[PDF] Top 20 Analysis of homozygosity disequilibrium using whole genome sequencing data
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Analysis of homozygosity disequilibrium using whole genome sequencing data
... Third, our GEE-based homozygosity association tests identified 5 DBP-associated ROHs and 3 hypertension- associated ROHs. Genes in these ROHs include some that are associated with calcium channels, renin ... See full document
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Rare variant analysis of blood pressure phenotypes in the Genetic Analysis Workshop 18 whole genome sequencing data using sequence kernel association test
... directions. Using SKAT, we were able to analyze the entire sequencing data for all 200 replications of both DBP and SBP simulated pheno- types under six different cases (3 weighting schemes times two ... See full document
6
An exploration of heterogeneity in genetic analysis of complex pedigrees: linkage and association using whole genome sequencing data in the MAP4 region
... In analysis of the original Genetic Analysis Workshop pedigree data (reported in detail in Chen et al [3]), we observed substantial between-pedigree heterogeneity and differences between linkage and ... See full document
6
Association analysis of whole genome sequencing data accounting for longitudinal and family designs
... genetic data from sequencing and imputation only on chromosome 3 because of limited computation ...missing data, as well as age, gender, smoking status, and antihy- pertensive medication ...consider ... See full document
7
Incorporating ENCODE information into association analysis of whole genome sequencing data
... next-generation sequencing (NGS) ...the whole exome sequencing (WES), the first wave of NGS-based association studies of complex diseases, ... See full document
5
Homozygosity disequilibrium and its gene regulation
... in homozygosity intensity ...previous homozygosity associ- ation test ...the homozygosity intensity for the common homozygote of an ...our homozygosity intensity ana- lyses of WGS data ... See full document
5
Higher criticism approach to detect rare variants using whole genome sequencing data
... real data with much larger sample ...for genome-wide type I error ...or data-driven weights ...family data analysis based on mixed effect models or for meta-analysis, which ... See full document
6
Quantifying the mapping precision of genome wide association studies using whole genome sequencing data
... GWAS using ei- ther WGS or imputed data and vice ...GWAS using HapMap2-imputed data to 98.3% using WGS data ...mapping analysis with epigenetic data) are within 100 ... See full document
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A goodness of fit association test for whole genome sequencing data
... For evaluating the above association tests, we used the WGS “dose” file of 1,215,399 SNVs and the GWAS file of 65,519 SNVs on chromosome 3 as the genotype data. The quantitative trait was the SBP for the 142 ... See full document
6
A mutation in the nucleoporin 107 gene causes XX gonadal dysgenesis
... performed using SNP arrays in affected females IV-1, IV-5, IV-6, and IV-7 and in the healthy female IV-2 (Figure 1A) to detect informative genomic regions that were homozygous and shared among affected individuals ... See full document
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Whole genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes
... Polymorphisms in genetic copy number can influence gene expression, coding sequence, and zygosity, making them pow- erful actors in the evolutionary process. Copy number variants (CNVs) are however understudied, being ... See full document
13
Comparison of Next Generation Sequencing Technologies for Comprehensive Assessment of Full Length Hepatitis C Viral Genomes
... targeted analysis of genomic regions that rely on PCR Sanger sequencing; the application of this method is limited by problems with primer design for highly divergent HCV genotypes, genome coverage, ... See full document
15
Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole genome sequencing
... for sequencing libraries (see Materials and methods). The sequencing reads were filtered and mapped using ...MegaMapper. Using our own (for SJD) and publicly available (for AB) ... See full document
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Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle
... SNP data set to generate a maximum likelihood (ML) phylogenetic tree ...this analysis, the BovineSNP50 data set was filtered using a linkage disequi- librium threshold (r 2 ≤ ...ated ... See full document
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Genome analysis and knowledge-driven variant interpretation with TGex
... ation Sequencing (NGS) candidate variant-containing genes and output a scored, prioritized gene list accord- ing to disease phenotype and symptom relationships, using the comprehensive GeneCards ...genetic ... See full document
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Application of resequencing to rice genomics, functional genomics and evolutionary analysis
... identified genome-wide variation patterns including the identification of more than ...for whole genome sequencing (He et ...generated genome sequences from 446 geographically diverse ... See full document
10
Genome sequencing and crop improvement
... unassembled genome sequence data and expressed sequence tags (EST). This data can also be applied for SNP and simple sequence repeats (SSR) molecular marker discovery, though without a reference ... See full document
5
Homozygosity and Linkage Disequilibrium
... linkage disequilibrium and systematic data are collected (Kidd et ...of disequilibrium ceived a great deal of ...LD genome screens example, disequilibrium between markers was used to ... See full document
14
Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics
... systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and ... See full document
19
Whole genome diversity, population structure and linkage disequilibrium analysis
... genotyped using sequencing-based DArT genotyping ...next-generation sequencing platforms as described before [28, ...the analysis. Data set filtered for minor allele frequency (MAF) ... See full document
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