scholarly journals Genetic Analysis of Deep Phenotyping Projects in Common Disorders

2017 ◽  
Author(s):  
Elliot S. Gershon ◽  
Godfrey Pearlson ◽  
Matcheri S. Keshavan ◽  
Carol Tamminga ◽  
Brett Clementz ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Multiple Testing ◽  
Genetic Architecture ◽  
Psychotic Disorders ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Large Numbers ◽  
Genome Wide ◽  
Phenotype Imputation ◽  
Deep Phenotyping

AbstractSeveral studies of complex psychotic disorders with large numbers of neurobiological phenotypes are currently under way, in living patients and controls, and on assemblies of brain specimens. Genetic analyses of such data typically present challenges, because of the choice of underlying hypotheses on genetic architecture of the studied disorders and phenotypes, large numbers of phenotypes, the appropriate multiple testing corrections, limited numbers of subjects, imputations required on missing phenotypes and genotypes, and the cross-disciplinary nature of the phenotype measures. Advances in genotype and phenotype imputation, and in genome-wide association (GWAS) methods, are useful in dealing with these challenges. As compared with the more traditional single-trait analyses, deep phenotyping with simultaneous genome-wide analyses serves as a discovery tool for previously unsuspected relationships of phenotypic traits with each other, and with specific molecular involvements.

scholarly journals A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shenping Zhou ◽  
Rongrong Ding ◽  
Fanming Meng ◽  
Xingwang Wang ◽  
Zhanwei Zhuang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth And Development ◽  
Genetic Architecture ◽  
Association Studies ◽  
Meta Analysis ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Daily Gain

Abstract Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

scholarly journals Identification of Bacterial Blight Resistance Loci in Rice (Oryza sativa L.) against Diverse Xoo Thai Strains by Genome-Wide Association Study

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 518
Author(s):  
Siriporn Korinsak ◽  
Clive T. Darwell ◽  
Samart Wanchana ◽  
Lawan Praphaisal ◽  
Siripar Korinsak ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Oryza Sativa L ◽  
Genome Wide Association ◽  
Rice Agriculture ◽  
Large Numbers ◽  
Genome Wide ◽  
Resistant Varieties ◽  
A Genome ◽  
Serious Disease

Bacterial leaf blight (BLB) is a serious disease affecting global rice agriculture caused by Xanthomonas oryzae pv. oryzae (Xoo). Most resistant rice lines are dependent on single genes that are vulnerable to resistance breakdown caused by pathogen mutation. Here we describe a genome-wide association study of 222 predominantly Thai rice accessions assayed by phenotypic screening against 20 Xoo isolates. Loci corresponding to BLB resistance were detected using >142,000 SNPs. We identified 147 genes according to employed significance thresholds across chromosomes 1–6, 8, 9 and 11. Moreover, 127 of identified genes are located on chromosomal regions outside estimated Linkage Disequilibrium influences of known resistance genes, potentially indicating novel BLB resistance markers. However, significantly associated SNPs only occurred across a maximum of six Xoo isolates indicating that the development of broad-spectrum Xoo strain varieties may prove challenging. Analyses indicated a range of gene functions likely underpinning BLB resistance. In accordance with previous studies of accession panels focusing on indica varieties, our germplasm displays large numbers of SNPs associated with resistance. Despite encouraging data suggesting that many loci contribute to resistance, our findings corroborate previous inferences that multi-strain resistant varieties may not be easily realised in breeding programs without resorting to multi-locus strategies.

scholarly journals Genetic architecture of common bunt resistance in winter wheat using genome-wide association study

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Amira M. I. Mourad ◽  
Ahmed Sallam ◽  
Vikas Belamkar ◽  
Ezzat Mahdy ◽  
Bahy Bakheit ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Association Study ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Common Bunt ◽  
Genome Wide ◽  
Bunt Resistance

scholarly journals A New Polygenic Model for Nonfamilial Colorectal Cancer Inheritance Based on the Genetic Architecture of the Azoxymethane-Induced Mouse Model

Genetics ◽  
2019 ◽  
Vol 214 (3) ◽  
pp. 691-702
Author(s):  
Anika C. Bissahoyo ◽  
Yuying Xie ◽  
Lynda Yang ◽  
R. Scott Pearsall ◽  
Daekee Lee ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Mouse Model ◽  
Genetic Architecture ◽  
Inbred Strains ◽  
Genome Wide Association ◽  
Polygenic Resistance ◽  
Genetic Studies ◽  
Polygenic Model ◽  
Genome Wide ◽  
Dominant Characteristic

The azoxymethane model of colorectal cancer (CRC) was used to gain insights into the genetic heterogeneity of nonfamilial CRC. We observed significant differences in susceptibility parameters across 40 mouse inbred strains, with 6 new and 18 of 24 previously identified mouse CRC modifier alleles detected using genome-wide association analysis. Tumor incidence varied in F1 as well as intercrosses and backcrosses between resistant and susceptible strains. Analysis of inheritance patterns indicates that resistance to CRC development is inherited as a dominant characteristic genome-wide, and that susceptibility appears to occur in individuals lacking a large-effect, or sufficient numbers of small-effect, polygenic resistance alleles. Our results suggest a new polygenic model for inheritance of nonfamilial CRC, and that genetic studies in humans aimed at identifying individuals with elevated susceptibility should be pursued through the lens of absence of dominant resistance alleles rather than for the presence of susceptibility alleles.

scholarly journals Generalised Anxiety Disorder – A Twin Study of Genetic Architecture, Genome-Wide Association and Differential Gene Expression

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0134865 ◽  
Author(s):  
Matthew N. Davies ◽  
Serena Verdi ◽  
Andrea Burri ◽  
Maciej Trzaskowski ◽  
Minyoung Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Anxiety Disorder ◽  
Differential Gene Expression ◽  
Twin Study ◽  
Genetic Architecture ◽  
Genome Wide Association ◽  
Generalised Anxiety Disorder ◽  
Genome Wide ◽  
Differential Gene
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