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Human Genetics

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https://www.readbyqxmd.com/read/29335774/genomic-trade-offs-are-autism-and-schizophrenia-the-steep-price-of-the-human-brain
#1
J M Sikela, V B Searles Quick
Evolution often deals in genomic trade-offs: changes in the genome that are beneficial overall persist even though they also produce disease in a subset of individuals. Here, we explore the possibility that such trade-offs have occurred as part of the evolution of the human brain. Specifically, we provide support for the possibility that the same key genes that have been major contributors to the rapid evolutionary expansion of the human brain and its exceptional cognitive capacity also, in different combinations, are significant contributors to autism and schizophrenia...
January 15, 2018: Human Genetics
https://www.readbyqxmd.com/read/29322246/de-novo-variants-in-setd1b-are-associated-with-intellectual-disability-epilepsy-and-autism
#2
Takuya Hiraide, Mitsuko Nakashima, Kaori Yamoto, Tokiko Fukuda, Mitsuhiro Kato, Hiroko Ikeda, Yoko Sugie, Kazushi Aoto, Tadashi Kaname, Kazuhiko Nakabayashi, Tsutomu Ogata, Naomichi Matsumoto, Hirotomo Saitsu
SETD1B (SET domain containing 1B) is a component of SET1 histone methyltransferase complex, which mediates the methylation of histone H3 on lysine 4 (H3K4). Here, we describe two unrelated individuals with de novo variants in SETD1B identified by trio-based whole exome sequencing: c.5524C>T, p.(Arg1842Trp) and c.5575C>T, p.(Arg1859Cy). The two missense variants occurred at evolutionarily conserved amino acids and are located within the SET domain, which plays a pivotal role in catalyzing histone methylation...
January 10, 2018: Human Genetics
https://www.readbyqxmd.com/read/29305691/the-capos-mutation-in-atp1a3-alters-na-k-atpase-function-and-results-in-auditory-neuropathy-which-has-implications-for-management
#3
Lisbeth Tranebjærg, Nicola Strenzke, Sture Lindholm, Nanna D Rendtorff, Hanne Poulsen, Himanshu Khandelia, Wojciech Kopec, Troels J Brünnich Lyngbye, Christian Hamel, Cecile Delettre, Beatrice Bocquet, Michael Bille, Hanne H Owen, Toke Bek, Hanne Jensen, Karen Østergaard, Claes Möller, Linda Luxon, Lucinda Carr, Louise Wilson, Kaukab Rajput, Tony Sirimanna, Katherine Harrop-Griffiths, Shamima Rahman, Barbara Vona, Julia Doll, Thomas Haaf, Oliver Bartsch, Hendrik Rosewich, Tobias Moser, Maria Bitner-Glindzicz
Cerebellar ataxia, areflexia, pes cavus, optic atrophy and sensorineural hearing impairment (CAPOS) is a rare clinically distinct syndrome caused by a single dominant missense mutation, c.2452G>A, p.Glu818Lys, in ATP1A3, encoding the neuron-specific alpha subunit of the Na+/K+-ATPase α3. Allelic mutations cause the neurological diseases rapid dystonia Parkinsonism and alternating hemiplegia of childhood, disorders which do not encompass hearing or visual impairment. We present detailed clinical phenotypic information in 18 genetically confirmed patients from 11 families (10 previously unreported) from Denmark, Sweden, UK and Germany indicating a specific type of hearing impairment-auditory neuropathy (AN)...
January 5, 2018: Human Genetics
https://www.readbyqxmd.com/read/29288389/principles-and-methods-of-in-silico-prioritization-of-non-coding-regulatory-variants
#4
REVIEW
Phil H Lee, Christian Lee, Xihao Li, Brian Wee, Tushar Dwivedi, Mark Daly
Over a decade of genome-wide association, studies have made great strides toward the detection of genes and genetic mechanisms underlying complex traits. However, the majority of associated loci reside in non-coding regions that are functionally uncharacterized in general. Now, the availability of large-scale tissue and cell type-specific transcriptome and epigenome data enables us to elucidate how non-coding genetic variants can affect gene expressions and are associated with phenotypic changes. Here, we provide an overview of this emerging field in human genomics, summarizing available data resources and state-of-the-art analytic methods to facilitate in-silico prioritization of non-coding regulatory mutations...
December 29, 2017: Human Genetics
https://www.readbyqxmd.com/read/29288388/correction-to-expanding-the-genetic-heterogeneity-of-intellectual-disability
#5
Shams Anazi, Sateesh Maddirevula, Vincenzo Salpietro, Yasmine T Asi, Saud Alsahli, Amal Alhashem, Hanan E Shamseldin, Fatema AlZahrani, Nisha Patel, Niema Ibrahim, Firdous M Abdulwahab, Mais Hashem, Nadia Alhashmi, Fathiya Al Murshedi, Adila Al Kindy, Ahmad Alshaer, Ahmed Rumayyan, Saeed Al Tala, Wesam Kurdi, Abdulaziz Alsaman, Ali Alasmari, Selina Banu, Tipu Sultan, Mohammed M Saleh, Hisham Alkuraya, Mustafa A Salih, Hesham Aldhalaan, Tawfeg Ben-Omran, Fatima Al Musafri, Rehab Ali, Jehan Suleiman, Brahim Tabarki, Ayman W El-Hattab, Caleb Bupp, Majid Alfadhel, Nada Al Tassan, Dorota Monies, Stefan T Arold, Mohamed Abouelhoda, Tammaryn Lashley, Henry Houlden, Eissa Faqeih, Fowzan S Alkuraya
Variant nomenclature discrepancy was identified in the article.
December 29, 2017: Human Genetics
https://www.readbyqxmd.com/read/29264654/genetic-variants-in-microrna-genes-and-targets-associated-with-cardiovascular-disease-risk-factors-in-the-african-american-population
#6
Chang Li, Megan L Grove, Bing Yu, Barbara C Jones, Alanna Morrison, Eric Boerwinkle, Xiaoming Liu
The purpose of this study is to identify microRNA (miRNA) related polymorphism, including single nucleotide variants (SNVs) in mature miRNA-encoding sequences or in miRNA-target sites, and their association with cardiovascular disease (CVD) risk factors in African-American population. To achieve our objective, we examined 1900 African-Americans from the Atherosclerosis Risk in Communities study using SNVs identified from whole-genome sequencing data. A total of 971 SNVs found in 726 different mature miRNA-encoding sequences and 16,057 SNVs found in the three prime untranslated region (3'UTR) of 3647 protein-coding genes were identified and interrogated their associations with 17 CVD risk factors...
December 20, 2017: Human Genetics
https://www.readbyqxmd.com/read/29209947/copy-number-variation-arising-from-gene-conversion-on-the-human-y-chromosome
#7
Wentao Shi, Andrea Massaia, Sandra Louzada, Ruby Banerjee, Pille Hallast, Yuan Chen, Anders Bergström, Yong Gu, Steven Leonard, Michael A Quail, Qasim Ayub, Fengtang Yang, Chris Tyler-Smith, Yali Xue
We describe the variation in copy number of a ~ 10 kb region overlapping the long intergenic noncoding RNA (lincRNA) gene, TTTY22, within the IR3 inverted repeat on the short arm of the human Y chromosome, leading to individuals with 0-3 copies of this region in the general population. Variation of this CNV is common, with 266 individuals having 0 copies, 943 (including the reference sequence) having 1, 23 having 2 copies, and two having 3 copies, and was validated by breakpoint PCR, fibre-FISH, and 10× Genomics Chromium linked-read sequencing in subsets of 1234 individuals from the 1000 Genomes Project...
December 5, 2017: Human Genetics
https://www.readbyqxmd.com/read/29204889/authorization-of-tissues-from-deceased-patients-for-genetic-research
#8
Maureen Wilson-Genderson, K Laura Barker, Heather M Gardiner, Maghboeba Mosavel, Jeffrey Thomas, Laura A Siminoff
Tissues from deceased donors provide important data for genomic research and Organ Procurement Organizations (OPOs) play a significant role. To understand the decisions of families who donated for transplantation and made decisions about donation to the Genotype-Tissue Expression Project (GTEx), we examined donation decisions of family decision makers (FDMs). 413 families were interviewed by telephone. The OPO staff who made the transplant and research requests completed self-administered surveys; a total of 309 matching surveys from 99 OPO staff were obtained...
December 4, 2017: Human Genetics
https://www.readbyqxmd.com/read/29196799/3c-pcr-a-novel-proximity-ligation-based-approach-to-phase-chromosomal-rearrangement-breakpoints-with-distal-allelic-variants
#9
Samantha L P Schilit, Cynthia C Morton
Recent advances in molecular cytogenetics highlight the importance of noncoding structural variation in human disease. Genomic rearrangements can disrupt chromatin architecture, leading to long-range alterations in gene expression. With increasing ability to assess distal gene dysregulation comes new challenges in clinical interpretation of rearrangements. While haplotyping methods to determine compound heterozygosity in a single gene with two pathogenic variants are established, such methods are insufficient for phasing larger distances between a pathogenic variant and a genomic rearrangement breakpoint...
December 1, 2017: Human Genetics
https://www.readbyqxmd.com/read/29181734/pleiotropy-of-cardiometabolic-syndrome-with-obesity-related-anthropometric-traits-determined-using-empirically-derived-kinships-from-the-busselton-health-study
#10
Gemma Cadby, Phillip E Melton, Nina S McCarthy, Marcio Almeida, Sarah Williams-Blangero, Joanne E Curran, John L VandeBerg, Jennie Hui, John Beilby, A W Musk, Alan L James, Joseph Hung, John Blangero, Eric K Moses
Over two billion adults are overweight or obese and therefore at an increased risk of cardiometabolic syndrome (CMS). Obesity-related anthropometric traits genetically correlated with CMS may provide insight into CMS aetiology. The aim of this study was to utilise an empirically derived genetic relatedness matrix to calculate heritabilities and genetic correlations between CMS and anthropometric traits to determine whether they share genetic risk factors (pleiotropy). We used genome-wide single nucleotide polymorphism (SNP) data on 4671 Busselton Health Study participants...
November 27, 2017: Human Genetics
https://www.readbyqxmd.com/read/29164333/the-ubiquity-of-pleiotropy-in-human-disease
#11
Kevin Chesmore, Jacquelaine Bartlett, Scott M Williams
Pleiotropy has long been thought to be a common phenomenon in the human genome; however, until recently appropriate data was unavailable to test this hypothesis. Prior studies focused on assessing the prevalence of pleiotropy in only small subsets of phenotypes (≤ 53 phenotypes), without a truly comprehensive assessment of pleiotropy in the human genome. In this study, we determined the prevalence of pleiotropy, using the entire GWAS catalog (1094 disease phenotypes, 14,459 genes), as well as investigate the relationship between the degree of pleiotropy and the average effect size for each associating gene...
November 21, 2017: Human Genetics
https://www.readbyqxmd.com/read/29128982/actionable-secondary-findings-from-whole-genome-sequencing-of-954-east-asians
#12
Clara Sze-Man Tang, Saloni Dattani, Man-Ting So, Stacey S Cherny, Paul K H Tam, Pak C Sham, Maria-Mercè Garcia-Barcelo
Recently, the American College of Medical Genetics (ACMG) recommended the return of actionable secondary findings detected from clinical sequencing. The reported frequency of secondary findings in Asian populations were highly variable and it is unclear whether the uniformity in coverage offered by whole-genome sequencing (WGS) may impact the estimate. In this analysis, we aimed to refine the rate of secondary findings on East Asians through a large-scale WGS study. We classified 1256 protein-altering or splicing variants of the 59 actionable genes detected from WGS of 954 East Asians in strict accordance with the ACMG and the Association for Molecular Pathology guidelines...
November 11, 2017: Human Genetics
https://www.readbyqxmd.com/read/29101457/a-functional-strategy-to-characterize-expression-quantitative-trait-loci
#13
Elena Grassi, Elisa Mariella, Mattia Forneris, Federico Marotta, Marika Catapano, Ivan Molineris, Paolo Provero
The study of genetic variation has been revolutionized by the advent of high-throughput technologies able to determine the complete genomic sequence of thousands of individuals. Understanding the functional relevance of variants is, however, still a difficult task, especially when focusing on non-coding variants. Most of the variants associated with disease by Genome-Wide Association Studies (GWAS) are indeed non-coding, and presumably exert their effects by altering gene regulation. Expression Quantitative Trait Loci (eQTL) studies represent an important step in understanding the functional relevance of regulatory variants...
November 3, 2017: Human Genetics
https://www.readbyqxmd.com/read/29094202/additive-effect-pattern-of-both-zp2-and-zp3-in-human-and-mouse
#14
LETTER
Wenqiang Liu, Dandan Bai, Jiayu Chen, Shaorong Gao
No abstract text is available yet for this article.
November 1, 2017: Human Genetics
https://www.readbyqxmd.com/read/29094203/creation-of-miniature-pig-model-of-human-waardenburg-syndrome-type-2a-by-enu-mutagenesis
#15
Tang Hai, Weiwei Guo, Jing Yao, Chunwei Cao, Ailing Luo, Meng Qi, Xianlong Wang, Xiao Wang, Jiaojiao Huang, Ying Zhang, Hongyong Zhang, Dayu Wang, Haitao Shang, Qianlong Hong, Rui Zhang, Qitao Jia, Qiantao Zheng, Guosong Qin, Yongshun Li, Tao Zhang, Weiwu Jin, Zheng-Yi Chen, Hongmei Wang, Qi Zhou, Anming Meng, Hong Wei, Shiming Yang, Jianguo Zhao
Human Waardenburg syndrome 2A (WS2A) is a dominant hearing loss (HL) syndrome caused by mutations in the microphthalmia-associated transcription factor (MITF) gene. In mouse models with MITF mutations, WS2A is transmitted in a recessive pattern, which limits the study of hearing loss (HL) pathology. In the current study, we performed ENU (ethylnitrosourea) mutagenesis that resulted in substituting a conserved lysine with a serine (p. L247S) in the DNA-binding domain of the MITF gene to generate a novel miniature pig model of WS2A...
November 2017: Human Genetics
https://www.readbyqxmd.com/read/29090338/mutations-of-ptpn23-in-developmental-and-epileptic-encephalopathy
#16
Nadine Sowada, Mais Omar Hashem, Rüstem Yilmaz, Muddathir Hamad, Naseebullah Kakar, Holger Thiele, Stefan T Arold, Harald Bode, Fowzan S Alkuraya, Guntram Borck
Developmental and epileptic encephalopathies (DEE) are a heterogeneous group of neurodevelopmental disorders with poor prognosis. Recent discoveries have greatly expanded the repertoire of genes that are mutated in epileptic encephalopathies and DEE, often in a de novo fashion, but in many patients, the disease remains molecularly uncharacterized. Here, we describe a new form of DEE in patients with likely deleterious biallelic variants in PTPN23. The phenotype is characterized by early onset drug-resistant epilepsy, severe and global developmental delay, microcephaly, and sometimes premature death...
November 2017: Human Genetics
https://www.readbyqxmd.com/read/29063188/world-wide-distributions-of-lactase-persistence-alleles-and-the-complex-effects-of-recombination-and-selection
#17
Anke Liebert, Saioa López, Bryony Leigh Jones, Nicolas Montalva, Pascale Gerbault, Winston Lau, Mark G Thomas, Neil Bradman, Nikolas Maniatis, Dallas M Swallow
The genetic trait of lactase persistence (LP) is associated with at least five independent functional single nucleotide variants in a regulatory region about 14 kb upstream of the lactase gene [-13910*T (rs4988235), -13907*G (rs41525747), -13915*G (rs41380347), -14009*G (rs869051967) and -14010*C (rs145946881)]. These alleles have been inferred to have spread recently and present-day frequencies have been attributed to positive selection for the ability of adult humans to digest lactose without risk of symptoms of lactose intolerance...
November 2017: Human Genetics
https://www.readbyqxmd.com/read/28975465/expanding-the-spectrum-of-germline-variants-in-cancer
#18
Abdul K Siraj, Tariq Masoodi, Rong Bu, Sandeep Kumar Parvathareddy, Ismail A Al-Badawi, Nasser Al-Sanea, Luai H Ashari, Alaa Abduljabbar, Samar Alhomoud, Saif S Al-Sobhi, Asma Tulbah, Dahish Ajarim, Khalid Alzoman, Muna Aljuboury, Hussam Bin Yousef, Mohammed Al-Dawish, Fouad Al-Dayel, Fowzan S Alkuraya, Khawla S Al-Kuraya
Our ability to identify germline variants in hereditary cancer cases remains challenged by the incomplete cataloging of relevant genes and lack of consensus on who should be tested. We designed a panel [hereditary oncogenesis predisposition evaluation (HOPE)] that encompasses most of the genes known to be associated with cancer development and tested its yield on more than 1300 samples of cancer patients. Pathogenic or likely pathogenic variants in high and intermediate risk genes were identified in 16, 23...
November 2017: Human Genetics
https://www.readbyqxmd.com/read/28940097/expanding-the-genetic-heterogeneity-of-intellectual-disability
#19
Shams Anazi, Sateesh Maddirevula, Vincenzo Salpietro, Yasmine T Asi, Saud Alsahli, Amal Alhashem, Hanan E Shamseldin, Fatema AlZahrani, Nisha Patel, Niema Ibrahim, Firdous M Abdulwahab, Mais Hashem, Nadia Alhashmi, Fathiya Al Murshedi, Adila Al Kindy, Ahmad Alshaer, Ahmed Rumayyan, Saeed Al Tala, Wesam Kurdi, Abdulaziz Alsaman, Ali Alasmari, Selina Banu, Tipu Sultan, Mohammed M Saleh, Hisham Alkuraya, Mustafa A Salih, Hesham Aldhalaan, Tawfeg Ben-Omran, Fatima Al Musafri, Rehab Ali, Jehan Suleiman, Brahim Tabarki, Ayman W El-Hattab, Caleb Bupp, Majid Alfadhel, Nada Al Tassan, Dorota Monies, Stefan T Arold, Mohamed Abouelhoda, Tammaryn Lashley, Henry Houlden, Eissa Faqeih, Fowzan S Alkuraya
Intellectual disability (ID) is a common morbid condition with a wide range of etiologies. The list of monogenic forms of ID has increased rapidly in recent years thanks to the implementation of genomic sequencing techniques. In this study, we describe the phenotypic and genetic findings of 68 families (105 patients) all with novel ID-related variants. In addition to established ID genes, including ones for which we describe unusual mutational mechanism, some of these variants represent the first confirmatory disease-gene links following previous reports (TRAK1, GTF3C3, SPTBN4 and NKX6-2), some of which were based on single families...
November 2017: Human Genetics
https://www.readbyqxmd.com/read/28975356/erratum-to-a-multi-stage-genome-wide-association-study-of-uterine-fibroids-in-african-americans
#20
Jacklyn N Hellwege, Janina M Jeff, Lauren A Wise, C Scott Gallagher, Melissa Wellons, Katherine E Hartmann, Sarah F Jones, Eric S Torstenson, Scott Dickinson, Edward A Ruiz-Narváez, Nadin Rohland, Alexander Allen, David Reich, Arti Tandon, Bogdan Pasaniuc, Nicholas Mancuso, Hae Kyung Im, David A Hinds, Julie R Palmer, Lynn Rosenberg, Joshua C Denny, Dan M Roden, Elizabeth A Stewart, Cynthia C Morton, Eimear E Kenny, Todd L Edwards, Digna R Velez Edwards
The article "A multi-stage genome-wide association study of uterine fibroids in African Americans", written by Jacklyn N. Hellwege, was originally published Online First without open access. After publication in volume 136, issue 10, page 1363-1373 the author decided to opt for Open Choice and to make the article an open access publication. Therefore, the copyright of the article has been changed to
October 4, 2017: Human Genetics
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