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Missing heritability

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https://www.readbyqxmd.com/read/28921393/genome-wide-compound-heterozygote-analysis-highlights-alleles-associated-with-adult-height-in-europeans
#1
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/28893854/will-big-data-close-the-missing-heritability-gap
#2
Hwasoon Kim, Alexander Grueneberg, Ana I Vazquez, Stephen Hsu, Gustavo de Los Campos
Despite the important discoveries reported by Genome-Wide Association studies, for most traits and diseases the prediction R-squared (R-sq.) achieved with genetic scores remains considerably lower than the trait heritability. Modern biobanks will soon deliver unprecedentedly large biomedical data sets: Will the advent of Big Data close the gap between the trait heritability and the proportion of variance that can be explained by a genomic predictor? We addressed this question using Bayesian methods and a data analysis approach that produces a surface response relating prediction R-sq...
September 11, 2017: Genetics
https://www.readbyqxmd.com/read/28886269/loss-of-function-grhl3-variants-detected-in-african-patients-with-isolated-cleft-palate
#3
M A Eshete, H Liu, M Li, W L Adeyemo, L J J Gowans, P A Mossey, T Busch, W Deressa, P Donkor, P B Olaitan, B S Aregbesola, R O Braimah, G O Oseni, F Oginni, R Audu, C Onwuamah, O James, E Augustine-Akpan, L A Rahman, M O Ogunlewe, F K N Arthur, S A Bello, P Agbenorku, P Twumasi, F Abate, T Hailu, Y Demissie, A Hailu, G Plange-Rhule, S Obiri-Yeboah, M M Dunnwald, P E Gravem, M L Marazita, A A Adeyemo, J C Murray, R A Cornell, A Butali
In contrast to the progress that has been made toward understanding the genetic etiology of cleft lip with or without cleft palate, relatively little is known about the genetic etiology for cleft palate only (CPO). A common coding variant of grainyhead like transcription factor 3 ( GRHL3) was recently shown to be associated with risk for CPO in Europeans. Mutations in this gene were also reported in families with Van der Woude syndrome. To identify rare mutations in GRHL3 that might explain the missing heritability for CPO, we sequenced GRHL3 in cases of CPO from Africa...
September 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28876085/joint-analysis-of-snp-snp-environment-interactions-for-chronic-dialysis-by-an-improved-branch-and-bound-algorithm
#4
Cheng-Hong Yang, Yu-Da Lin, Li-Yeh Chuang, Jin-Bor Chen, Hsueh-Wei Chang
In previous studies, both single-nucleotide polymorphism (SNP)-SNP or gene-gene (G × G) interactions and SNP-environmental factor (G × E) interactions were reported to partially account for "missing" heritability. However, (G × G) × E interactions were less commonly addressed. The purpose of this study was to develop a novel strategy to evaluate possible (G × G) × E interactions in D-loop-based chronic dialysis association. Using values from our previously published data set (704 controls and 193 cases) of 77 D-loop SNPs and 7 environmental factors (coronary heart disease, hypertension, diabetes mellitus, triglyceride, cholesterol, blood thiol, and TBARS levels), we compared the performances of G, G × G, G × E, and (G × G) × E...
September 6, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28873162/mutation-detection-in-patients-with-advanced-cancer-by-universal-sequencing-of-cancer-related-genes-in-tumor-and-normal-dna-vs-guideline-based-germline-testing
#5
Diana Mandelker, Liying Zhang, Yelena Kemel, Zsofia K Stadler, Vijai Joseph, Ahmet Zehir, Nisha Pradhan, Angela Arnold, Michael F Walsh, Yirong Li, Anoop R Balakrishnan, Aijazuddin Syed, Meera Prasad, Khedoudja Nafa, Maria I Carlo, Karen A Cadoo, Meg Sheehan, Megan H Fleischut, Erin Salo-Mullen, Magan Trottier, Steven M Lipkin, Anne Lincoln, Semanti Mukherjee, Vignesh Ravichandran, Roy Cambria, Jesse Galle, Wassim Abida, Marcia E Arcila, Ryma Benayed, Ronak Shah, Kenneth Yu, Dean F Bajorin, Jonathan A Coleman, Steven D Leach, Maeve A Lowery, Julio Garcia-Aguilar, Philip W Kantoff, Charles L Sawyers, Maura N Dickler, Leonard Saltz, Robert J Motzer, Eileen M O'Reilly, Howard I Scher, Jose Baselga, David S Klimstra, David B Solit, David M Hyman, Michael F Berger, Marc Ladanyi, Mark E Robson, Kenneth Offit
Importance: Guidelines for cancer genetic testing based on family history may miss clinically actionable genetic changes with established implications for cancer screening or prevention. Objective: To determine the proportion and potential clinical implications of inherited variants detected using simultaneous sequencing of the tumor and normal tissue ("tumor-normal sequencing") compared with genetic test results based on current guidelines. Design, Setting, and Participants: From January 2014 until May 2016 at Memorial Sloan Kettering Cancer Center, 10 336 patients consented to tumor DNA sequencing...
September 5, 2017: JAMA: the Journal of the American Medical Association
https://www.readbyqxmd.com/read/28856828/effects-of-correcting-missing-daily-feed-intake-values-on-the-genetic-parameters-and-estimated-breeding-values-for-feeding-traits-in-pigs
#6
Tetsuya Ito, Kazuo Fukawa, Mai Kamikawa, Satoshi Nikaidou, Masaaki Taniguchi, Aisaku Arakawa, Genki Tanaka, Satoshi Mikawa, Tsutomu Furukawa, Kensuke Hirose
Daily feed intake (DFI) is an important consideration for improving feed efficiency, but measurements using electronic feeder systems contain many missing and incorrect values. Therefore, we evaluated three methods for correcting missing DFI data (quadratic, orthogonal polynomial, and locally weighted (Loess) regression equations) and assessed the effects of these missing values on the genetic parameters and the estimated breeding values (EBV) for feeding traits. DFI records were obtained from 1622 Duroc pigs, comprising 902 individuals without missing DFI and 720 individuals with missing DFI...
August 30, 2017: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/28809852/the-snp-set-based-association-study-identifies-itga1-as-a-susceptibility-gene-of-attention-deficit-hyperactivity-disorder-in-han-chinese
#7
L Liu, L Zhang, H M Li, Z R Wang, X F Xie, J P Mei, J L Jin, J Shi, L Sun, S C Li, Y L Tan, L Yang, J Wang, H M Yang, Q J Qian, Y F Wang
Genome-wide association studies, which detect the association between single-nucleotide polymorphisms (SNPs) and disease susceptibility, have been extensively applied to study attention-deficit/hyperactivity disorder (ADHD), but genome-wide significant associations have not been found yet. Genetic heterogeneity and insufficient genomic coverage may account for the missing heritability. We performed a two-stage association study for ADHD in the Han Chinese population. In the discovery stage, 1033 ADHD patients and 950 healthy controls were genotyped using both the Affymetrix Genome-Wide Human SNP Array 6...
August 15, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28799029/detecting-the-qtl-allele-system-conferring-flowering-date-in-a-nested-association-mapping-population-of-soybean-using-a-novel-procedure
#8
Shuguang Li, Yongce Cao, Jianbo He, Tuanjie Zhao, Junyi Gai
The RTM-GWAS was chosen among five procedures to identify DTF QTL-allele constitution in a soybean NAM population; 139 QTLs with 496 alleles accounting for 81.7% of phenotypic variance were detected. Flowering date (days to flowering, DTF) is an ecological trait in soybean, closely related to its ability to adapt to areas. A nested association mapping (NAM) population consisting of four RIL populations (LM, ZM, MT and MW with M8206 as their common parent) was established and tested for their DTF under five environments...
August 10, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28766213/expanded-gene-panel-use-for-women-with-breast-cancer-identification-and-intervention-beyond-breast-cancer-risk
#9
Erin O'Leary, Daniela Iacoboni, Jennifer Holle, Scott T Michalski, Edward D Esplin, Shan Yang, Karen Ouyang
BACKGROUND: Clinicians ordering multi-gene next-generation sequencing panels for hereditary breast cancer risk have a variety of test panel options. Many panels include lesser known breast cancer genes or genes associated with other cancers. The authors hypothesized that using broader gene panels increases the identification of clinically significant findings, some relevant and others incidental to the testing indication. They examined clinician ordering patterns and compared the yield of pathogenic or likely pathogenic (P/LP) variants in non-BRCA genes of female breast cancer patients...
August 1, 2017: Annals of Surgical Oncology
https://www.readbyqxmd.com/read/28738478/-less-common-variants-association-study-and-statistical-analysis
#10
X Liao, J Deng, J Y Xun, J X Yan
In the past decade, based on the "common disease-common variant" hypothesis, genomewide association studies (GWAS) have been extensively used to dissect the genetic components of complex diseases and quantitative traits. However, the identified disease-associated common variants by GWASs can only explain small part of the corresponding disease heritability. "Common disease-rare variant" hypothesis has been proposed to explore the missed heritability. With the development of the next generation sequencing technology, various association studies of less common variants are ongoing...
July 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28726280/an-efficient-study-design-to-test-parent-of-origin-effects-in-family-trios
#11
Xiaobo Yu, Gao Chen, Rui Feng
Increasing evidence has shown that genes may cause prenatal, neonatal, and pediatric diseases depending on their parental origins. Statistical models that incorporate parent-of-origin effects (POEs) can improve the power of detecting disease-associated genes and help explain the missing heritability of diseases. In many studies, children have been sequenced for genome-wide association testing. But it may become unaffordable to sequence their parents and evaluate POEs. Motivated by the reality, we proposed a budget-friendly study design of sequencing children and only genotyping their parents through single nucleotide polymorphism array...
July 20, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28711250/genetic-analysis-for-quality-of-frozen-embryos-produced-by-holstein-cattle-donors-in-canada
#12
C Jaton, F S Schenkel, F Malchiodi, M Sargolzaei, C A Price, C Baes, F Miglior
The number of embryos produced by Holstein donors has been shown to be heritable, so it could be possible to genetically select for this trait to improve the efficiency of the assisted reproductive technology (ART) in dairy cattle. Another important parameter to consider for achieving good results from ART is embryo quality because embryos of good quality have more chance of producing live offspring. The possibility of using genetic selection for increasing the quality of embryo produced from ART has yet to be assessed...
September 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28711145/integrative-approaches-to-understanding-the-pathogenic-role-of-genetic-variation-in-rheumatic-diseases
#13
REVIEW
Vincent A Laufer, Jake Y Chen, Carl D Langefeld, S Louis Bridges
The use of high-throughput omics may help to understand the contribution of genetic variants to the pathogenesis of rheumatic diseases. We discuss the concept of missing heritability: that genetic variants do not explain the heritability of rheumatoid arthritis and related rheumatologic conditions. In addition to an overview of how integrative data analysis can lead to novel insights into mechanisms of rheumatic diseases, we describe statistical approaches to prioritizing genetic variants for future functional analyses...
August 2017: Rheumatic Diseases Clinics of North America
https://www.readbyqxmd.com/read/28705779/autoimmune-aspects-of-psoriasis-heritability-and-autoantigens
#14
REVIEW
Jörg Christoph Prinz
Chronic immune-mediated disorders (IMDs) constitute a major health burden. Understanding IMD pathogenesis is facing two major constraints: Missing heritability explaining familial clustering, and missing autoantigens. Pinpointing IMD risk genes and autoimmune targets, however, is of fundamental importance for developing novel causal therapies. The strongest association of all IMDs is seen with human leukocyte antigen (HLA) alleles. Using psoriasis as an IMD model this article reviews the pathogenic role HLA molecules may have within the polygenic predisposition of IMDs...
July 10, 2017: Autoimmunity Reviews
https://www.readbyqxmd.com/read/28702320/parental-obesity-leads-to-metabolic-changes-in-the-f2-generation-in-drosophila
#15
Rebecca A S Palu, Sophia A Praggastis, Carl S Thummel
OBJECTIVE: A significant portion of the heritable risk for complex metabolic disorders cannot be attributed to classic Mendelian genetic factors. At least some of this missing heritability is thought to be due to the epigenetic influence of parental and grandparental metabolic state on offspring health. Previous work suggests that this transgenerational phenomenon is evolutionarily conserved in Drosophila. These studies, however, have all depended on dietary paradigms to alter parental metabolic state, which can have inconsistent heritable effects on the metabolism of offspring...
July 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/28696413/genome-wide-meta-analysis-of-copy-number-variations-with-alcohol-dependence
#16
A Sulovari, Z Liu, Z Zhu, D Li
Genetic association studies and meta-analyses of alcohol dependence (AD) have reported AD-associated single nucleotide polymorphisms (SNPs). These SNPs collectively account for a small portion of estimated heritability in AD. Recent genome-wide copy number variation (CNV) studies have identified CNVs associated with AD and substance dependence, suggesting that a portion of the missing heritability is explained by CNV. We applied PennCNV and QuantiSNP CNV calling algorithms to identify consensus CNVs in five AD cohorts of European and African origins...
July 11, 2017: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/28667292/identification-of-a-functionally-significant-tri-allelic-genotype-in-the-tyrosinase-gene-tyr-causing-hypomorphic-oculocutaneous-albinism-oca1b
#17
Chelsea S Norman, Luke O'Gorman, Jane Gibson, Reuben J Pengelly, Diana Baralle, J Arjuna Ratnayaka, Helen Griffiths, Matthew Rose-Zerilli, Megan Ranger, David Bunyan, Helena Lee, Rhiannon Page, Tutte Newall, Fatima Shawkat, Christopher Mattocks, Daniel Ward, Sarah Ennis, Jay E Self
Oculocutaneous albinism (OCA) and ocular albinism (OA) are inherited disorders of melanin biosynthesis, resulting in loss of pigment and severe visual deficits. OCA encompasses a range of subtypes with overlapping, often hypomorphic phenotypes. OCA1 is the most common cause of albinism in European populations and is inherited through autosomal recessive mutations in the Tyrosinase (TYR) gene. However, there is a high level of reported missing heritability, where only a single heterozygous mutation is found in TYR...
June 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28659968/the-human-microbiome-and-the-missing-heritability-problem
#18
Santiago Sandoval-Motta, Maximino Aldana, Esperanza Martínez-Romero, Alejandro Frank
The "missing heritability" problem states that genetic variants in Genome-Wide Association Studies (GWAS) cannot completely explain the heritability of complex traits. Traditionally, the heritability of a phenotype is measured through familial studies using twins, siblings and other close relatives, making assumptions on the genetic similarities between them. When this heritability is compared to the one obtained through GWAS for the same traits, a substantial gap between both measurements arise with genome wide studies reporting significantly smaller values...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28651948/genetic-sharing-with-coronary-artery-disease-identifies-potential-novel-loci-for-bone-mineral-density
#19
Cheng Peng, Jie Shen, Xu Lin, Kuan-Jui Su, Jonathan Greenbaum, Wei Zhu, Hui-Ling Lou, Feng Liu, Chun-Ping Zeng, Wei-Feng Deng, Hong-Wen Deng
Bone mineral density (BMD) is a complex trait with high missing heritability. Numerous evidences have shown that BMD variation has a relationship with coronary artery disease (CAD). This relationship may come from a common genetic basis called pleiotropy. By leveraging the pleiotropy with CAD, we may be able to improve the detection power of genetic variants associated with BMD. Using a recently developed conditional false discovery rate (cFDR) method, we jointly analyzed summary statistics from two large independent genome wide association studies (GWAS) of lumbar spine (LS) BMD and CAD...
June 23, 2017: Bone
https://www.readbyqxmd.com/read/28646452/dosage-effects-of-zp2-and-zp3-heterozygous-mutations-cause-human-infertility
#20
Wenqiang Liu, Kunming Li, Dandan Bai, Jiqing Yin, Yuanyuan Tang, Fengli Chi, Linfeng Zhang, Yu Wang, Jiaping Pan, Shanshan Liang, Yi Guo, Jingling Ruan, Xiaochen Kou, Yanhong Zhao, Hong Wang, Jiayu Chen, Xiaoming Teng, Shaorong Gao
The zona pellucida (ZP) is an extracellular matrix universally surrounding mammalian eggs, which is essential for oogenesis, fertilization, and pre-implantation embryo development. Here, we identified two novel heritable mutations of ZP2 and ZP3, both occurring in an infertile female patient with ZP-abnormal eggs. Mouse models with the same mutations were generated by CRISPR/Cas9 gene editing system, and oocytes obtained from female mice with either single heterozygous mutation showed approximately half of the normal ZP thickness compared to wild-type oocytes...
August 2017: Human Genetics
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