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Missing heritability

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https://www.readbyqxmd.com/read/27903611/the-genomic-architecture-of-interactions-between-natural-genetic-polymorphisms-and-environments-in-yeast-growth
#1
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)...
November 30, 2016: Genetics
https://www.readbyqxmd.com/read/27896934/increased-identification-of-novel-variants-in-type-2-diabetes-birth-weight-and-their-pleiotropic-loci
#2
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
https://www.readbyqxmd.com/read/27888432/candidate-predisposing-germline-copy-number-variants-in-early-onset-colorectal-cancer-patients
#3
A J Brea-Fernandez, C Fernandez-Rozadilla, M Alvarez-Barona, D Azuara, M M Ginesta, J Clofent, L de Castro, D Gonzalez, M Andreu, X Bessa, X Llor, R Xicola, R Jover, A Castells, S Castellvi-Bel, G Capella, A Carracedo, C Ruiz-Ponte
PURPOSE: A great proportion of the heritability of colorectal cancer (CRC) still remains unexplained, and rare variants, as well as copy number changes, have been proposed as potential candidates to explain the so-called 'missing heritability'. We aimed to identify rare high-to-moderately penetrant copy number variants (CNVs) in patients suspected of having hereditary CRC due to an early onset. METHODS/PATIENTS: We have selected for genome-wide copy number analysis, 27 MMR-proficient early onset CRC patients (<50 years) without identifiable germline mutations in Mendelian genes related to this phenotype...
November 25, 2016: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/27883230/missing-heritability-illegitimate-quantitative-comparison-of-holistic-and-reductionist-data-response-to-doi-10-1002-bies-201600084
#4
Eugene Sverdlov
No abstract text is available yet for this article.
December 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/27859906/human-recq-helicase-pathogenic-variants-population-variation-and-missing-diseases
#5
Wenqing Fu, Alessio Ligabue, Kai J Rogers, Joshua M Akey, Raymond J Monnat
Heritable loss of function mutations in the human RECQ helicase genes BLM, WRN and RECQL4 cause Bloom, Werner and Rothmund-Thomson syndromes, cancer predispositions with additional developmental or progeroid features. In order to better understand RECQ pathogenic and population variation, we systematically analyzed genetic variation in all five human RECQ helicase genes. A total of 3,741 unique basepair-level variants were identified, across 17,605 potential mutation sites. Direct counting of BLM, RECQL4 and WRN pathogenic variants was used to determine aggregate and disease-specific carrier frequencies...
November 17, 2016: Human Mutation
https://www.readbyqxmd.com/read/27852354/exploring-the-genetic-etiology-of-trust-in-adolescents-combined-twin-and-dna-analyses
#6
Robyn E Wootton, Oliver S P Davis, Abigail L Mottershaw, R Adele H Wang, Claire M A Haworth
Behavioral traits generally show moderate to strong genetic influence, with heritability estimates of around 50%. Some recent research has suggested that trust may be an exception because it is more strongly influenced by social interactions. In a sample of over 7,000 adolescent twins from the United Kingdom's Twins Early Development Study, we found broad sense heritability estimates of 57% for generalized trust and 51% for trust in friends. Genomic-relatedness-matrix restricted maximum likelihood (GREML) estimates in the same sample indicate that 21% of the narrow sense genetic variance can be explained by common single nucleotide polymorphisms for generalized trust and 43% for trust in friends...
December 2016: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/27848076/identifying-gene-gene-interactions-that-are-highly-associated-with-four-quantitative-lipid-traits-across-multiple-cohorts
#7
Rishika De, Shefali S Verma, Emily Holzinger, Molly Hall, Amber Burt, David S Carrell, David R Crosslin, Gail P Jarvik, Helena Kuivaniemi, Iftikhar J Kullo, Leslie A Lange, Matthew B Lanktree, Eric B Larson, Kari E North, Alex P Reiner, Vinicius Tragante, Gerard Tromp, James G Wilson, Folkert W Asselbergs, Fotios Drenos, Jason H Moore, Marylyn D Ritchie, Brendan Keating, Diane Gilbert-Diamond
Genetic loci explain only 25-30 % of the heritability observed in plasma lipid traits. Epistasis, or gene-gene interactions may contribute to a portion of this missing heritability. Using the genetic data from five NHLBI cohorts of 24,837 individuals, we combined the use of the quantitative multifactor dimensionality reduction (QMDR) algorithm with two SNP-filtering methods to exhaustively search for SNP-SNP interactions that are associated with HDL cholesterol (HDL-C), LDL cholesterol (LDL-C), total cholesterol (TC) and triglycerides (TG)...
November 15, 2016: Human Genetics
https://www.readbyqxmd.com/read/27830690/-detection-of-novel-genetic-markers-of-susceptibility-to-preeclampsia-based-on-an-analysis-of-the-regulatory-genes-in-the-placental-tissue
#8
V N Serebrova, E A Trifonova, T V Gabidulina, I Yu Bukharina, T A Agarkova, I D Evtushenko, N R Maksimova, V A Stepanov
Regulatory single nucleotide polymorphisms (rSNPs) are the least-studied group of SNP; however, they play an essential role in the development of human pathology by altering the level of candidate genes expression. In this work, we analyzed 29 rSNPs in 17 new candidate genes associated with preeclampsia (PE) according to the analysis of the transcriptome in placental tissue. Three ethnic groups have been studied (yakut, russian, and buryat). We have detected significant associations of PE with eight rSNPs in six differentially expressed genes, i...
September 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/27808177/a-short-insertion-mutation-disrupts-genesis-of-mir-16-and-causes-increased-body-weight-in-domesticated-chicken
#9
Xinzheng Jia, Huiran Lin, Qinghua Nie, Xiquan Zhang, Susan J Lamont
Body weight is one of the most important quantitative traits with high heritability in chicken. We previously mapped a quantitative trait locus (QTL) for body weight by genome-wide association study (GWAS) in an F2 chicken resource population. To identify the causal mutations linked to this QTL, expression profiles were determined on livers of high-weight and low-weight chicken lines by microarray. Combining the expression pattern with SNP effects by GWAS, miR-16 was identified as the most likely potential candidate with a 3...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27799157/prevalence-and-penetrance-of-major-genes-and-polygenes-for-colorectal-cancer
#10
Aung Ko Win, Mark A Jenkins, James G Dowty, Antonis C Antoniou, Andrew Lee, Graham G Giles, Daniel D Buchanan, Mark Clendenning, Christophe Rosty, Dennis J Ahnen, Stephen N Thibodeau, Graham Casey, Steven Gallinger, Loic Le Marchand, Robert W Haile, John D Potter, Yingye Zheng, Noralane M Lindor, Polly A Newcomb, John L Hopper, Robert J MacInnis
BACKGROUND: While high-risk mutations in identified major susceptibility genes (DNA mismatch repair genes and MUTYH) account for some familial aggregation of colorectal cancer, their population prevalence and the causes of the remaining familial aggregation are not known. METHODS: We studied the families of 5,744 colorectal cancer cases (probands) recruited from population cancer registries in the USA, Canada and Australia and screened probands for mutations in mismatch repair genes and MUTYH...
October 31, 2016: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/27789554/lnc-ing-notch1-to-idiopathic-calcific-aortic-valve-disease
#11
W David Merryman, Cynthia R Clark
Calcific aortic valve disease (CAVD) is an age-related disorder that causes significant cardiovascular morbidity and mortality, and is directly responsible for ~15,000 patient deaths per year in the USA. Currently, the molecular mechanism by which CAVD initiates is unknown, making discovery of a non-surgical strategy challenging (reviewed in (1)). Garg et al. made a seminal discovery in 2005 when they showed NOTCH1 mutations led to heritable CAVD.(2) Since then, the heart valve research community has sought a causal mechanism that could connect NOTCH1 dysfunction to idiopathic CAVD...
October 27, 2016: Circulation
https://www.readbyqxmd.com/read/27777418/the-phf21b-gene-is-associated-with-major-depression-and-modulates-the-stress-response
#12
M-L Wong, M Arcos-Burgos, S Liu, J I Vélez, C Yu, B T Baune, M C Jawahar, V Arolt, U Dannlowski, A Chuah, G A Huttley, R Fogarty, M D Lewis, S R Bornstein, J Licinio
Major depressive disorder (MDD) affects around 350 million people worldwide; however, the underlying genetic basis remains largely unknown. In this study, we took into account that MDD is a gene-environment disorder, in which stress is a critical component, and used whole-genome screening of functional variants to investigate the 'missing heritability' in MDD. Genome-wide association studies (GWAS) using single- and multi-locus linear mixed-effect models were performed in a Los Angeles Mexican-American cohort (196 controls, 203 MDD) and in a replication European-ancestry cohort (499 controls, 473 MDD)...
October 25, 2016: Molecular Psychiatry
https://www.readbyqxmd.com/read/27771416/candidate-gene-analysis-of-the-fibrinogen-phenotype-reveals-the-importance-of-polygenic-co-regulation
#13
H Toinét Cronjé, Cornelie Nienaber-Rousseau, Lizelle Zandberg, Tinashe Chikowore, Zelda de Lange, Tertia van Zyl, Marlien Pieters
Fibrinogen and its functional aspects have been linked to cardiovascular disease. There is vast discrepancy between the heritability of fibrinogen concentrations observed in twin studies and the heritability uncovered by genome wide association studies. We postulate that some of the missing heritability might be explained by the pleiotropic and polygenic co-regulation of fibrinogen through multiple targeted genes, apart from the fibrinogen genes themselves. To this end we investigated single nucleotide polymorphisms (SNPs) in genes coding for phenotypes associated with total and γ' fibrinogen concentrations and clot properties...
October 19, 2016: Matrix Biology: Journal of the International Society for Matrix Biology
https://www.readbyqxmd.com/read/27766458/evaluating-mendelian-nephrotic-syndrome-genes-for-evidence-for-risk-alleles-or-oligogenicity-that-explain-heritability
#14
Brendan D Crawford, Christopher E Gillies, Catherine C Robertson, Matthias Kretzler, Edgar Otto, Virginia Vega-Wagner, Matthew G Sampson
BACKGROUND: More than 30 genes can harbor rare exonic variants sufficient to cause nephrotic syndrome (NS), and the number of genes implicated in monogenic NS continues to grow. However, outside the first year of life, the majority of affected patients, particularly in ancestrally mixed populations, do not have a known monogenic form of NS. Even in those children classified with a monogenic form of NS, there is phenotypic heterogeneity. Thus, we have only discovered a fraction of the heritability of NS-the underlying genetic factors contributing to phenotypic variation...
October 20, 2016: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
https://www.readbyqxmd.com/read/27765491/a-novel-fuzzy-set-based-multifactor-dimensionality-reduction-method-for-detecting-gene-gene-interaction
#15
Hye-Young Jung, Sangseob Leem, Sungyoung Lee, Taesung Park
BACKGROUND: Gene-gene interaction (GGI) is one of the most popular approaches for finding the missing heritability of common complex traits in genetic association studies. The multifactor dimensionality reduction (MDR) method has been widely studied for detecting GGIs. In order to identify the best interaction model associated with disease susceptibility, MDR compares all possible genotype combinations in terms of their predictability of disease status from a simple binary high(H) and low(L) risk classification...
September 29, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27759029/a-cross-ethnic-survey-of-cfb-and-slc44a4-indian-ulcerative-colitis-gwas-hits-underscores-their-potential-role-in-disease-susceptibility
#16
Aditi Gupta, Garima Juyal, Ajit Sood, Vandana Midha, Keiko Yamazaki, Arnau Vich Vila, Motohiro Esaki, Toshiyuki Matsui, Atsushi Takahashi, Michiaki Kubo, Rinse K Weersma, B K Thelma
The first ever genome-wide association study (GWAS) of ulcerative colitis in genetically distinct north Indian population identified two novel genes namely CFB and SLC44A4. Considering their biological relevance, we investigated allelic/genetic heterogeneity in these genes among ulcerative colitis cohorts of north Indian, Japanese and Dutch origin using high-density ImmunoChip case-control genotype data. Comparative linkage disequilibrium profiling and test of association were performed. Of the 28 CFB SNPs, similar strength of association was observed for rs4151657 (novel ulcerative colitis GWAS SNP) in north Indians (P=1...
October 19, 2016: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/27754287/br-07-2-the-linking-in-the-human-observational-and-clinical-study
#17
Peter Nilsson
A number of chronic disease conditions tend to cluster in families with an increased risk in first-degree relatives, but also an increased risk in second-degree relatives. This fact is most often referred to as the heritability (heredity) of these diseases and explained by the influence of genetic factors, or shared environment, even if the more specific details or mechanism leading to disease are not known. New methods have to be explored in screening studies and register linkage studies to define and measure consequences of a positive family history of disease...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27753954/os-08-04-epistatic-and-sex-dependent-association-analyses-of-genes-of-the-renin-angiotensin-aldosterone-system-and-blood-pressure-in-families
#18
Stephen Harrap, Katrina Scurrah, Angela Lamantia, Justine Ellis
OBJECTIVE: Genes encoding key elements of the renin-angiotensin-aldosterone system (RAAS) cascade have been previously but inconsistently associated with blood pressure. Sex-dependency might be important here and functional genetic polymorphisms might exhibit epistatic effects. DESIGN AND METHOD: We assessed variation in the genes encoding renin (REN), angiotensinogen (AGT), angiotensin converting enzyme (ACE), angiotensin II type 1 receptor (AGTR1) and aldosterone synthase (CYP11B2)...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27716388/the-genetics-of-breast-cancer-risk-in-the-post-genome-era-thoughts-on-study-design-to-move-past-brca-and-towards-clinical-relevance
#19
Andrew D Skol, Mark M Sasaki, Kenan Onel
More than 12 % of women will be diagnosed with breast cancer in their lifetime. Although there have been tremendous advances in elucidating genetic risk factors underlying both familial and sporadic breast cancer, much of the genetic contribution to breast cancer etiology remains unknown. The discovery of BRCA1 and BRCA2 over 20 years ago remains the seminal event in the field and has paved the way for the discovery of other high-penetrance susceptibility genes by linkage analysis. The advent of genome-wide association studies made possible the next wave of discoveries, in which over 80 low-penetrance and moderate-penetrance variants were identified...
October 3, 2016: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/27687928/bovine-spastic-paresis-a-review-of-the-genetic-background-and-perspectives-for-the-future
#20
REVIEW
Victoria Goeckmann, Sophie Rothammer, Ivica Medugorac
Bovine spastic paresis (BSP) is a sporadic, progressive neuromuscular disease that is thought to affect all breeds of cattle. The disease manifests as a unilateral or bilateral hyperextension of the hind limb due to increased muscle tone or permanent spasm of mainly the gastrocnemius and/or the quadriceps muscle. Clinical signs only appear in rising, standing and moving animals, which is an important diagnostic feature. Although several medical treatments have been described, surgical procedures such as neurectomy or tenectomy are generally indicated...
October 2016: Veterinary Journal
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