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Missing heritability

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https://www.readbyqxmd.com/read/28634715/regulatory-element-based-prediction-identifies-new-susceptibility-regulatory-variants-for-osteoporosis
#1
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...
June 20, 2017: Human Genetics
https://www.readbyqxmd.com/read/28628480/kernel-based-measure-of-variable-importance-for-genetic-association-studies
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/28561745/hiseeker-detecting-high-order-snp-interactions-based-on-pairwise-snp-combinations
#9
Jie Liu, Guoxian Yu, Yuan Jiang, Jun Wang
Detecting single nucleotide polymorphisms' (SNPs) interaction is one of the most popular approaches for explaining the missing heritability of common complex diseases in genome-wide association studies. Many methods have been proposed for SNP interaction detection, but most of them only focus on pairwise interactions and ignore high-order ones, which may also contribute to complex traits. Existing methods for high-order interaction detection can hardly handle genome-wide data and suffer from low detection power, due to the exponential growth of search space...
May 31, 2017: Genes
https://www.readbyqxmd.com/read/28550290/differential-methylation-is-associated-with-non-syndromic-cleft-lip-and-palate-and-contributes-to-penetrance-effects
#10
Lucas Alvizi, Xiayi Ke, Luciano Abreu Brito, Rimante Seselgyte, Gudrun E Moore, Philip Stanier, Maria Rita Passos-Bueno
Non-syndromic cleft lip and/or palate (NSCLP) is a common congenital malformation with a multifactorial model of inheritance. Although several at-risk alleles have been identified, they do not completely explain the high heritability. We postulate that epigenetic factors as DNA methylation might contribute to this missing heritability. Using a Methylome-wide association study in a Brazilian cohort (67 NSCLP, 59 controls), we found 578 methylation variable positions (MVPs) that were significantly associated with NSCLP...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28537275/a-rare-variant-test-for-high-dimensional-data
#11
Marika Kaakinen, Reedik Mägi, Krista Fischer, Jani Heikkinen, Marjo-Riitta Järvelin, Andrew P Morris, Inga Prokopenko
Genome-wide association studies have facilitated the discovery of thousands of loci for hundreds of phenotypes. However, the issue of missing heritability remains unsolved for most complex traits. Locus discovery could be enhanced with both improved power through multi-phenotype analysis (MPA) and use of a wider allele frequency range, including rare variants (RVs). MPA methods for single-variant association have been proposed, but given their low power for RVs, more efficient approaches are required. We propose multi-phenotype analysis of rare variants (MARV), a burden test-based method for RVs extended to the joint analysis of multiple phenotypes through a powerful reverse regression technique...
May 24, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28530468/genetic-susceptibility-contributing-to-periodontal-and-cardiovascular-disease
#12
G Aarabi, T Zeller, H Seedorf, D R Reissmann, G Heydecke, A S Schaefer, U Seedorf
Periodontal disease (PD) and coronary artery disease (CAD) are common diseases characterized by an overaggressive inflammatory response to diverse stimuli. Whereas PD leads to destruction of the tooth-supporting structures, CAD is a chronic inflammatory condition ultimately causing myocardial infarction via narrowing and occluding of blood vessels. Classical twin studies led to the conclusion that both complex diseases have a similar degree of heritability and that a significant fraction of the genetic factors accounting for this heritability is shared...
June 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28506960/familial-analysis-of-epistatic-and-sex-dependent-association-of-genes-of-the-renin-angiotensin-aldosterone-system-and-blood-pressure
#13
Katrina J Scurrah, Angela Lamantia, Justine A Ellis, Stephen B Harrap
BACKGROUND: Renin-angiotensin-aldosterone system genes have been inconsistently associated with blood pressure, possibly because of unrecognized influences of sex-dependent genetic effects or gene-gene interactions (epistasis). METHODS AND RESULTS: We tested association of systolic blood pressure with single-nucleotide polymorphisms (SNPs) at renin (REN), angiotensinogen (AGT), angiotensin-converting enzyme (ACE), angiotensin II type 1 receptor (AGTR1), and aldosterone synthase (CYP11B2), including sex-SNP or SNP-SNP interactions...
June 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28505210/whole-exome-sequencing-of-a-consanguineous-family-identifies-the-possible-modifying-effect-of-a-globally-rare-ak5-allelic-variant-in-celiac-disease-development-among-saudi-patients
#14
Jumana Yousuf Al-Aama, Noor Ahmad Shaik, Babajan Banaganapalli, Mohammed A Salama, Omran Rashidi, Ahmed N Sahly, Mohammed O Mohsen, Harbi A Shawoosh, Hebah Ahmad Shalabi, Mohammad Al Edreesi, Sameer E Alharthi, Jun Wang, Ramu Elango, Omar I Saadah
Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD's heritability. In order to discover the missing heritability due to rare variants, we have exome sequenced a consanguineous Saudi family presenting CD in an autosomal recessive (AR) pattern. We have identified a rare homozygous insertion c.1683_1684insATT, in the conserved coding region of AK5 gene that showed classical AR model segregation in this family...
2017: PloS One
https://www.readbyqxmd.com/read/28494787/missing-heritability-and-where-to-find-it
#15
Santhosh Girirajan
A report on the 11th Genomics of Rare Disease meeting held at the Wellcome Genome Campus, Hinxton, Cambridge, UK, 5-7 April, 2017.
May 11, 2017: Genome Biology
https://www.readbyqxmd.com/read/28464315/selection-of-core-animals-in-the-algorithm-for-proven-and-young-using-a-simulation-model
#16
H L Bradford, I Pocrnić, B O Fragomeni, D A L Lourenco, I Misztal
The Algorithm for Proven and Young (APY) enables the implementation of single-step genomic BLUP (ssGBLUP) in large, genotyped populations by separating genotyped animals into core and non-core subsets and creating a computationally efficient inverse for the genomic relationship matrix (G). As APY became the choice for large-scale genomic evaluations in BLUP-based methods, a common question is how to choose the animals in the core subset. We compared several core definitions to answer this question. Simulations comprised a moderately heritable trait for 95,010 animals and 50,000 genotypes for animals across five generations...
May 2, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28442163/the-search-for-the-missing-heritability-of-prostate-cancer
#17
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
#18
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
#19
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...
June 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
#20
Bret M Boyd, Julie M Allen, Nam-Phuong Nguyen, Pranjal Vachaspati, Zachary S 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...
July 1, 2017: Molecular Biology and Evolution
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