Yeung,Richard J T Rodenburg,Jan A M Smeitink,Rachel Chan,Thomas Tsoi,Joannie Hui,Shelia S N Wong,Shuk-Mui Tai,Victor C M Chan,Che-Kwan Ma,Sharon T H Fung,Shun-Ping Wu,W K Chak,Brian H Y Chung,Cheuk-Wing Fung
Mitochondrial diseases (MDs) are a group of clinically and genetically heterogeneous disorders characterized by defects in oxidative phosphorylation. Since clinical phenotypes of MDs may be non-specific, genetic diagnosis is crucial for guiding disease management. In the current study, whole-exome sequencing (WES) was performed for our paediatric-onset MD cohort of a Southern Chinese origin, with the
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Human genetics and genomics meetings going virtual: practical lessons learned from two international meetings in early 2020. Hum. Genomics (IF 3.351) Pub Date : 2020-07-08 Alistair R R Forrest,Gabriela M Repetto,Juergen K V Reichardt
The recent coronavirus disease 2019 (COVID-19) pandemic has caused worldwide disruption which also extends to the arena of scientific meetings around the world. Here, we explore the lessons learned from moving two human genetics and genomics meetings quickly to an online format in early 2020. The tips presented herein may be useful not only for future virtual meetings but may also enrich future physical
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Novel biallelic loss-of-function variants in CEP290 cause Joubert syndrome in two siblings. Hum. Genomics (IF 3.351) Pub Date : 2020-06-29 Xiang Wang,Zhu Zhang,Xueguang Zhang,Ying Shen,Hongqian Liu
Joubert syndrome (JS) is a rare genetic disorder, which can be defined by brain stem malformation, cerebellar vermis hypoplasia, and consequent “molar tooth sign” (MTS). JS always shares variety of phenotypes in development defects. With the development of next-generation sequencing, dozens of causative genes have been identified to JS so far. Here, we investigated two male siblings with JS and uncovered
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Application of CRISPR/Cas9 to human-induced pluripotent stem cells: from gene editing to drug discovery. Hum. Genomics (IF 3.351) Pub Date : 2020-06-26 Claudia De Masi,Paola Spitalieri,Michela Murdocca,Giuseppe Novelli,Federica Sangiuolo
Human-induced pluripotent stem cells (hiPSCs) and CRISPR/Cas9 gene editing system represent two instruments of basic and translational research, which both allow to acquire deep insight about the molecular bases of many diseases but also to develop pharmacological research. This review is focused to draw up the latest technique of gene editing applied on hiPSCs, exploiting some of the genetic manipulation
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A potential prognostic prediction model of colon adenocarcinoma with recurrence based on prognostic lncRNA signatures. Hum. Genomics (IF 3.351) Pub Date : 2020-06-10 Lipeng Jin,Chenyao Li,Tao Liu,Lei Wang
Colon adenocarcinoma (COAD) is one of the common gastrointestinal malignant diseases, with high mortality rate and poor prognosis due to delayed diagnosis. This study aimed to construct a prognostic prediction model for patients with colon adenocarcinoma (COAD) recurrence. Differently expressed RNAs (DERs) between recurrence and non-recurrence COAD samples were identified based on expression profile
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Whole-genome sequencing of Chinese centenarians reveals important genetic variants in aging WGS of centenarian for genetic analysis of aging. Hum. Genomics (IF 3.351) Pub Date : 2020-06-10 Shuhua Shen,Chao Li,Luwei Xiao,Xiaoming Wang,Hang Lv,Yuan Shi,Yixue Li,Qi Huang
Genetic research on longevity has provided important insights into the mechanism of aging and aging-related diseases. Pinpointing import genetic variants associated with aging could provide insights for aging research. We performed a whole-genome sequencing in 19 centenarians to establish the genetic basis of human longevity. Using SKAT analysis, we found 41 significantly correlated genes in centenarians
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Genomics of COVID-19: molecular mechanisms going from susceptibility to severity of the disease. Hum. Genomics (IF 3.351) Pub Date : 2020-06-10 Ruty Mehrian-Shai,Giuseppe Novelli,Vasilis Vasiliou,Jessica Watt,Juergen K V Reichardt
The current COVID-19 pandemic (https://www.who.int/dg/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19%2D%2D-11-march-2020) has highlighted the importance of science and medicine, specifically public health, in our modern societies. Countries have taken different approaches to the pandemic. Science and medicine will play an important role in our way forward.
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Clinical performance of non-invasive prenatal served as a first-tier screening test for trisomy 21, 18, 13 and sex chromosome aneuploidy in a pilot city in China. Hum. Genomics (IF 3.351) Pub Date : 2020-06-05 Yanhui Liu,Hailiang Liu,Yi He,Wanfang Xu,Qiulin Ma,Yuzhen He,Wei Lei,Guoquan Chen,Zheng He,Jiayi Huang,Jianan Liu,Yuanru Liu,Quanfei Huang,Fubing Yu
Cell-free fetal DNA (cffDNA) has opened up new approaches for non-invasive prenatal testing (NIPT), and it is often used as the second-tier test for high-risk pregnant women in detecting trisomy (T) 21, T18, and T13 after serum biochemistry screening. This study aims to discuss the clinical performance of NIPT as an alternative first-tier screening test for pregnant women in detecting T21, T18, T13
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COVID-19 preclinical models: human angiotensin-converting enzyme 2 transgenic mice. Hum. Genomics (IF 3.351) Pub Date : 2020-06-04 Cathleen Lutz,Leigh Maher,Charles Lee,Wonyoung Kang
Coronavirus disease 2019 (COVID-19) is a declared pandemic that is spreading all over the world at a dreadfully fast rate. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the pathogen of COVID-19, infects the human body using angiotensin-converting enzyme 2 (ACE2) as a receptor identical to the severe acute respiratory syndrome (SARS) pandemic that occurred in 2002–2003. SARS-CoV-2 has
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Gene X environment: the cellular environment governs the transcriptional response to environmental chemicals. Hum. Genomics (IF 3.351) Pub Date : 2020-05-24 Andreanna Burman,Rolando Garcia-Milian,Shannon Whirledge
BACKGROUND An individual's response to environmental exposures varies depending on their genotype, which has been termed the gene-environment interaction. The phenotype of cell exposed can also be a key determinant in the response to physiological cues, indicating that a cell-gene-environment interaction may exist. We investigated whether the cellular environment could alter the transcriptional response
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An investigation of genetic polymorphisms in heparan sulfate proteoglycan core proteins and key modification enzymes in an Australian Caucasian multiple sclerosis population. Hum. Genomics (IF 3.351) Pub Date : 2020-05-12 Rachel K Okolicsanyi,Julia Bluhm,Cassandra Miller,Lyn R Griffiths,Larisa M Haupt
Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease affecting the central nervous system in young adults. Heparan sulfate proteoglycans (HSPGs) are ubiquitous to the cell surface and the extracellular matrix. HSPG biosynthesis is a complex process involving enzymatic attachment of heparan sulfate (HS) chains to a core protein. HS side chains mediate specific ligand and growth factor
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COVID-19 vulnerability: the potential impact of genetic susceptibility and airborne transmission. Hum. Genomics (IF 3.351) Pub Date : 2020-05-12 Krystal J Godri Pollitt,Jordan Peccia,Albert I Ko,Naftali Kaminski,Charles S Dela Cruz,Daniel W Nebert,Juergen K V Reichardt,David C Thompson,Vasilis Vasiliou
The recent coronavirus disease (COVID-19), caused by SARS-CoV-2, is inarguably the most challenging coronavirus outbreak relative to the previous outbreaks involving SARS-CoV and MERS-CoV. With the number of COVID-19 cases now exceeding 2 million worldwide, it is apparent that (i) transmission of SARS-CoV-2 is very high and (ii) there are large variations in disease severity, one component of which
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Identification of rare and common variants in BNIP3L: a schizophrenia susceptibility gene. Hum. Genomics (IF 3.351) Pub Date : 2020-05-11 Juan Zhou,Chuanchuan Ma,Ke Wang,Xiuli Li,Xuemin Jian,Han Zhang,Jianmin Yuan,Jiajun Yin,Jianhua Chen,Yongyong Shi
BACKGROUND Schizophrenia is a chronic and severe mental disorder, and it has been predicted to be highly polygenic. Common SNPs located in or near BNIP3L were found to be genome-wide significantly associated with schizophrenia in recent genome-wide association studies. The purpose of our study is to investigate potential causal variants in BNIP3L gene. RESULTS We performed targeted sequencing for all
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Hydroxymethylation and tumors: can 5-hydroxymethylation be used as a marker for tumor diagnosis and treatment? Hum. Genomics (IF 3.351) Pub Date : 2020-05-06 Tianmin Xu,Haoyue Gao
5-Methylcytosine (5mC) is considered as a common epigenetic modification that plays an important role in the regulation of gene expression. At the same time, 5-hydroxymethylcytosine (5hmC) has been found as an emerging modification of cytosine bases of recent years. Unlike 5mC, global 5hmC levels vary from tissues that have differential distribution both in mammalian tissues and in the genome. DNA
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A novel method to predict essential proteins based on tensor and HITS algorithm. Hum. Genomics (IF 3.351) Pub Date : 2020-04-06 Zhihong Zhang,Yingchun Luo,Sai Hu,Xueyong Li,Lei Wang,Bihai Zhao
Essential proteins are an important part of the cell and closely related to the life activities of the cell. Hitherto, Protein-Protein Interaction (PPI) networks have been adopted by many computational methods to predict essential proteins. Most of the current approaches focus mainly on the topological structure of PPI networks. However, those methods relying solely on the PPI network have low detection
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Reply to "Is the number of DNA repair genes associated with evolution rate and size of genomes?" Hum. Genomics (IF 3.351) Pub Date : 2020-03-16 Konstantinos Voskarides
Dear Editor, I appreciate the fact that our manuscript “Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes” [1] has gained attention by other scientists. Comments by Dr. I. Undroiu [2] are interesting but I think that some points of our work have been misunderstood. Below, I am answering to all the comments, one by one, since we
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Is the number of DNA repair genes associated with evolution rate and size of genomes? Hum. Genomics (IF 3.351) Pub Date : 2020-03-16 Ion Udroiu
In a recent article, Voskarides et al. [1] investigated the relationship between DNA repair genes and evolution rates in vertebrates. In the last decade, there was an increase in comparative studies seeking correlation between DNA repair and longevity [2,3,4,5]. One of the reasons is also to translate this knowledge to human health and understand phenomena like aging and carcinogenesis. The authors
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Do epigenetic changes caused by commensal microbiota contribute to development of ocular disease? A review of evidence. Hum. Genomics (IF 3.351) Pub Date : 2020-03-13 Ashima Nayyar,Sofya Gindina,Arturo Barron,Yan Hu,John Danias
There is evidence that genetic polymorphisms and environmentally induced epigenetic changes play an important role in modifying disease risk. The commensal microbiota has the ability to affect the cellular environment throughout the body without requiring direct contact; for example, through the generation of a pro-inflammatory state. In this review, we discuss evidence that dysbiosis in intestinal
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Metabolomic profiling of metoprolol hypertension treatment reveals altered gut microbiota-derived urinary metabolites. Hum. Genomics (IF 3.351) Pub Date : 2020-03-11 Chad N Brocker,Thomas Velenosi,Hania K Flaten,Glenn McWilliams,Kyle McDaniel,Shelby K Shelton,Jessica Saben,Kristopher W Krausz,Frank J Gonzalez,Andrew A Monte
Metoprolol succinate is a long-acting beta-blocker prescribed for the management of hypertension (HTN) and other cardiovascular diseases. Metabolomics, the study of end-stage metabolites of upstream biologic processes, yield insight into mechanisms of drug effectiveness and safety. Our aim was to determine metabolomic profiles associated with metoprolol effectiveness for the treatment of hypertension
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Hyperinsulinism associated with GLUD1 mutation: allosteric regulation and functional characterization of p.G446V glutamate dehydrogenase. Hum. Genomics (IF 3.351) Pub Date : 2020-03-06 Karolina Luczkowska,Caroline Stekelenburg,Frédérique Sloan-Béna,Emmanuelle Ranza,Giacomo Gastaldi,Valérie Schwitzgebel,Pierre Maechler
BACKGROUND Gain-of-function mutations in the GLUD1 gene, encoding for glutamate dehydrogenase (GDH), result in the hyperinsulinism/hyperammonemia HI/HA syndrome. HI/HA patients present with harmful hypoglycemia secondary to protein-induced HI and elevated plasma ammonia levels. These symptoms may be accompanied by seizures and mental retardation. GDH is a mitochondrial enzyme that catalyzes the oxidative
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TRPM3_miR-204: a complex locus for eye development and disease. Hum. Genomics (IF 3.351) Pub Date : 2020-02-18 Alan Shiels
First discovered in a light-sensitive retinal mutant of Drosophila, the transient receptor potential (TRP) superfamily of non-selective cation channels serve as polymodal cellular sensors that participate in diverse physiological processes across the animal kingdom including the perception of light, temperature, pressure, and pain. TRPM3 belongs to the melastatin sub-family of TRP channels and has
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Identification and characterization of methylation-mediated transcriptional dysregulation dictate methylation roles in preeclampsia. Hum. Genomics (IF 3.351) Pub Date : 2020-01-30 Shuyu Zhao,Nan Lv,Yan Li,Tianyi Liu,Yuhong Sun,Xiaodan Chu
BACKGROUND Preeclampsia (PE) is a heterogeneous, hypertensive disorder of pregnancy, with no robust biomarkers or effective treatments. PE increases the risk of poor outcomes for both the mother and the baby. Methylation-mediated transcriptional dysregulation motifs (methTDMs) could contribute the PE development. However, precise functional roles of methTDMs in PE have not been globally described.
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Delineating significant genome-wide associations of variants with antipsychotic and antidepressant treatment response: implications for clinical pharmacogenomics. Hum. Genomics (IF 3.351) Pub Date : 2020-01-15 Maria Koromina,Stefania Koutsilieri,George P Patrinos
BACKGROUND Genome-wide association studies (GWAS) have significantly contributed to the association of many clinical conditions and phenotypic characteristics with genomic variants. The majority of these genomic findings have been deposited to the GWAS catalog. So far, findings uncovering associations of single nucleotide polymorphisms (SNPs) with treatment efficacy in mood disorders are encouraging
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Re-analysis of whole blastocysts after trophectoderm biopsy indicated chromosome aneuploidy. Hum. Genomics (IF 3.351) Pub Date : 2020-01-13 Zhanhui Ou,Zhiheng Chen,Minna Yin,Yu Deng,Yunhao Liang,Wenjun Wang,Yuanqing Yao,Ling Sun
BACKGROUND To compare the concordance between trophectoderm (TE) analysis and whole blastocyst analysis of embryos from chromosomal structural rearrangement (SR) carriers. METHOD Sixty-three abnormal blastocysts identified by preimplantation genetic testing for chromosomal structural rearrangement (PGT-SR) were included. The whole blastocysts were processed through multiple displacement amplification
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Investigating diagnostic sequencing techniques for CADASIL diagnosis. Hum. Genomics (IF 3.351) Pub Date : 2020-01-08 P J Dunn,N Maksemous,R A Smith,H G Sutherland,L M Haupt,L R Griffiths
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a cerebral small vessel disease caused by mutations in the NOTCH3 gene. Our laboratory has been undertaking genetic diagnostic testing for CADASIL since 1997. Work originally utilised Sanger sequencing methods targeting specific NOTCH3 exons. More recently, next-generation sequencing (NGS)-based
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Associations between microRNA (miR-25, miR-32, miR-125, and miR-222) polymorphisms and recurrent implantation failure in Korean women. Hum. Genomics (IF 3.351) Pub Date : 2019-12-16 Jeong Yong Lee,Eun Hee Ahn,Jung Oh Kim,Han Sung Park,Chang Soo Ryu,Ji Hyang Kim,Young Ran Kim,Woo Sik Lee,Nam Keun Kim
BACKGROUND Recurrent implantation failure (RIF) is the failure of embryos to implant more than two times in a given individual. There is debate about a precise definition for RIF, but we consider more than two implantation failures for individuals who undergo in vitro fertilization-embryo transfer (IVF-ET) to constitute RIF. There are many potential reasons for RIF, including embryonic factors, immunological
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Downregulation of miR-542-3p promotes osteogenic transition of vascular smooth muscle cells in the aging rat by targeting BMP7. Hum. Genomics (IF 3.351) Pub Date : 2019-12-11 Huan Liu,Hongwei Wang,Sijin Yang,Dehui Qian
BACKGROUND Aging is believed to have a close association with cardiovascular diseases, resulting in various pathological alterations in blood vessels, including vascular cell phenotypic shifts. In aging vessels, the microRNA(miRNA)-mediated mechanism regulating the vascular smooth muscle cell (VSMC) phenotype remains unclarified. MiRNA microarray was used to compare the expressions of miRNAs in VSMCs
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The multi-faceted functioning portrait of LRF/ZBTB7A. Hum. Genomics (IF 3.351) Pub Date : 2019-12-10 Caterina Constantinou,Magda Spella,Vasiliki Chondrou,George P Patrinos,Adamantia Papachatzopoulou,Argyro Sgourou
Transcription factors (TFs) consisting of zinc fingers combined with BTB (for broad-complex, tram-track, and bric-a-brac) domain (ZBTB) are a highly conserved protein family that comprises a multifunctional and heterogeneous group of TFs, mainly modulating cell developmental events and cell fate. LRF/ZBTB7A, in particular, is reported to be implicated in a wide variety of physiological and cancer-related
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Investigating RNA expression profiles altered by nicotinamide mononucleotide therapy in a chronic model of alcoholic liver disease. Hum. Genomics (IF 3.351) Pub Date : 2019-12-10 Mohammed A Assiri,Hadi R Ali,John O Marentette,Youngho Yun,Juan Liu,Matthew D Hirschey,Laura M Saba,Peter S Harris,Kristofer S Fritz
BACKGROUND Chronic alcohol consumption is a significant cause of liver disease worldwide. Several biochemical mechanisms have been linked to the initiation and progression of alcoholic liver disease (ALD) such as oxidative stress, inflammation, and metabolic dysregulation, including the disruption of NAD+/NADH. Indeed, an ethanol-mediated reduction in hepatic NAD+ levels is thought to be one factor
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Human genetics and genomics research in Ecuador: historical survey, current state, and future directions. Hum. Genomics (IF 3.351) Pub Date : 2019-12-10 Marlon S Zambrano-Mila,Spiros N Agathos,Juergen K V Reichardt
BACKGROUND In South America, the history of human genetics is extensive and its beginnings go back to the onset of the twentieth century. In Ecuador, the historical record of human genetics and genomics research is limited. In this context, our work analyzes the current status and historical panorama of these fields, based on bibliographic searches in Scopus, Google Scholar, PubMed, and Web of Science
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EFTUD2 gene deficiency disrupts osteoblast maturation and inhibits chondrocyte differentiation via activation of the p53 signaling pathway. Hum. Genomics (IF 3.351) Pub Date : 2019-12-05 Jing Wu,Yi Yang,You He,Qiang Li,Xu Wang,Chengjun Sun,Lishun Wang,Yu An,Feihong Luo
BACKGROUND Mandibulofacial dysostosis with microcephaly (MFDM) is characteristic of multiple skeletal anomalies comprising craniofacial anomalies/dysplasia, microcephaly, dysplastic ears, choanal atresia, and short stature. Heterozygous loss of function variants of EFTUD2 was previously reported in MFDM; however, the mechanism underlying EFTUD2-associated skeletal dysplasia remains unclear. RESULTS
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Factors affecting cell-free DNA fetal fraction: statistical analysis of 13,661 maternal plasmas for non-invasive prenatal screening. Hum. Genomics (IF 3.351) Pub Date : 2019-12-04 Yaping Hou,Jiexia Yang,Yiming Qi,Fangfang Guo,Haishan Peng,Dongmei Wang,Yixia Wang,Xiaohui Luo,Yi Li,Aihua Yin
BACKGROUND The identification of cell-free fetal DNA (cffDNA) facilitated non-invasive prenatal screening (NIPS) through analysis of cffDNA in maternal plasma. However, challenges regarding its clinical implementation become apparent. Factors affecting fetal fraction should be clarified to guide its clinical application. RESULTS A total of 13,661 pregnant subjects with singleton pregnancies who undertook
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Genetics and functions of the retinoic acid pathway, with special emphasis on the eye. Hum. Genomics (IF 3.351) Pub Date : 2019-12-03 Brian Thompson,Nicholas Katsanis,Nicholas Apostolopoulos,David C Thompson,Daniel W Nebert,Vasilis Vasiliou
Retinoic acid (RA) is a potent morphogen required for embryonic development. RA is formed in a multistep process from vitamin A (retinol); RA acts in a paracrine fashion to shape the developing eye and is essential for normal optic vesicle and anterior segment formation. Perturbation in RA-signaling can result in severe ocular developmental diseases-including microphthalmia, anophthalmia, and coloboma
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Noninvasive prenatal testing for chromosome aneuploidies and subchromosomal microdeletions/microduplications in a cohort of 42,910 single pregnancies with different clinical features. Hum. Genomics (IF 3.351) Pub Date : 2019-11-29 Yibo Chen,Qi Yu,Xiongying Mao,Wei Lei,Miaonan He,Wenbo Lu
BACKGROUND Since the discovery of cell-free DNA (cfDNA) in maternal plasma, it has opened up new approaches for non-invasive prenatal testing. With the development of whole-genome sequencing, small subchromosomal deletions and duplications could be found by NIPT. This study is to review the efficacy of NIPT as a screening test for aneuploidies and CNVs in 42,910 single pregnancies. METHODS A total
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