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Human Genetics

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https://www.readbyqxmd.com/read/29128982/actionable-secondary-findings-from-whole-genome-sequencing-of-954-east-asians
#1
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
#2
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/29094203/creation-of-miniature-pig-model-of-human-waardenburg-syndrome-type-2a-by-enu-mutagenesis
#3
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 1, 2017: Human Genetics
https://www.readbyqxmd.com/read/29094202/additive-effect-pattern-of-both-zp2-and-zp3-in-human-and-mouse
#4
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/29090338/mutations-of-ptpn23-in-developmental-and-epileptic-encephalopathy
#5
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...
October 31, 2017: Human Genetics
https://www.readbyqxmd.com/read/29063188/world-wide-distributions-of-lactase-persistence-alleles-and-the-complex-effects-of-recombination-and-selection
#6
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...
October 23, 2017: Human Genetics
https://www.readbyqxmd.com/read/28975356/erratum-to-a-multi-stage-genome-wide-association-study-of-uterine-fibroids-in-african-americans
#7
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
https://www.readbyqxmd.com/read/28975465/expanding-the-spectrum-of-germline-variants-in-cancer
#8
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...
October 3, 2017: Human Genetics
https://www.readbyqxmd.com/read/28971300/zp2-heterozygous-mutation-in-an-infertile-woman
#9
LETTER
Sandrine Barbaux, Laïla El Khattabi, Ahmed Ziyyat
No abstract text is available yet for this article.
October 3, 2017: Human Genetics
https://www.readbyqxmd.com/read/28940097/expanding-the-genetic-heterogeneity-of-intellectual-disability
#10
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...
September 22, 2017: Human Genetics
https://www.readbyqxmd.com/read/28921393/genome-wide-compound-heterozygote-analysis-highlights-alleles-associated-with-adult-height-in-europeans
#11
Kaiyin Zhong, Gu Zhu, Xiaoxi Jing, A Emile J Hendriks, Sten L S Drop, M Arfan Ikram, Scott Gordon, Changqing Zeng, Andre G Uitterlinden, Nicholas G Martin, Fan Liu, Manfred Kayser
Adult height is the most widely genetically studied common trait in humans; however, the trait variance explainable by currently known height-associated single nucleotide polymorphisms (SNPs) identified from the previous genome-wide association studies (GWAS) is yet far from complete given the high heritability of this complex trait. To exam if compound heterozygotes (CH) may explain extra height variance, we conducted a genome-wide analysis to screen for CH in association with adult height in 10,631 Dutch Europeans enriched with extremely tall people, using our recently developed method implemented in the software package CollapsABEL...
September 18, 2017: Human Genetics
https://www.readbyqxmd.com/read/28913566/adar-rna-editing-in-human-disease-more-to-it-than-meets-the-i
#12
REVIEW
Angela Gallo, Dragana Vukic, David Michalík, Mary A O'Connell, Liam P Keegan
We review the structures and functions of ADARs and their involvements in human diseases. ADAR1 is widely expressed, particularly in the myeloid component of the blood system, and plays a prominent role in promiscuous editing of long dsRNA. Missense mutations that change ADAR1 residues and reduce RNA editing activity cause Aicardi-Goutières Syndrome, a childhood encephalitis and interferonopathy that mimics viral infection and resembles an extreme form of Systemic Lupus Erythmatosus (SLE). In Adar1 mouse mutant models aberrant interferon expression is prevented by eliminating interferon activation signaling from cytoplasmic dsRNA sensors, indicating that unedited cytoplasmic dsRNA drives the immune induction...
September 14, 2017: Human Genetics
https://www.readbyqxmd.com/read/28866814/from-mechanisms-to-therapy-rna-processing-s-impact-on-human-genetics
#13
EDITORIAL
Luiz O Penalva, Jeremy R Sanford
No abstract text is available yet for this article.
September 2, 2017: Human Genetics
https://www.readbyqxmd.com/read/28866801/recent-advances-in-assays-for-the-fragile-x-related-disorders
#14
REVIEW
Bruce E Hayward, Daman Kumari, Karen Usdin
The fragile X-related disorders are a group of three clinical conditions resulting from the instability of a CGG-repeat tract at the 5' end of the FMR1 transcript. Fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X-associated primary ovarian insufficiency (FXPOI) are disorders seen in carriers of FMR1 alleles with 55-200 repeats. Female carriers of these premutation (PM) alleles are also at risk of having a child who has an FMR1 allele with >200 repeats. Most of these full mutation (FM) alleles are epigenetically silenced resulting in a deficit of the FMR1 gene product, FMRP...
September 2, 2017: Human Genetics
https://www.readbyqxmd.com/read/28866788/enrichment-of-putatively-damaging-rare-variants-in-the-dyx2-locus-and-the-reading-related-genes-ccdc136-and-flnc
#15
Andrew K Adams, Shelley D Smith, Dongnhu T Truong, Erik G Willcutt, Richard K Olson, John C DeFries, Bruce F Pennington, Jeffrey R Gruen
Eleven loci with prior evidence for association with reading and language phenotypes were sequenced in 96 unrelated subjects with significant impairment in reading performance drawn from the Colorado Learning Disability Research Center collection. Out of 148 total individual missense variants identified, the chromosome 7 genes CCDC136 and FLNC contained 19. In addition, a region corresponding to the well-known DYX2 locus for RD contained 74 missense variants. Both allele sets were filtered for a minor allele frequency ≤0...
September 2, 2017: Human Genetics
https://www.readbyqxmd.com/read/28864994/a-genetic-variant-in-the-placenta-derived-mhc-class-i-chain-related-gene-a-increases-the-risk-of-preterm-birth-in-a-chinese-population
#16
Junjiao Song, Jing Li, Han Liu, Yuexin Gan, Yang Sun, Min Yu, Yongjun Zhang, Fei Luo, Ying Tian, Weiye Wang, Jun Zhang, Julian Little, Haidong Cheng, Dan Chen
Preterm birth (PTB) is a predominant contributor to neonatal mortality and morbidity worldwide. However, the pathophysiology of PTB is not well-understood. We tested the hypothesis that single-nucleotide polymorphisms (SNPs) in the placenta-derived MHC class I chain-related gene A (MICA) could disrupt placental development and hence result in PTB. Nineteen selected SNPs in MICA were genotyped in a case-control study of 127 premature infants and 634 term controls in a Chinese Han population. We found that significantly increased PTB risk was associated with homozygosity for the A variant of rs2256318 (adjusted odds ratio = 6...
September 1, 2017: Human Genetics
https://www.readbyqxmd.com/read/28864915/a-gene-based-test-of-association-through-an-orthogonal-decomposition-of-genotype-scores
#17
Zhongxue Chen, Kai Wang
The burden test and the sequence kernel association test (SKAT) are two popular methods for detecting association with rare variants. Treated as two different sources of association information, they are adaptively combined to form an optimal SKAT (SKAT-O) method for optimal power. We show that the burden test is part of rather than independent of the SKAT. We introduce a new test statistic that is the sum of the burden statistic and a statistic asymptotically independent of the burden statistic. The performance of this new test statistic is demonstrated through extensive simulation studies and applications to a Genetic Analysis Workshop 17 data set and the Ocular Hypertension Treatment Study data...
September 1, 2017: Human Genetics
https://www.readbyqxmd.com/read/28852871/smn-regulation-in-sma-and-in-response-to-stress-new-paradigms-and-therapeutic-possibilities
#18
REVIEW
Catherine E Dominguez, David Cunningham, Dawn S Chandler
Low levels of the survival of motor neuron (SMN) protein cause the neurodegenerative disease spinal muscular atrophy (SMA). SMA is a pediatric disease characterized by spinal motor neuron degeneration. SMA exhibits several levels of severity ranging from early antenatal fatality to only mild muscular weakness, and disease prognosis is related directly to the amount of functional SMN protein that a patient is able to express. Current therapies are being developed to increase the production of functional SMN protein; however, understanding the effect that natural stresses have on the production and function of SMN is of critical importance to ensuring that these therapies will have the greatest possible effect for patients...
August 29, 2017: Human Genetics
https://www.readbyqxmd.com/read/28836065/a-multi-stage-genome-wide-association-study-of-uterine-fibroids-in-african-americans
#19
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
Uterine fibroids are benign tumors of the uterus affecting up to 77% of women by menopause. They are the leading indication for hysterectomy, and account for $34 billion annually in the United States. Race/ethnicity and age are the strongest known risk factors. African American (AA) women have higher prevalence, earlier onset, and larger and more numerous fibroids than European American women. We conducted a multi-stage genome-wide association study (GWAS) of fibroid risk among AA women followed by in silico genetically predicted gene expression profiling of top hits...
August 23, 2017: Human Genetics
https://www.readbyqxmd.com/read/28799012/mtdna-genomes-reveal-a-relaxation-of-selective-constraints-in-low-bmi-individuals-in-a-uyghur-population
#20
Hong-Xiang Zheng, Lei Li, Xiao-Yan Jiang, Shi Yan, Zhendong Qin, Xiaofeng Wang, Li Jin
Considerable attention has been focused on the effect of deleterious mutations caused by the recent relaxation of selective constraints on human health, including the prevalence of obesity, which might represent an adaptive response of energy-conserving metabolism under the conditions of modern society. Mitochondrial DNA (mtDNA) encoding 13 core subunits of oxidative phosphorylation plays an important role in metabolism. Therefore, we hypothesized that a relaxation of selection constraints on mtDNA and an increase in the proportion of deleterious mutations have played a role in obesity prevalence...
August 10, 2017: Human Genetics
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