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Missing heritability

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https://www.readbyqxmd.com/read/28726280/an-efficient-study-design-to-test-parent-of-origin-effects-in-family-trios
#1
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
#2
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...
July 12, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28711145/integrative-approaches-to-understanding-the-pathogenic-role-of-genetic-variation-in-rheumatic-diseases
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28642868/an-exploration-of-gene-gene-interactions-and-their-effects-on-hypertension
#11
Ying Meng, Susan Groth, Jill R Quinn, John Bisognano, Tong Tong Wu
Hypertension tends to perpetuate in families and the heritability of hypertension is estimated to be around 20-60%. So far, the main proportion of this heritability has not been found by single-locus genome-wide association studies. Therefore, the current study explored gene-gene interactions that have the potential to partially fill in the missing heritability. A two-stage discovery-confirmatory analysis was carried out in the Framingham Heart Study cohorts. The first stage was an exhaustive pairwise search performed in 2320 early-onset hypertensive cases with matched normotensive controls from the offspring cohort...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28641921/genome-wide-association-and-interaction-studies-of-csf-t-tau-a%C3%AE-42-ratio-in-adni-cohort
#12
Jin Li, Qiushi Zhang, Feng Chen, Xianglian Meng, Wenjie Liu, Dandan Chen, Jingwen Yan, Sungeun Kim, Lei Wang, Weixing Feng, Andrew J Saykin, Hong Liang, Li Shen
The pathogenic relevance in Alzheimer's disease (AD) presents a decrease of cerebrospinal fluid amyloid-ß42 (Aß42) burden and an increase in cerebrospinal fluid total tau (T-tau) levels. In this work, we performed genome-wide association study (GWAS) and genome-wide interaction study of T-tau/Aß42 ratio as an AD imaging quantitative trait on 843 subjects and 563,980 single-nucleotide polymorphisms (SNPs) in ADNI cohort. We aim to identify not only SNPs with significant main effects but also SNPs with interaction effects to help explain "missing heritability"...
May 15, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28634715/regulatory-element-based-prediction-identifies-new-susceptibility-regulatory-variants-for-osteoporosis
#13
Shi Yao, Yan Guo, Shan-Shan Dong, Ruo-Han Hao, Xiao-Feng Chen, Yi-Xiao Chen, Jia-Bin Chen, Qing Tian, Hong-Wen Deng, Tie-Lin Yang
Despite genome-wide association studies (GWASs) have identified many susceptibility genes for osteoporosis, it still leaves a large part of missing heritability to be discovered. Integrating regulatory information and GWASs could offer new insights into the biological link between the susceptibility SNPs and osteoporosis. We generated five machine learning classifiers with osteoporosis-associated variants and regulatory features data. We gained the optimal classifier and predicted genome-wide SNPs to discover susceptibility regulatory variants...
August 2017: Human Genetics
https://www.readbyqxmd.com/read/28628480/kernel-based-measure-of-variable-importance-for-genetic-association-studies
#14
Vicente Gallego, M Luz Calle, Ramon Oller
The identification of genetic variants that are associated with disease risk is an important goal of genetic association studies. Standard approaches perform univariate analysis where each genetic variant, usually Single Nucleotide Polymorphisms (SNPs), is tested for association with disease status. Though many genetic variants have been identified and validated so far using this univariate approach, for most complex diseases a large part of their genetic component is still unknown, the so called missing heritability...
June 17, 2017: International Journal of Biostatistics
https://www.readbyqxmd.com/read/28598419/genome-wide-approach-identifies-a-novel-gene-maternal-pre-pregnancy-bmi-interaction-on-preterm-birth
#15
Xiumei Hong, Ke Hao, Hongkai Ji, Shouneng Peng, Ben Sherwood, Antonio Di Narzo, Hui-Ju Tsai, Xin Liu, Irina Burd, Guoying Wang, Yuelong Ji, Deanna Caruso, Guangyun Mao, Tami R Bartell, Zhongyang Zhang, Colleen Pearson, Linda Heffner, Sandra Cerda, Terri H Beaty, M Daniele Fallin, Aviva Lee-Parritz, Barry Zuckerman, Daniel E Weeks, Xiaobin Wang
Preterm birth (PTB) contributes significantly to infant mortality and morbidity with lifelong impact. Few robust genetic factors of PTB have been identified. Such 'missing heritability' may be partly due to gene × environment interactions (G × E), which is largely unexplored. Here we conduct genome-wide G × E analyses of PTB in 1,733 African-American women (698 mothers of PTB; 1,035 of term birth) from the Boston Birth Cohort. We show that maternal COL24A1 variants have a significant genome-wide interaction with maternal pre-pregnancy overweight/obesity on PTB risk, with rs11161721 (PG × E=1...
June 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28591191/reanalysis-of-brca1-2-negative-high-risk-ovarian-cancer-patients-reveals-novel-germline-risk-loci-and-insights-into-missing-heritability
#16
Jaime L Stafford, Gregory Dyson, Nancy K Levin, Sophia Chaudhry, Rita Rosati, Hasini Kalpage, Courtney Wernette, Nancie Petrucelli, Michael S Simon, Michael A Tainsky
While up to 25% of ovarian cancer (OVCA) cases are thought to be due to inherited factors, the majority of genetic risk remains unexplained. To address this gap, we sought to identify previously undescribed OVCA risk variants through the whole exome sequencing (WES) and candidate gene analysis of 48 women with ovarian cancer and selected for high risk of genetic inheritance, yet negative for any known pathogenic variants in either BRCA1 or BRCA2. In silico SNP analysis was employed to identify suspect variants followed by validation using Sanger DNA sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28589856/association-analysis-of-rare-variants-near-the-apoe-region-with-csf-and-neuroimaging-biomarkers-of-alzheimer-s-disease
#17
Kwangsik Nho, Sungeun Kim, Emrin Horgusluoglu, Shannon L Risacher, Li Shen, Dokyoon Kim, Seunggeun Lee, Tatiana Foroud, Leslie M Shaw, John Q Trojanowski, Paul S Aisen, Ronald C Petersen, Clifford R Jack, Michael W Weiner, Robert C Green, Arthur W Toga, Andrew J Saykin
BACKGROUND: The APOE ε4 allele is the most significant common genetic risk factor for late-onset Alzheimer's disease (LOAD). The region surrounding APOE on chromosome 19 has also shown consistent association with LOAD. However, no common variants in the region remain significant after adjusting for APOE genotype. We report a rare variant association analysis of genes in the vicinity of APOE with cerebrospinal fluid (CSF) and neuroimaging biomarkers of LOAD. METHODS: Whole genome sequencing (WGS) was performed on 817 blood DNA samples from the Alzheimer's Disease Neuroimaging Initiative (ADNI)...
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28587112/is-there-a-role-for-genomics-in-the-management-of-hypertension
#18
REVIEW
Jacopo Burrello, Silvia Monticone, Fabrizio Buffolo, Martina Tetti, Franco Veglio, Tracy A Williams, Paolo Mulatero
Hypertension (HTN) affects about 1 billion people worldwide and the lack of a single identifiable cause complicates its treatment. Blood pressure (BP) levels are influenced by environmental factors, but there is a strong genetic component. Linkage analysis has identified several genes involved in Mendelian forms of HTN and the associated pathophysiological mechanisms have been unravelled, leading to targeted therapies. The majority of these syndromes are due to gain-of-function or loss-of-functions mutations, resulting in an alteration of mineralocorticoid, glucocorticoid, or sympathetic pathways...
May 26, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28583089/genome-enabled-predictions-for-fruit-weight-and-quality-from-repeated-records-in-european-peach-progenies
#19
Filippo Biscarini, Nelson Nazzicari, Marco Bink, Pere Arús, Maria José Aranzana, Ignazio Verde, Sabrina Micali, Thierry Pascal, Benedicte Quilot-Turion, Patrick Lambert, Cassia da Silva Linge, Igor Pacheco, Daniele Bassi, Alessandra Stella, Laura Rossini
BACKGROUND: Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach. RESULTS: A repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented...
June 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28582595/why-the-missing-heritability-might-not-be-in-the-dna
#20
Pierrick Bourrat, Qiaoying Lu, Eva Jablonka
There are four major hypotheses (H1, H2, H3, and H4) as to the source of missing heritability. We propose that estimates obtained from GWAS underestimate heritability by not taking into account non-DNA (epigenetic) sources of heritability. Taking those factors into account (H4) should result in increased heritability estimates.
June 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
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