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Missing heritability

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https://www.readbyqxmd.com/read/28442163/the-search-for-the-missing-heritability-of-prostate-cancer
#1
EDITORIAL
Patrick C Walsh
Scientists and clinicians at Johns Hopkins have been working since 1987 to uncover the genetic pathogenesis of prostate cancer. A patient query about the hereditary nature of the disease led to data collection on family history, followed by segregation and linkage analyses. Collaborative investigations using next-generation sequencing to identify genetic variants associated with prostate cancer risk have revealed the significance of HOXB13, BRCA 1/2, and DNA repair mutations.
April 22, 2017: European Urology
https://www.readbyqxmd.com/read/28441463/rapidsnps-a-new-computational-pipeline-for-rapidly-identifying-key-genetic-variants-reveals-previously-unidentified-snps-that-are-significantly-associated-with-individual-platelet-responses
#2
Bajuna Rashid Salehe, Chris Ian Jones, Giuseppe Di Fatta, Liam James McGuffin
Advances in omics technologies have led to the discovery of genetic markers, or single nucleotide polymorphisms (SNPs), that are associated with particular diseases or complex traits. Although there have been significant improvements in the approaches used to analyse associations of SNPs with disease, further optimised and rapid techniques are needed to keep up with the rate of SNP discovery, which has exacerbated the 'missing heritability' problem. Here, we have devised a novel, integrated, heuristic-based, hybrid analytical computational pipeline, for rapidly detecting novel or key genetic variants that are associated with diseases or complex traits...
2017: PloS One
https://www.readbyqxmd.com/read/28425186/association-studies-of-low-frequency-coding-variants-in-nonsyndromic-cleft-lip-with-or-without-cleft-palate
#3
Elizabeth J Leslie, Jenna C Carlson, John R Shaffer, Carmen J Buxó, Eduardo E Castilla, Kaare Christensen, Frederic W B Deleyiannis, Leigh L Field, Jacqueline T Hecht, Lina Moreno, Ieda M Orioli, Carmencita Padilla, Alexandre R Vieira, George L Wehby, Eleanor Feingold, Seth M Weinberg, Jeffrey C Murray, Mary L Marazita
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a group of common human birth defects with complex etiology. Although genome-wide association studies have successfully identified a number of risk loci, these loci only account for about 20% of the heritability of orofacial clefts. The "missing" heritability may be found in rare variants, copy number variants, or interactions. In this study, we investigated the role of low-frequency variants genotyped in 1995 cases and 1626 controls on the Illumina HumanCore + Exome chip...
April 19, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28419279/primates-lice-and-bacteria-speciation-and-genome-evolution-in-the-symbionts-of-hominid-lice
#4
Bret M Boyd, Julie M Allen, Nam-Phuong Nguyen, Pranjal Vachaspati, Zach Quicksall, Tandy Warnow, Lawrence Mugisha, Kevin P Johnson, David L Reed
Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood-sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins. Here we sequenced the genomes of symbiotic and heritable bacterial of human, chimpanzee, gorilla, and monkey lice and used phylogenomics to investigate their evolutionary relationships. We find that these symbionts have a phylogenetic history reflecting the louse phylogeny, a finding contrary to previous reports of symbiont replacement...
April 14, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28411841/the-molecular-revolution-in-cutaneous-biology-the-era-of-genome-wide-association-studies-and-statistical-big%C3%A2-data-and-computational-topics
#5
REVIEW
Hima Anbunathan, Anne M Bowcock
The investigation of biological systems involving all organs of the body including the skin is in era of big data. This requires heavy-duty computational tools, and novel statistical methods. Microarrays have allowed the interrogation of thousands of common genetic markers in thousands of individuals from the same population (termed genome wide association studies or GWAS) to reveal common variation associated with disease or phenotype. These markers are usually single nucleotide polymorphisms (SNPs) that are relatively common in the population...
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28404137/genetics-of-inflammatory-bowel-disease-beyond-nod2
#6
REVIEW
Maša Umićević Mirkov, Bram Verstockt, Isabelle Cleynen
The study of the genetic underpinnings of inflammatory bowel disease has made great progress since the identification of NOD2 as a major susceptibility gene. Novel genotyping and sequencing technologies have led to the discovery of 242 common susceptibility loci, 45 of which have been fine-mapped to statistically conclusive causal variants; 50 genes associated with very-early-onset inflammatory disease have been identified. The evolving genetic architecture of inflammatory bowel disease has deepened our understanding of its pathogenesis through identification of major disease associated pathways-knowledge that has the potential to indicate novel drug targets or markers for personalised medicine...
March 2017: Lancet. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28401901/missing-heritability-is-the-gap-closing-an-analysis-of-32-complex-traits-in-the-lifelines-cohort-study
#7
Ilja M Nolte, Peter J van der Most, Behrooz Z Alizadeh, Paul Iw de Bakker, H Marike Boezen, Marcel Bruinenberg, Lude Franke, Pim van der Harst, Gerjan Navis, Dirkje S Postma, Marianne G Rots, Ronald P Stolk, Morris A Swertz, Bruce Hr Wolffenbuttel, Cisca Wijmenga, Harold Snieder
Despite the recent explosive rise in number of genetic markers for complex disease traits identified in genome-wide association studies, there is still a large gap between the known heritability of these traits and the part explained by these markers. To gauge whether this 'heritability gap' is closing, we first identified genome-wide significant SNPs from the literature and performed replication analyses for 32 highly relevant traits from five broad disease areas in 13 436 subjects of the Lifelines Cohort...
April 12, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28398343/large-scale-interaction-effects-reveal-missing-heritability-in-schizophrenia-bipolar-disorder-and-posttraumatic-stress-disorder
#8
H J Woo, C Yu, K Kumar, J Reifman
Genetic susceptibility factors behind psychiatric disorders typically contribute small effects individually. A possible explanation for the missing heritability is that the effects of common variants are not only polygenic but also non-additive, appearing only when interactions within large groups are taken into account. Here, we tested this hypothesis for schizophrenia (SZ) and bipolar disorder (BP) disease risks, and identified genetic factors shared with posttraumatic stress disorder (PTSD). When considered independently, few single-nucleotide polymorphisms (SNPs) reached genome-wide significance...
April 11, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28361694/an-empirical-fuzzy-multifactor-dimensionality-reduction-method-for-detecting-gene-gene-interactions
#9
Sangseob Leem, Taesung Park
BACKGROUND: Detection of gene-gene interaction (GGI) is a key challenge towards solving the problem of missing heritability in genetics. The multifactor dimensionality reduction (MDR) method has been widely studied for detecting GGIs. MDR reduces the dimensionality of multi-factor by means of binary classification into high-risk (H) or low-risk (L) groups. Unfortunately, this simple binary classification does not reflect the uncertainty of H/L classification. Thus, we proposed Fuzzy MDR to overcome limitations of binary classification by introducing the degree of membership of two fuzzy sets H/L...
March 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28334077/a-powerful-and-efficient-two-stage-method-for-detecting-gene-to-gene-interactions-in-gwas
#10
Jakub Pecanka, Marianne A Jonker, Zoltan Bochdanovits, Aad W Van Der Vaart
For over a decade functional gene-to-gene interaction (epistasis) has been suspected to be a determinant in the "missing heritability" of complex traits. However, searching for epistasis on the genome-wide scale has been challenging due to the prohibitively large number of tests which result in a serious loss of statistical power as well as computational challenges. In this article, we propose a two-stage method applicable to existing case-control data sets, which aims to lessen both of these problems by pre-assessing whether a candidate pair of genetic loci is involved in epistasis before it is actually tested for interaction with respect to a complex phenotype...
February 6, 2017: Biostatistics
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
#11
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
#12
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...
May 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28222494/selecting-cases-and-controls-for-dna-sequencing-studies-using-family-histories-of-disease
#13
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
#14
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
#15
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 nucleolus organizer regions (NORs). Instead, GWAS implicated a trans-acting locus, as if rRNA gene 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...
April 3, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28187711/poppante-population-and-pedigree-association-testing-for-quantitative-data
#16
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
#17
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
#18
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
#19
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
#20
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
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