[PDF] Top 20 On combining family and population based sequencing data
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On combining family and population based sequencing data
... exome sequencing studies provide the resolution necessary to identify both com- mon and rare genetic variants associated with com- plex disease ...to combining association signals across a genetic region/ ... See full document
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A comparative analysis of family based and population based association tests using whole genome sequence data
... both family-based and population-based designs, to detect association with variants in the MAP4 gene region and on chromosome 3 with blood ...(eQTLs) data. Four set-based tests ... See full document
5
Factors Influencing the Sensitivity and Specificity of Conventional Sequencing in Human Immunodeficiency Virus Type 1 Tropism Testing
... deep sequencing on a GS FLX (454) sequencer (Roche, Basel, Switzer- land); this method allows the parallel sequencing of thousands of clones from a single ...conventional sequencing results as this ... See full document
8
Two stage family based designs for sequencing studies
... relatives, based on their population frequency and degree of relationship, add these scores over all families, and compare it to an approximate null mean and var- ... See full document
5
Identity by descent estimation with population and pedigree based imputation in admixed family data
... pedigree- based imputation, we used a set of 351 well-spaced SNPs (Marker Set 2 [MS-2]; Table 1) extracted from the SNP data of all genotyped individuals in these 16 ...positions based on the Haldane ... See full document
7
A Bayesian approach to combining population and survey data for male fertility estimation
... survey data are used for quantitative assessment of the relationship of socio- economic variables to male fertility, data quality is a ...Survey data on male fertility are known to be worse for men ... See full document
6
Combining DNA methylation and RNA sequencing data of cancer for supervised knowledge extraction
... three data matrices (RNA sequencing, DNA methylation, and their combination) of each considered cancer, resulting in 36 different knowledge discovery ... See full document
23
Logistic Bayesian LASSO for detecting association combining family and case control data
... is based on an MCMC proced- ure to sample from the posterior distribution, it is com- putationally intensive, and thus not suitable for whole-genome ...a family-based single-SNP association testing ... See full document
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Extended T2 tests for longitudinal family data in whole genome sequencing studies
... To compare the overall capabilities of these tests, we studied their power (i.e., true positive rates) in detecting each of all windows over 200 simulation replicates. As illu- strated in Figure 4, there are 4 ... See full document
6
A multi level model for analyzing whole genome sequencing family data with longitudinal traits
... genome sequencing (WGS) studies have the strength to provide greater information for the identification of rare variants, which likely account for a significant portion of missing heritability of common human ... See full document
5
Association analysis of whole genome sequencing data accounting for longitudinal and family designs
... next-generation sequencing studies, the family-based design has the unique advantages of pro- tecting against population stratification, detecting geno- typing errors, and facilitating ... See full document
7
Whole-genome haplotyping approaches and genomic medicine
... and population- based methods may work better than any single approach, by combining strengths and minimizing weaknesses (Table ...Hap-seqX, combining haplotype assembly with a reference ... See full document
16
Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data
... primarily based on direct counting of sequencing reads, provide inaccurate estimates of local nucleotide diversity (Nielsen et ...NGS data to provide more accurate estimates of allele ...timate ... See full document
37
PD_NGSAtlas: a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders
... All of the subjects were diagnosed by consensus for ei- ther BP or SZ according to DSM-IV-TR criteria and the control samples had no history of an Axis I disorder. The diverse types of clinical characteristics were also ... See full document
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Exploration and comparison of methods for combining population and family based genetic association using the Genetic Analysis Workshop 17 mini exome
... Epstein et al. [6] generalized this work by relaxing the assumptions of HWE, random mating, and the assumed multiplicative mode of inheritance. In addition, they described a formal test for the appropriateness of combin- ... See full document
6
Combining multiple family based association studies
... We implement the imputation step using the loess func- tion in R. The choice of the smoothing parameter depends on many factors such as the age of the disease mutation, the population under study, and the marker ... See full document
6
Risk Prediction Modeling on Family-Based Sequencing Data Using a Random Field Method
... ABSTRACT Family-based design is one of the most popular designs in genetic studies and has many unique features for risk-prediction ...among family members can be informative for predicting an ... See full document
11
Combining information from linkage and association mapping for next generation sequencing longitudinal family data
... 2 data sets: one containing approximately 50,000 GWAS markers, which we refer to as the AllMark data set, and 1 contain- ing only 784 LD-pruned GWAS markers, the NoLD data ...both data sets we ... See full document
5
Adjusting for population stratification and relatedness with sequencing data
... for population stratification and known/unknown subject ...genome-wide sequencing data, the question of whether it is preferable to use common variants or rare variants for such an adjustment remains ... See full document
5
A comparison of whole genome sequencing with exome sequencing for family based association studies
... DNA sequencing decreases, association studies based on whole genome sequencing are now becoming ...genome sequencing compared to exome sequencing, which has been widely used to study a ... See full document
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