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Missing heritability

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https://www.readbyqxmd.com/read/28302160/increased-genomic-burden-of-germline-copy-number-variants-is-associated-with-early-onset-breast-cancer-australian-breast-cancer-family-registry
#1
Logan C Walker, John F Pearson, George A R Wiggins, Graham G Giles, John L Hopper, Melissa C Southey
BACKGROUND: Women with breast cancer who have multiple affected relatives are more likely to have inherited genetic risk factors for the disease. All the currently known genetic risk factors for breast cancer account for less than half of the average familial risk. Furthermore, the genetic factor(s) underlying an increased cancer risk for many women from multiple-case families remain unknown. Rare genomic duplications and deletions, known as copy number variants (CNVs), cover more than 10% of a human genome, are often not assessed in studies of genetic predisposition, and could account for some of the so-called "missing heritability"...
March 16, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28256260/genetics-of-early-onset-parkinson-s-disease-in-finland-exome-sequencing-and-genome-wide-association-study
#2
Ari Siitonen, Michael A Nalls, Dena Hernández, J Raphael Gibbs, Jinhui Ding, Pauli Ylikotila, Connor Edsall, Andrew Singleton, Kari Majamaa
Several genes and risk factors are associated with Parkinson's disease (PD). Although many of the genetic markers belong to a common pathway, a unifying pathogenetic mechanism is yet to be found. Also, missing heritability analyses have estimated that only part of the genetic influence contributing to PD has been found. Here, we carried out whole-exome sequencing (WES) on 438 Finnish patients with early-onset PD. We also reanalyzed previous data from genome-wide association studies (GWAS) on the same cohort...
February 2, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28222494/selecting-cases-and-controls-for-dna-sequencing-studies-using-family-histories-of-disease
#3
Wonji Kim, Dandi Qiao, Michael H Cho, Soo Heon Kwak, Kyong Soo Park, Edwin K Silverman, Pak Sham, Sungho Won
Recent improvements in sequencing technology have enabled the investigation of so-called missing heritability, and a large number of affected subjects have been sequenced in order to detect significant associations between human diseases and rare variants. However, the cost of genome sequencing is still high, and a statistically powerful strategy for selecting informative subjects would be useful. Therefore, in this report, we propose a new statistical method for selecting cases and controls for sequencing studies based on family history...
February 21, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28201496/other-side-of-the-coin-the-missing-heritability-in-hypertrophic-cardiomyopathy
#4
Adam S Helms, Sharlene M Day
No abstract text is available yet for this article.
February 13, 2017: European Heart Journal
https://www.readbyqxmd.com/read/28188182/unstable-inheritance-of-45s-rrna-genes-in-arabidopsis-thaliana
#5
Fernando A Rabanal, Viktoria Nizhynska, Terezie Mandáková, Polina Yu Novikova, Martin A Lysak, Richard Mott, Magnus Nordborg
The considerable genome size variation in Arabidopsis thaliana has been shown largely to be due to copy number variation (CNV) in 45S ribosomal RNA (rRNA) genes. Surprisingly, attempts to map this variation by means of genome-wide association studies (GWAS) failed to identify either of the two likely sources, namely the nucleolar organizer regions (NORs). Instead, GWAS implicated a trans-acting locus, as if rRNA CNV was a phenotype rather than a genotype. To explain these results, we investigated the inheritance and stability of rRNA gene copy number using the variety of genetic resources available in A...
February 10, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28187711/poppante-population-and-pedigree-association-testing-for-quantitative-data
#6
Alessia Visconti, Mashael Al-Shafai, Wadha A Al Muftah, Shaza B Zaghlool, Massimo Mangino, Karsten Suhre, Mario Falchi
BACKGROUND: Family-based designs, from twin studies to isolated populations with their complex genealogical data, are a valuable resource for genetic studies of heritable molecular biomarkers. Existing software for family-based studies have mainly focused on facilitating association between response phenotypes and genetic markers, and no user-friendly tools are at present available to straightforwardly extend association studies in related samples to large datasets of generic quantitative data, as those generated by current -omics technologies...
February 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28177346/how-to-improve-breeding-value-prediction-for-feed-conversion-ratio-in-the-case-of-incomplete-longitudinal-body-weights
#7
V H Huynh Tran, H Gilbert, I David
With the development of automatic self-feeders, repeated measurements of feed intake are becoming easier in an increasing number of species. However, the corresponding BW are not always recorded, and these missing values complicate the longitudinal analysis of the feed conversion ratio (FCR). Our aim was to evaluate the impact of missing BW data on estimations of the genetic parameters of FCR and ways to improve the estimations. On the basis of the missing BW profile in French Large White pigs (male pigs weighed weekly, females and castrated males weighed monthly), we compared 2 different ways of predicting missing BW, 1 using a Gompertz model and 1 using a linear interpolation...
January 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28154507/gene-gene-interaction-analysis-for-the-accelerated-failure-time-model-using-a-unified-model-based-multifactor-dimensionality-reduction-method
#8
Seungyeoun Lee, Donghee Son, Wenbao Yu, Taesung Park
Although a large number of genetic variants have been identified to be associated with common diseases through genome-wide association studies, there still exits limitations in explaining the missing heritability. One approach to solving this missing heritability problem is to investigate gene-gene interactions, rather than a single-locus approach. For gene-gene interaction analysis, the multifactor dimensionality reduction (MDR) method has been widely applied, since the constructive induction algorithm of MDR efficiently reduces high-order dimensions into one dimension by classifying multi-level genotypes into high- and low-risk groups...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28121987/genetic-variation-in-the-social-environment-contributes-to-health-and-disease
#9
Amelie Baud, Megan K Mulligan, Francesco Paolo Casale, Jesse F Ingels, Casey J Bohl, Jacques Callebert, Jean-Marie Launay, Jon Krohn, Andres Legarra, Robert W Williams, Oliver Stegle
Assessing the impact of the social environment on health and disease is challenging. As social effects are in part determined by the genetic makeup of social partners, they can be studied from associations between genotypes of one individual and phenotype of another (social genetic effects, SGE, also called indirect genetic effects). For the first time we quantified the contribution of SGE to more than 100 organismal phenotypes and genome-wide gene expression measured in laboratory mice. We find that genetic variation in cage mates (i...
January 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28117369/fine-mapping-genetic-associations-between-the-hla-region-and-extremely-high-intelligence
#10
Delilah Zabaneh, Eva Krapohl, Michael A Simpson, Mike B Miller, William G Iacono, Matt McGue, Martha Putallaz, David Lubinski, Robert Plomin, Gerome Breen
General cognitive ability (intelligence) is one of the most heritable behavioural traits and most predictive of socially important outcomes and health. We hypothesized that some of the missing heritability of IQ might lie hidden in the human leukocyte antigen (HLA) region, which plays a critical role in many diseases and traits but is not well tagged in conventional GWAS. Using a uniquely powered design, we investigated whether fine-mapping of the HLA region could narrow the missing heritability gap. Our case-control design included 1,393 cases with extremely high intelligence scores (top 0...
January 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28114305/targeted-sequencing-of-lung-function-loci-in-chronic-obstructive-pulmonary-disease-cases-and-controls
#11
María Soler Artigas, Louise V Wain, Nick Shrine, Tricia M McKeever, Ian Sayers, Ian P Hall, Martin D Tobin
Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide; smoking is the main risk factor for COPD, but genetic factors are also relevant contributors. Genome-wide association studies (GWAS) of the lung function measures used in the diagnosis of COPD have identified a number of loci, however association signals are often broad and collectively these loci only explain a small proportion of the heritability. In order to examine the association with COPD risk of genetic variants down to low allele frequencies, to aid fine-mapping of association signals and to explain more of the missing heritability, we undertook a targeted sequencing study in 300 COPD cases and 300 smoking controls for 26 loci previously reported to be associated with lung function...
2017: PloS One
https://www.readbyqxmd.com/read/28105966/a-novel-approach-for-pathway-analysis-of-gwas-data-highlights-role-of-bmp-signaling-and-muscle-cell-differentiation-in-colorectal-cancer-susceptibility
#12
Aniket Mishra, Stuart MacGregor
Genome-wide association studies (GWAS) have revolutionized the field of gene mapping. As the GWAS field matures, it is becoming clear that for many complex traits, a proportion of the missing heritability is attributable to common variants of individually small effect. Detecting these small effects individually can be difficult, and statistical power would be increased if relevant variants could be grouped together for testing. Here, we propose a VEGAS2Pathway approach that aggregates association strength of individual markers into pre-specified biological pathways...
February 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28105963/prevalence-and-heritability-of-early-childhood-caries-among-monozygotic-and-dizygotic-twins
#13
Anuradha Kuppan, Steven Rodrigues, Victor Samuel, Mahesh Ramakrishnan, Hassan S Halawany, Nimmi B Abraham, Vimal Jacob, Sukumaran Anil
Deciphering the relative importance of genetic and environmental factors, which play a major role in the prevalence of early childhood caries (ECC), can help clinicians with planning a long-term preventive treatment. The objective of the study was to determine the prevalence and heritability of ECC among monozygotic (MZ) and dizygotic (DZ) twins in Chennai, India, in the year 2013. A cross-sectional study was designed to estimate the prevalence of ECC among twins. Zygosity classification for the survey framework was adapted from a highly accurate parental report questionnaire pertaining to the physical similarity between twins...
February 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28095416/meta-gwas-accuracy-and-power-metagap-calculator-shows-that-hiding-heritability-is-partially-due-to-imperfect-genetic-correlations-across-studies
#14
Ronald de Vlaming, Aysu Okbay, Cornelius A Rietveld, Magnus Johannesson, Patrik K E Magnusson, André G Uitterlinden, Frank J A van Rooij, Albert Hofman, Patrick J F Groenen, A Roy Thurik, Philipp D Koellinger
Large-scale genome-wide association results are typically obtained from a fixed-effects meta-analysis of GWAS summary statistics from multiple studies spanning different regions and/or time periods. This approach averages the estimated effects of genetic variants across studies. In case genetic effects are heterogeneous across studies, the statistical power of a GWAS and the predictive accuracy of polygenic scores are attenuated, contributing to the so-called 'missing heritability'. Here, we describe the online Meta-GWAS Accuracy and Power (MetaGAP) calculator (available at www...
January 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28065468/the-genetic-architecture-of-gene-expression-in-peripheral-blood
#15
Luke R Lloyd-Jones, Alexander Holloway, Allan McRae, Jian Yang, Kerrin Small, Jing Zhao, Biao Zeng, Andrew Bakshi, Andres Metspalu, Manolis Dermitzakis, Greg Gibson, Tim Spector, Grant Montgomery, Tonu Esko, Peter M Visscher, Joseph E Powell
We analyzed the mRNA levels for 36,778 transcript expression traits (probes) from 2,765 individuals to comprehensively investigate the genetic architecture and degree of missing heritability for gene expression in peripheral blood. We identified 11,204 cis and 3,791 trans independent expression quantitative trait loci (eQTL) by using linear mixed models to perform genome-wide association analyses. Furthermore, using information on both closely and distantly related individuals, heritability was estimated for all expression traits...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28039885/rare-variant-association-test-with-multiple-phenotypes
#16
Selyeong Lee, Sungho Won, Young Jin Kim, Yongkang Kim, Bong-Jo Kim, Taesung Park
Although genome-wide association studies (GWAS) have now discovered thousands of genetic variants associated with common traits, such variants cannot explain the large degree of "missing heritability," likely due to rare variants. The advent of next generation sequencing technology has allowed rare variant detection and association with common traits, often by investigating specific genomic regions for rare variant effects on a trait. Although multiple correlated phenotypes are often concurrently observed in GWAS, most studies analyze only single phenotypes, which may lessen statistical power...
April 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28028462/network-based-analysis-of-differentially-expressed-genes-in-cerebrospinal-fluid-csf-and-blood-reveals-new-candidate-genes-for-multiple-sclerosis
#17
Nahid Safari-Alighiarloo, Mostafa Rezaei-Tavirani, Mohammad Taghizadeh, Seyyed Mohammad Tabatabaei, Saeed Namaki
BACKGROUND: The involvement of multiple genes and missing heritability, which are dominant in complex diseases such as multiple sclerosis (MS), entail using network biology to better elucidate their molecular basis and genetic factors. We therefore aimed to integrate interactome (protein-protein interaction (PPI)) and transcriptomes data to construct and analyze PPI networks for MS disease. METHODS: Gene expression profiles in paired cerebrospinal fluid (CSF) and peripheral blood mononuclear cells (PBMCs) samples from MS patients, sampled in relapse or remission and controls, were analyzed...
2016: PeerJ
https://www.readbyqxmd.com/read/27995669/perch-a-unified-framework-for-disease-gene-prioritization
#18
Bing-Jian Feng
To interpret genetic variants discovered from next-generation sequencing, integration of heterogeneous information is vital for success. This article describes a framework named PERCH (Polymorphism Evaluation, Ranking, and Classification for a Heritable trait), available at http://BJFengLab.org/. It can prioritize disease genes by quantitatively unifying a new deleteriousness measure called BayesDel, an improved assessment of the biological relevance of genes to the disease, a modified linkage analysis, a novel rare-variant association test, and a converted variant call quality score...
March 2017: Human Mutation
https://www.readbyqxmd.com/read/27903611/the-genomic-architecture-of-interactions-between-natural-genetic-polymorphisms-and-environments-in-yeast-growth
#19
Xinzhu Wei, Jianzhi Zhang
Gene-environment interaction (G×E) refers to the phenomenon that the same mutation has different phenotypic effects in different environments. Although quantitative trait loci (QTLs) exhibiting G×E have been reported, little is known about the general properties of G×E, and those of its underlying QTLs. Here, we use the genotypes of 1005 segregants from a cross between two Saccharomyces cerevisiae strains, and the growth rates of these segregants in 47 environments, to identify growth rate QTLs (gQTLs) in each environment, and QTLs that have different growth effects in each pair of environments (g×eQTLs) ...
February 2017: Genetics
https://www.readbyqxmd.com/read/27896934/increased-identification-of-novel-variants-in-type-2-diabetes-birth-weight-and-their-pleiotropic-loci
#20
Chun-Ping Zeng, Yuan-Cheng Chen, Xu Lin, Jonathan Greenbaum, You-Ping Chen, Cheng Peng, Xia-Fang Wang, Rou Zhou, Wei-Min Deng, Jie Shen, Hong-Wen Deng
BACKGROUND: Clinical and epidemiological findings point to an association between type 2 diabetes (T2D) and low birth weight (BW). However, the nature underlying their relationship is largely unknown. Here, we aim to identify novel single-nucleotide polymorphisms (SNPs) in T2D, BW and their pleiotropic loci. METHODS: We applied a pleiotropy-informed conditional false discovery rate (cFDR) method to two independent GWAS summary statistics of T2D (n = 149,821) and BW (n = 26,836)...
November 29, 2016: Journal of Diabetes
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