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Human Genetics

Qian Wang, Renato Polimanti, Henry R Kranzler, Lindsay A Farrer, Hongyu Zhao, Joel Gelernter
Schizophrenia (SZ) and HIV infection are serious disorders with a complex phenotypic relationship. Observational studies have described their comorbidity; their genetic correlation is not well studied. We performed extensive analysis in search of common genetic factors for SZ and HIV, and their relationship with risky sexual behavior (RSB). Summary statistics from genome-wide association studies of HIV infection and schizophrenia were obtained and 2379 European Americans were genotyped and assessed for RSB score...
October 17, 2016: Human Genetics
Jung-Ho Park, Munjin Kwon, Yoshihiro Yamaguchi, Bonnie L Firestein, Ji-Young Park, Jieun Yun, Jeong-Ook Yang, Masayori Inouye
More than 31,000 protein-coding sequences (CCDS) have been identified in the human genome. Here, we analyzed codon usage in all human CCDS and found that there is a preferential usage of minor codons for Ala (CGC), Pro (CCG), Ser (UCG), and Thr (ACG) in the initial 50-codon sequences of the CCDS. These codons, with consensus XCG sequences, are most infrequently used among their synonymous codons. Thus, the tRNA concentrations per codon are considered to be highest for the minor codons for Ala, Pro, Ser and Thr in comparison with other synonymous codons for each of them to enhance the translation efficiency...
October 11, 2016: Human Genetics
Simon C Johnson, Brenda Gonzalez, Quanwei Zhang, Brandon Milholland, Zhengdong Zhang, Yousin Suh
While mitochondria have been linked to many human diseases through genetic association and functional studies, the precise role of mitochondria in specific pathologies, such as cardiovascular, neurodegenerative, and metabolic diseases, is often unclear. Here, we take advantage of the catalog of human genome-wide associations, whole-genome tissue expression and expression quantitative trait loci datasets, and annotated mitochondrial proteome databases to examine the role of common genetic variation in mitonuclear genes in human disease...
October 4, 2016: Human Genetics
Arvis Sulovari, Yolanda H Chen, James J Hudziak, Dawei Li
Genetic variants with extreme allele frequency differences (EAFD) may underlie some human health disparities across populations. To identify EAFD loci, we systematically analyzed and characterized 81 million genomic variants from 2504 unrelated individuals of 26 world populations (phase III of the 1000 Genomes Project). Our analyses revealed a total of 434 genes, 15 pathways, and 18 diseases and traits influenced by EAFD variants from five continental populations. They included known EAFD genes, such as LCT (lactose tolerance), SLC24A5 (skin pigmentation), and EDAR (hair morphology)...
October 3, 2016: Human Genetics
M Phan, F Conte, K D Khandelwal, C W Ockeloen, T Bartzela, T Kleefstra, H van Bokhoven, M Rubini, H Zhou, C E L Carels
Tooth agenesis and orofacial clefts represent the most common developmental anomalies and their co-occurrence is often reported in patients as well in animal models. The aim of the present systematic review is to thoroughly investigate the current literature (PubMed, EMBASE) to identify the genes and genomic loci contributing to syndromic or non-syndromic co-occurrence of tooth agenesis and orofacial clefts, to gain insight into the molecular mechanisms underlying their dual involvement in the development of teeth and facial primordia...
December 2016: Human Genetics
Lijiang Ma, Yavuz Bayram, Heather M McLaughlin, Megan T Cho, Alyson Krokosky, Clesson E Turner, Kristin Lindstrom, Caleb P Bupp, Katey Mayberry, Weiyi Mu, Joann Bodurtha, Veronique Weinstein, Neda Zadeh, Wendy Alcaraz, Zöe Powis, Yunru Shao, Daryl A Scott, Andrea M Lewis, Janson J White, Shalani N Jhangiani, Elif Yilmaz Gulec, Seema R Lalani, James R Lupski, Kyle Retterer, Rhonda E Schnur, Ingrid M Wentzensen, Sherri Bale, Wendy K Chung
Intellectual disabilities are genetically heterogeneous and can be associated with congenital anomalies. Using whole-exome sequencing (WES), we identified five different de novo missense variants in the protein phosphatase-1 catalytic subunit beta (PPP1CB) gene in eight unrelated individuals who share an overlapping phenotype of dysmorphic features, macrocephaly, developmental delay or intellectual disability (ID), congenital heart disease, short stature, and skeletal and connective tissue abnormalities. Protein phosphatase-1 (PP1) is a serine/threonine-specific protein phosphatase involved in the dephosphorylation of a variety of proteins...
December 2016: Human Genetics
Huijie Li, Suyun Li, Qiang Wang, Chongqi Jia
Recently, a single nucleotide polymorphism (SNP) A503V (rs1057868) in cytochrome P450 oxidoreductase (POR) gene was reported to influence nicotine metabolism. Considering the importance of nicotine metabolism to smoking cessation, the aim of this study was to investigate the association between POR gene polymorphisms and smoking cessation in a Chinese population. A case-control study was conducted with 363 successful smoking quitters as the cases, and 345 failed smoking quitters as the controls. Eight tagSNPs which cover the entire gene and four functional SNPs were selected and genotyped...
December 2016: Human Genetics
Jinlu Zhang, Changguan Wang, Yan Shen, Ningning Chen, Likun Wang, Ling Liang, Tong Guo, Xiaobei Yin, Zhizhong Ma, Bo Zhang, Liping Yang
Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous disorder characterized by night blindness, visual field constriction, and severely reduced visual acuity. Despite a number of genes being implicated in RP pathogenesis, the genetic etiology of the disease remains unknown in many patients. In this study, our aim was to identify the disease-causing mutation of a large Chinese family with autosomal dominant RP (adRP). Targeted exon capture sequencing was initially performed to screen mutations in known disease-causing genes, followed by exome sequencing...
December 2016: Human Genetics
Carina M Schlebusch, Frans Prins, Marlize Lombard, Mattias Jakobsson, Himla Soodyall
Southern Africa was likely exclusively inhabited by San hunter-gatherers before ~2000 years ago. Around that time, East African groups assimilated with local San groups and gave rise to the Khoekhoe herders. Subsequently, Bantu-speaking farmers, arriving from the north (~1800 years ago), assimilated and displaced San and Khoekhoe groups, a process that intensified with the arrival of European colonists ~350 years ago. In contrast to the western parts of southern Africa, where several Khoe-San groups still live today, the eastern parts are largely populated by Bantu speakers and individuals of non-African descent...
December 2016: Human Genetics
Erin M Hagen, Robert J Sicko, Denise M Kay, Shannon L Rigler, Aggeliki Dimopoulos, Shabbir Ahmad, Margaret H Doleman, Ruzong Fan, Paul A Romitti, Marilyn L Browne, Michele Caggana, Lawrence C Brody, Gary M Shaw, Laura L Jelliffe-Pawlowski, James L Mills
Classic heterotaxy consists of congenital heart defects with abnormally positioned thoracic and abdominal organs. We aimed to uncover novel, genomic copy-number variants (CNVs) in classic heterotaxy cases. A microarray containing 2.5 million single-nucleotide polymorphisms (SNPs) was used to genotype 69 infants (cases) with classic heterotaxy identified from California live births from 1998 to 2009. CNVs were identified using the PennCNV software. We identified 56 rare CNVs encompassing genes in the NODAL (NIPBL, TBX6), BMP (PPP4C), and WNT (FZD3) signaling pathways, not previously linked to classic heterotaxy...
December 2016: Human Genetics
Mario Lucariello, Enrique Vidal, Silvia Vidal, Mauricio Saez, Laura Roa, Dori Huertas, Mercè Pineda, Esther Dalfó, Joaquin Dopazo, Paola Jurado, Judith Armstrong, Manel Esteller
Classical Rett syndrome (RTT) is a neurodevelopmental disorder where most of cases carry MECP2 mutations. Atypical RTT variants involve mutations in CDKL5 and FOXG1. However, a subset of RTT patients remains that do not carry any mutation in the described genes. Whole exome sequencing was carried out in a cohort of 21 female probands with clinical features overlapping with those of RTT, but without mutations in the customarily studied genes. Candidates were functionally validated by assessing the appearance of a neurological phenotype in Caenorhabditis elegans upon disruption of the corresponding ortholog gene...
December 2016: Human Genetics
D T Truong, L D Shriberg, S D Smith, K L Chapman, A R Scheer-Cohen, M M C DeMille, A K Adams, A Q Nato, E M Wijsman, J D Eicher, J R Gruen
Verbal trait disorders encompass a wide range of conditions and are marked by deficits in five domains that impair a person's ability to communicate: speech, language, reading, spelling, and writing. Nonword repetition is a robust endophenotype for verbal trait disorders that is sensitive to cognitive processes critical to verbal development, including auditory processing, phonological working memory, and motor planning and programming. In the present study, we present a six-generation extended pedigree with a history of verbal trait disorders...
December 2016: Human Genetics
Brahim Tabarki, Nabil AlMajhad, Amal AlHashem, Ranad Shaheen, Fowzan S Alkuraya
Dominant gain-of-function mutations of the KCNMA1 gene, encoding the pore-forming subunit of the large conductance voltage- and Ca(2+)-activated K+ channel, have been described in a few patients with the syndrome of epilepsy, paroxysmal dyskinesias and developmental delay. In this report, we describe the loss-of-function phenotype of this newly described disease gene. In two siblings from a consanguineous family with epilepsy, developmental delay and severe cerebellar atrophy, combined exome/autozygome analysis identified a homozygous frameshift duplication in KCNMA1 (c...
November 2016: Human Genetics
I-Wen Song, Hsiang-Cheng Chen, Yuh-Feng Lin, Jenn-Hwai Yang, Chi-Ching Chang, Chung-Tei Chou, Ming-Ta Michael Lee, Yi-Chun Chou, Chien-Hsiun Chen, Yuan-Tsong Chen, Chen-Hung Chen, Jer-Yuarn Wu
Primary Sjögren's syndrome (PSS) is an autoimmune disease targeting exocrine glands. It ten times more dominantly affects women than men with an onset peak at menopause. The genetic factor predisposing women to PSS remains unclear. Therefore, we aimed to identify susceptibility loci for PSS in women. We performed genome-wide association study (GWAS) using 242 female PSS patients and 1444 female control in Han Chinese population residing in Taiwan. Replication was conducted in an independent cohort of 178 female PSS and 14,432 control subjects...
November 2016: Human Genetics
Sijie Wu, Jingze Tan, Yajun Yang, Qianqian Peng, Manfei Zhang, Jinxi Li, Dongsheng Lu, Yu Liu, Haiyi Lou, Qidi Feng, Yan Lu, Yaqun Guan, Zhaoxia Zhang, Yi Jiao, Pardis Sabeti, Jean Krutmann, Kun Tang, Li Jin, Shuhua Xu, Sijia Wang
Hair straightness/curliness is one of the most conspicuous features of human variation and is particularly diverse among populations. A recent genome-wide scan found common variants in the Trichohyalin (TCHH) gene that are associated with hair straightness in Europeans, but different genes might affect this phenotype in other populations. By sampling 2899 Han Chinese, we performed the first genome-wide scan of hair straightness in East Asians, and found EDAR (rs3827760) as the predominant gene (P = 4.67 × 10(-16)), accounting for 3...
November 2016: Human Genetics
Alexander P Drew, Anthony N Cutrupi, Megan H Brewer, Garth A Nicholson, Marina L Kennerson
Distal hereditary motor neuropathies predominantly affect the motor neurons of the peripheral nervous system leading to chronic disability. Using whole genome sequencing (WGS) we have identified a novel structural variation (SV) within the distal hereditary motor neuropathy locus on chromosome 7q34-q36.2 (DHMN1). The SV involves the insertion of a 1.35 Mb DNA fragment into the DHMN1 disease locus. The source of the inserted sequence is 2.3 Mb distal to the disease locus at chromosome 7q36.3. The insertion involves the duplication of five genes (LOC389602, RNF32, LMBR1, NOM1, MNX1) and partial duplication of UBE3C...
November 2016: Human Genetics
Majid Alfadhel, Marwan Nashabat, Hanan Al Qahtani, Ahmed Alfares, Fuad Al Mutairi, Hesham Al Shaalan, Ganka V Douglas, Klaas Wierenga, Jane Juusola, Muhammad Talal Alrifai, Stefan T Arold, Fowzan Alkuraya, Qais Abu Ali
Glycine cleavage system (GCS) catalyzes the degradation of glycine and disruption of its components encoded by GLDC, AMT and GCSH are the only known causes of glycine encephalopathy, also known as non-ketotic hyperglycinemia (NKH). In this report, we describe a consanguineous family with one child who presented with NKH, but harbored no pathogenic variants in any of the three genes linked to this condition. Whole-exome sequencing revealed a novel homozygous missense variant in exon 9 of SLC6A9 NM_201649.3: c...
November 2016: Human Genetics
Meijian Guan, Jun Ma, Jacob M Keaton, Latchezar Dimitrov, Poorva Mudgal, Mary Stromberg, Jason A Bonomo, Pamela J Hicks, Barry I Freedman, Donald W Bowden, Maggie C Y Ng
African Americans (AAs) are at higher risk for developing end-stage kidney disease (ESKD) compared to European Americans. Genome-wide association studies have identified variants associated with diabetic and non-diabetic kidney diseases. Nephropathy loci, including SLC7A9, UMOD, and SHROOM3, have been implicated in the maintenance of normal glomerular and renal tubular structure and function. Herein, 47 genes important in podocyte, glomerular basement membrane, mesangial cell, mesangial matrix, renal tubular cell, and renal interstitium structure were examined for association with type 2 diabetes (T2D)-attributed ESKD in AAs...
November 2016: Human Genetics
Xiaohong R Yang, Melissa Rotunno, Yanzi Xiao, Christian Ingvar, Hildur Helgadottir, Lorenza Pastorino, Remco van Doorn, Hunter Bennett, Cole Graham, Joshua N Sampson, Michael Malasky, Aurelie Vogt, Bin Zhu, Giovanna Bianchi-Scarra, William Bruno, Paola Queirolo, Giuseppe Fornarini, Johan Hansson, Rainer Tuominen, Laurie Burdett, Belynda Hicks, Amy Hutchinson, Kristine Jones, Meredith Yeager, Stephen J Chanock, Maria Teresa Landi, Veronica Höiom, Håkan Olsson, Nelleke Gruis, Paola Ghiorzo, Margaret A Tucker, Alisa M Goldstein
The risk of pancreatic cancer (PC) is increased in melanoma-prone families but the causal relationship between germline CDKN2A mutations and PC risk is uncertain, suggesting the existence of non-CDKN2A factors. One genetic possibility involves patients having mutations in multiple high-risk PC-related genes; however, no systematic examination has yet been conducted. We used next-generation sequencing data to examine 24 putative PC-related genes in 43 PC patients with and 23 PC patients without germline CDKN2A mutations and 1001 controls...
November 2016: Human Genetics
Sulman Basit, Khalid M Al-Harbi, Sabri A M Alhijji, Alia M Albalawi, Essa Alharby, Amr Eldardear, Mohammed I Samman
Autosomal recessive primary microcephaly (MCPH) is a static neurodevelopmental disorder characterized by congenital small head circumference and non-progressive intellectual disability without additional severe brain malformations. MCPH is a genetically heterogeneous disorder. Sixteen genes (MCPH1-MCPH16) have been discovered so far, mutations thereof lead to autosomal recessive primary microcephaly. In a family, segregating MCPH in an autosomal recessive manner, genome-wide homozygosity mapping mapped a disease locus to 16...
October 2016: Human Genetics
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