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https://www.readbyqxmd.com/read/28651334/tsgsis-a-high-dimensional-grouped-variable-selection-approach-for-detection-of-whole-genome-snp-snp-interactions
#1
Yao-Hwei Fang, Jie-Huei Wang, Chao A Hsiung
Motivation: Identification of single nucleotide polymorphism (SNP) interactions is an important and challenging topic in genome-wide association studies (GWAS). Many approaches have been applied to detecting whole-genome interactions. However, these approaches to interaction analysis tend to miss causal interaction effects when the individual marginal effects are uncorrelated to trait, while their interaction effects are highly associated with the trait. Results: A grouped variable selection technique, called two-stage grouped sure independence screening (TS-GSIS), is developed to study interactions that may not have marginal effects...
June 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28650998/functional-annotation-of-alzheimer-s-disease-associated-loci-revealed-by-gwass
#2
Zengpeng Han, Han Huang, Yue Gao, Qingyang Huang
Genome-wide association studies (GWASs) discovered a number of SNPs and genes associated with Alzheimer's disease (AD). However, how these SNPs and genes influence the liability to AD is not fully understood. We deployed computational approaches to explore the function and action mechanisms of AD -related SNPs and genes identified by GWASs, including the effects of 195 GWAS lead SNPs and 338 proxy SNPs on miRNAs binding and protein phosphorylation, their RegulomeDB and 3DSNP scores, and gene ontology, pathway enrichment and protein-protein interaction network of 126 AD-associated genes...
2017: PloS One
https://www.readbyqxmd.com/read/28650150/genome-wide-association-mapping-of-seed-coat-color-in-brassica-napus
#3
Jia Wang, Xiaohua Xian, Xinfu Xu, Cunmin Qu, Kun Lu, Jiana Li, Liezhao Liu
Seed coat color is an extremely important breeding characteristic of Brassica napus. To elucidate the factors affecting the genetic architecture of seed coat color, a genome-wide association study (GWAS) of seed coat color was conducted with a diversity panel comprising 520 B. napus cultivars and inbred lines. In total, 22 single-nucleotide polymorphisms (SNPs) distributed on 7 chromosomes were found to be associated with seed coat color. The most significant SNPs were found in 2014 near Bn-scaff_15763_1-p233999, only 43...
June 26, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28649937/the-genetics-of-platelet-count-and-volume-in-humans
#4
John D Eicher, Guillaume Lettre, Andrew D Johnson
The last decade has witnessed an explosion in the depth, variety, and amount of human genetic data that can be generated. This revolution in technical and analytical capacities has enabled the genetic investigation of human traits and disease in thousands to now millions of participants. Investigators have taken advantage of these advancements to gain insight into platelet biology and the platelet's role in human disease. To do so, large human genetics studies have examined the association of genetic variation with two quantitative traits measured in many population and patient based cohorts: platelet count (PLT) and mean platelet volume (MPV)...
June 26, 2017: Platelets
https://www.readbyqxmd.com/read/28648959/a-study-of-gwas-supported-variants-of-rs9943582-in-a-chinese-han-population-with-ischemic-stroke-no-associations-with-disease-onset-and-clinical-outcomes
#5
Hao Zhang, Lingli Sun, Huaiming Wang, Huan Cai, Guozhong Niu, Yongjie Bai, Yun Zhang, Dong Yang, Mengmeng Gu, Pengfei Xu, Xinying Fan, Xinfeng Liu, Gelin Xu
BACKGROUND: The variant rs9943582 of APLNR (apelin receptor) was identified by a large-scale study to be associated with an increased risk of ischemic stroke in a Japanese population. We conducted this study to investigate the association between the variant and age of onset and clinical outcomes of ischemic stroke in a Chinese population. METHODS: Improved multiple ligase detection reaction was used to genotype the variant. We compared the mean age at ischemic stroke onset with one-way ANOVA...
June 22, 2017: Journal of Stroke and Cerebrovascular Diseases: the Official Journal of National Stroke Association
https://www.readbyqxmd.com/read/28648753/association-of-increased-genotypes-risk-for-bipolar-disorder-with-brain-white-matter-integrity-investigated-with-tract-based-spatial-statistics
#6
REVIEW
L Squarcina, J Houenou, A C Altamura, J Soares, P Brambilla
BACKGROUND: Diffusion tensor imaging (DTI) studies, which allow the in-vivo investigation of brain tissue integrity, have shown that bipolar disorder (BD) patients present signs of white matter dysconnectivity. In parallel, genome-wide association studies (GWAS) identified several risk genetic variants for BD. I METHODS: In this mini-review, we summarized DTI studies coupling tract-based spatial statistics (TBSS), a reliable technique exploring white matter axon bundles, and genetics in BD...
June 15, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28645536/imaging-genetics-of-schizophrenia-in-the-post-gwas-era
#7
REVIEW
Ayla Arslan
Imaging genetics is a research methodology studying the effect of genetic variation on brain structure, function, behavior, and risk for psychopathology. Since the early 2000s, imaging genetics has been increasingly used in the research of schizophrenia (SZ). SZ is a severe mental disorder with no precise knowledge of its underlying neurobiology, however, new genetic and neurobiological data generate a climate for new avenues. The accumulating data of genome wide association studies (GWAS) continuously decode SZ risk genes...
June 20, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28644415/genome-wide-association-study-of-dietary-pattern-scores
#8
Frédéric Guénard, Annie Bouchard-Mercier, Iwona Rudkowska, Simone Lemieux, Patrick Couture, Marie-Claude Vohl
Dietary patterns, representing global food supplies rather than specific nutrients or food intakes, have been associated with cardiovascular disease (CVD) incidence and mortality. The contribution of genetic factors in the determination of food intakes, preferences and dietary patterns has been previously established. The current study aimed to identify novel genetic factors associated with reported dietary pattern scores. Reported dietary patterns scores were derived from reported dietary intakes for the preceding month and were obtained through a food frequency questionnaire and genome-wide association study (GWAS) conducted in a study sample of 141 individuals...
June 23, 2017: Nutrients
https://www.readbyqxmd.com/read/28642772/assessment-of-five-chilling-tolerance-traits-and-gwas-mapping-in-rice-using-the-usda-mini-core-collection
#9
Michael R Schläppi, Aaron K Jackson, Georgia C Eizenga, Aiju Wang, Chengcai Chu, Yao Shi, Naoki Shimoyama, Debbie L Boykin
Rice (Oryza sativa L.) is often exposed to cool temperatures during spring planting in temperate climates. A better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. To dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. Based on these assays, five chilling tolerance indices were calculated and assessed using 202 O...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642624/whole-exome-sequencing-to-identify-genetic-variants-associated-with-raised-atherosclerotic-lesions-in-young-persons
#10
James E Hixson, Goo Jun, Lawrence C Shimmin, Yizhi Wang, Guoqiang Yu, Chunhong Mao, Andrew S Warren, Timothy D Howard, Richard S Vander Heide, Jennifer Van Eyk, Yue Wang, David M Herrington
We investigated the influence of genetic variants on atherosclerosis using whole exome sequencing in cases and controls from the autopsy study "Pathobiological Determinants of Atherosclerosis in Youth (PDAY)". We identified a PDAY case group with the highest total amounts of raised lesions (n = 359) for comparisons with a control group with no detectable raised lesions (n = 626). In addition to the standard exome capture, we included genome-wide proximal promoter regions that contain sequences that regulate gene expression...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642574/replication-of-gout-urate-concentrations-gwas-susceptibility-loci-associated-with-gout-in-a-han-chinese-population
#11
Zhiqiang Li, Zhaowei Zhou, Xu Hou, Dajiang Lu, Xuan Yuan, Jie Lu, Can Wang, Lin Han, Lingling Cui, Zhen Liu, Jianhua Chen, Xiaoyu Cheng, Keke Zhang, Jue Ji, Zhaotong Jia, Lidan Ma, Ying Xin, Tian Liu, Qing Yu, Wei Ren, Xuefeng Wang, Xinde Li, Qing-Sheng Mi, Yongyong Shi, Changgui Li
Gout is a chronic disease resulting from elevated serum urate (SU). Previous genome-wide association studies (GWAS) have identified dozens of susceptibility loci for SU/gout, but few have been conducted for Chinese descent. Here, we try to extensively investigate whether these loci contribute to gout risk in Han Chinese. A total of 2255 variants in linkage disequilibrium (LD) with GWAS identified SU/gout associated variants were analyzed in a Han Chinese cohort of 1255 gout patients and 1848 controls. Cumulative genetic risk score analysis was performed to assess the cumulative effect of multiple "risk" variants on gout incidence...
June 22, 2017: Scientific Reports
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/28641744/polygenic-risk-score-and-heritability-estimates-reveals-a-genetic-relationship-between-asd-and-ocd
#13
W Guo, J F Samuels, Y Wang, H Cao, M Ritter, P S Nestadt, J Krasnow, B D Greenberg, A J Fyer, J T McCracken, D A Geller, D L Murphy, J A Knowles, M A Grados, M A Riddle, S A Rasmussen, N C McLaughlin, E L Nurmi, K D Askland, B A Cullen, J Piacentini, D L Pauls, O J Bienvenu, S E Stewart, F S Goes, B Maher, A E Pulver, D Valle, M Mattheisen, J Qian, G Nestadt, Y Y Shugart
Obsessive-compulsive disorder (OCD) and Autism spectrum disorder (ASD) are both highly heritable neurodevelopmental disorders that conceivably share genetic risk factors. However, the underlying genetic determinants remain largely unknown. In this work, the authors describe a combined genome-wide association study (GWAS) of ASD and OCD. The OCD dataset includes 2998 individuals in nuclear families. The ASD dataset includes 6898 individuals in case-parents trios. GWAS summary statistics were examined for potential enrichment of functional variants associated with gene expression levels in brain regions...
July 2017: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28641133/abc-transporters-in-megakaryopoiesis-and-platelet-activity
#14
REVIEW
Wei Wang, Lorena Buitrago, Ying Wang
ATP-binding cassette (ABC) is a family of transporters that facilitates the translocation of substrates across cell membrane using its ATPase subunit. These transporters have key roles in multidrug resistance, lipid homeostasis, antigen processing, immunity, cell proliferation and hematopoiesis. Some ABC transporters are selectively expressed on megakaryocyte progenitor, megakaryocyte and its cellular fragment platelet. However, the role of ABC transporters in hemostasis and thrombosis were not well explored until recently...
June 14, 2017: Thrombosis Research
https://www.readbyqxmd.com/read/28641109/rare-copy-number-variants-in-nrxn1-and-cntn6-increase-risk-for-tourette-syndrome
#15
Alden Y Huang, Dongmei Yu, Lea K Davis, Jae Hoon Sul, Fotis Tsetsos, Vasily Ramensky, Ivette Zelaya, Eliana Marisa Ramos, Lisa Osiecki, Jason A Chen, Lauren M McGrath, Cornelia Illmann, Paul Sandor, Cathy L Barr, Marco Grados, Harvey S Singer, Markus M Nöthen, Johannes Hebebrand, Robert A King, Yves Dion, Guy Rouleau, Cathy L Budman, Christel Depienne, Yulia Worbe, Andreas Hartmann, Kirsten R Müller-Vahl, Manfred Stuhrmann, Harald Aschauer, Mara Stamenkovic, Monika Schloegelhofer, Anastasios Konstantinidis, Gholson J Lyon, William M McMahon, Csaba Barta, Zsanett Tarnok, Peter Nagy, James R Batterson, Renata Rizzo, Danielle C Cath, Tomasz Wolanczyk, Cheston Berlin, Irene A Malaty, Michael S Okun, Douglas W Woods, Elliott Rees, Carlos N Pato, Michele T Pato, James A Knowles, Danielle Posthuma, David L Pauls, Nancy J Cox, Benjamin M Neale, Nelson B Freimer, Peristera Paschou, Carol A Mathews, Jeremiah M Scharf, Giovanni Coppola
Tourette syndrome (TS) is a model neuropsychiatric disorder thought to arise from abnormal development and/or maintenance of cortico-striato-thalamo-cortical circuits. TS is highly heritable, but its underlying genetic causes are still elusive, and no genome-wide significant loci have been discovered to date. We analyzed a European ancestry sample of 2,434 TS cases and 4,093 ancestry-matched controls for rare (< 1% frequency) copy-number variants (CNVs) using SNP microarray data. We observed an enrichment of global CNV burden that was prominent for large (> 1 Mb), singleton events (OR = 2...
June 21, 2017: Neuron
https://www.readbyqxmd.com/read/28640246/gwas-signals-revisited-using-human-knockouts
#16
Sateesh Maddirevula, Fatema AlZahrani, Shams Anazi, Mariam Almureikhi, Tawfeg Ben-Omran, Ghada M H Abdel-Salam, Mais Hashem, Niema Ibrahim, Firdous M Abdulwahab, Neama Meriki, Fahad A Bashiri, Meow-Keong Thong, Premala Muthukumarasamy, Rifhan Azwani Mazlan, Ranad Shaheen, Fowzan S Alkuraya
PurposeGenome-wide association studies (GWAS) have been instrumental to our understanding of the genetic risk determinants of complex traits. A common challenge in GWAS is the interpretation of signals, which are usually attributed to the genes closest to the polymorphic markers that display the strongest statistical association. Naturally occurring complete loss of function (knockout) of these genes in humans can inform GWAS interpretation by unmasking their deficiency state in a clinical context.MethodsWe exploited the unique population structure of Saudi Arabia to identify novel knockout events in genes previously highlighted in GWAS using combined autozygome/exome analysis...
June 22, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28639238/multiple-sclerosis-in-latin-americans-genetic-aspects
#17
REVIEW
Victor M Rivera
Latin Americans (LA) are a heterogeneous, multiethnic group of individuals who inhabit the continental countries in Latin America (LATAM), Caribbean islands and constitute the largest ethnic minority in the USA. Commonly used terminology and ethno racial classifications to define these groups may not be accurate. Risk for multiple sclerosis (MS) among LA is generally low to medium but frequencies are increasing in the American hemisphere. Genome-Wide Association Studies (GWAS) in LA show diverse variants and genetic proportions among Mestizos, the most representative ethnic population, who themselves are the product of centuries of interracial mixing between Native Americans (or Amerindians), White Caucasian Europeans, and Black Africans...
August 2017: Current Neurology and Neuroscience Reports
https://www.readbyqxmd.com/read/28639078/a-genome-wide-expression-association-analysis-identifies-genes-and-pathways-associated-with-amyotrophic-lateral-sclerosis
#18
Yanan Du, Yan Wen, Xiong Guo, Jingcan Hao, Wenyu Wang, Awen He, Qianrui Fan, Ping Li, Li Liu, Xiao Liang, Feng Zhang
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with strong genetic components. To identity novel risk variants for ALS, utilizing the latest genome-wide association studies (GWAS) and eQTL study data, we conducted a genome-wide expression association analysis by summary data-based Mendelian randomization (SMR) method. Summary data were derived from a large-scale GWAS of ALS, involving 12577 cases and 23475 controls. The eQTL annotation dataset included 923,021 cis-eQTL for 14,329 genes and 4732 trans-eQTL for 2612 genes...
June 21, 2017: Cellular and Molecular Neurobiology
https://www.readbyqxmd.com/read/28637796/quantifying-the-genetic-correlation-between-multiple-cancer-types
#19
Sara Lindström, Hilary Finucane, Brendan Bulik-Sullivan, Fredrick R Schumacher, Christopher I Amos, Rayjean J Hung, Kristin Rand, Stephen B Gruber, David Conti, Jennifer B Permuth, Hui-Yi Lin, Ellen L Goode, Thomas A Sellers, Laufey T Amundadottir, Rachael Stolzenberg-Solomon, Alison Klein, Gloria Petersen, Harvey Risch, Brian Wolpin, Li Hsu, Jeroen R Huyghe, Jenny Chang Claude, Andrew Chan, Sonja Berndt, Rosalind A Eeles, Douglas Easton, Christopher A Haiman, David J Hunter, Benjamin Neale, Alkes Price, Peter Kraft
Many cancers share specific genetic risk factors including both rare high-penetrance mutations and common single nucleotide polymorphisms (SNPs) identified through genome-wide association studies (GWAS). However, little is known about the overall shared heritability across cancers. Quantifying the extent to which two distinct cancers share genetic origin will give insights to shared biological mechanisms underlying cancer and inform design for future genetic association studies. In this study, we estimated the pair-wise genetic correlation between six cancer types (breast, colorectal, lung, ovarian, pancreatic and prostate) using cancer-specific GWAS summary statistics data based on 66,958 case and 70,665 control subjects of European ancestry...
June 21, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28637795/genome-wide-association-studies-of-cancer-in-diverse-populations
#20
Sungshim L Park, Iona Cheng, Christopher A Haiman
Genome-wide association studies (GWAS) of cancer have identified more than 700 risk loci, of which ~80% of were first discovered in European ancestry populations, ~15% in East Asians, 3% in multiethnic scans, and less than 1% in African and Latin American populations. These percentages closely mirror the distribution of samples included in the discovery phase of cancer GWAS to date (84% European, 11% East Asian, 4% African and 1% Latin American ancestry). GWAS in non-European populations have provided insight into ancestry-specific variation in cancer and have pointed to regions of susceptibility that are of particular importance in certain populations...
June 21, 2017: Cancer Epidemiology, Biomarkers & Prevention
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