[PDF] Top 20 Higher criticism approach to detect rare variants using whole genome sequencing data
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Higher criticism approach to detect rare variants using whole genome sequencing data
... Whole genome sequencing (WGS) is able to reveal complete genetic variations across the entire ...grouped variants potentially provide higher power for detecting genetic factors ... See full document
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Transmission and decorrelation methods for detecting rare variants using sequencing data from related individuals
... much higher power for the MAP4 gene, which explained the highest percent of variance of the genes assessed, FBAT-LC had higher power for the LEPR gene, which explained the lowest percent of ...of ... See full document
5
Whole-genome sequencing of clarithromycin resistant Helicobacter pylori characterizes unidentified variants of multidrug resistant efflux pump genes
... pylori genome with sufficient sequencing coverage. Illumina sequencing technique produces large amounts of short overlapping reads from the target genome ...analysis. Sequencing-based ... See full document
14
Quantifying the mapping precision of genome wide association studies using whole genome sequencing data
... WGS data, however, 5e-8 seems inadequate to control the GWFPR at ...1KGP3-imputed data) (Additional file 1: Figure S2), consistent with the result from a previous study ...imputed data was not due to ... See full document
10
A goodness of fit association test for whole genome sequencing data
... in genome-wide association studies, genes discovered to date only account for a small proportion of overall genetic contributions to many complex ...genetic variants that are either common variants ... See full document
6
Rare variant analysis of blood pressure phenotypes in the Genetic Analysis Workshop 18 whole genome sequencing data using sequence kernel association test
... 60x sequencing depth, with a goal of finding novel ...these rare variant approaches because available annota- tion information does not contain these novel ...GAW18 data, they may be shared with ... See full document
6
Prediction of genetic contributions to complex traits using whole genome sequencing data
... total variants (ie, 141,278 SNPs), on average, in TRN contributed when using SNPset 1, and 32% of the additive variance was explained by these ...the whole genome sequence variants ... See full document
6
Genetic data: The new challenge of personalized medicine, insights for rheumatoid arthritis patients
... such variants despite being common have a modest-effect size and thus a substantial fraction of heritability remains unexplained and/or hidden (Manolio et ...and rare variants, which would be ... See full document
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Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci
... in genome sequencing data is an active area of research, and many studies have demon- strated the difficulty of calling variants in sequencing data [25, 30, ...common ... See full document
15
Successful identification of rare variants using oligogenic segregation analysis as a prioritizing tool for whole exome sequencing studies
... reducing sequencing costs and to using resources conservatively by correctly elimi- nating traits unlikely to yield detectable ...the data set and was correctly eliminated based on our oligogenic ... See full document
5
Genome sequence of Coxiella burnetii strain Namibia
... The sequenced reads were filtered against the draft gen- ome assembly of Chlorocebus sabaeus (assembly AQIB01), Macaca mulatta (assembly AANU01), and Papio anubis (assembly AHZZ01) as well as four bacterial contaminants: ... See full document
9
Genome sequencing and crop improvement
... sequence data are being generated by the latest second generation sequencing technologies and these provide a valuable resource for the mining of molecular markers (Imelfort et ...plant genome ... See full document
5
Systematic analysis of the clinical and biochemical characteristics of maternally inherited hypertension in Chinese Han families associated with mitochondrial
... were higher than those of the control group (P < ...The whole mitochondrial DNA sequence analysis revealed a total of 172 base changes, including 17 in ribosomal RNA (rRNA) genes, four in transfer RNA ... See full document
8
Clinical and genomic evaluation of a Chinese patient with a novel deletion associated with Phelan–McDermid syndrome
... In principle, chimeric-read pairs should be observed in translocations and inversion events. These chimeric- read pairs suggested possible candidate BCA “clusters” throughout the genome. According to the insert ... See full document
9
Exome Sequencing to Detect Rare Variants Associated With General Cognitive Ability: A Pilot Study
... on rare genetic variants –– usu- ally defined as those occurring with less than ...chip variants in relation to normal varia- tion in cognitive ability measured in childhood and old age in a Scottish ... See full document
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A rare functional variant of SHARPIN attenuates the inflammatory response and associates with increased risk of late-onset Alzheimer’s disease
... performed whole-exome sequencing analyses of 202 LOAD patients lacking the APOE ε4 risk allele (Additional file 1: Table ...All variants derived from exome sequencing analysis were annotated ... See full document
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Whole Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe
... sequence data in a blinded ...phenotypic data and genotypic predictions (8, 13, 28), we sought to extend these studies by including a greater number of antibiotics (19 in total) and by including a ... See full document
15
Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle
... DNA sequencing error for the CPC98 specimen by counting non-consensus nucleotide calls from individual mtDNA reads that dif- fered from the CPC98 mtDNA consensus sequence ...analysis using the larger number ... See full document
15
Application of resequencing to rice genomics, functional genomics and evolutionary analysis
... constructed using a novel data-imputation ...cultivars using 1,917 SNPs to clarify the dynamics of the pedigree haplotypes (Yamamoto et ...on genome-wide SNP ana- lysis, these studies revealed ... See full document
10
Comparing strategies for combined testing of rare and common variants in whole sequence and genome wide genotype data
... 200 data replicates of simulated SBP. Sequence-derived variants were often more powerful than GWAS with some exceptions ...on rare SNPs ...On rare MAP4 SNPs, 1/ν-weights lowered the power, ... See full document
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