Rare variants
Imputing rare variants in families using a two stage approach
... are 0, 0, and 1.0, respectively, for BEAGLE and 0, 0.5, and 0.5 for GIGI, Saad et al’s method would choose BEAGLE for that variant, because the larger variance indicates more certainty in the call. Saad et al found that ...
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Prioritization of family member sequencing for the detection of rare variants
... Whole-genome sequencing (WGS) is an important tool in the discovery of rare variants that influence disease. Family-based association studies have likewise been crucial in the fine-mapping of genetic ...
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Identification of rare variants for hypertension with incorporation of linkage information
... and rare variants of genes located in the regions showing evidence of ...The rare variants were collapsed if their minor allele frequencies were less than or equal to the thresholds: ...
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A Powerful and Adaptive Association Test for Rare Variants
... of rare variants (RVs), although its application can be much broader to other types of traits, common variants (CVs), and gene set or pathway ...
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Methods for detecting associations between phenotype and aggregations of rare variants
... uncovered variants associated with more than 150 traits, the percentage of phenotypic variation explained by these associations remains ...is rare variants, and several statistics have been devised ...
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Enriching rare variants using family specific linkage information
... carry rare causal ...of rare variants are not large and the aggregate linkage evidence for the entire sample (a repli- cation in this case) is ...causal variants, for example, a locus ...
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Application of family based tests of association for rare variants to pathways
... single-nucleotide variants [SNVs]) when the number of SNVs in the gene or in the pathway is very large and the genotypes come from sequence data organized in large ...for rare variants from complex ...
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Does the inclusion of rare variants improve risk prediction?
... both rare variants (RVs) and common variants (CVs) to link previously unidentified genome loci to disease-related ...of variants provide better predictions of SBP than those using only CVs or ...
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Rare variants and de novo variants in mesial temporal lobe epilepsy with hippocampal sclerosis
... particular, rare variants of fragile X mental retardation protein (FMRP)-targeted genes have been found to be enriched in multiple psychiatric disorders (fragile X, ASD, and schizo- ...
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Methods to evaluate rare variants gene age interaction for triglycerides
... of rare variants cannot be readily applied for testing the gene environment interaction effect of rare variants, as those methods either have unstable results or inflated Type I error rates ...
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The UK10K project identifies rare variants in health and disease
... novel variants from nearly 4,000 European-ancestry ...and rare variants compared to existing panels such as the 1000GP phase 1 ...and rare genetic variants with a large variety of ...
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A clustering approach to identify rare variants associated with hypertension
... In this paper, we propose a clustering-based test to detect rare variants when continuous phenotypes are available. There are three advantages of doing this: First, the CST can make better use of phenotype ...
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Multiple common and rare variants of ABCG2 cause gout
... the rare variants identified by targeted exon ...identified rare variants (n=9, table ...missense variants (n=9) (see online supplementary table S2) with the protein prediction ...
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Identifying rare variants using a Bayesian regression approach
... Rare variants are genetic variants that have a minor allele frequency (MAF) less than ...that rare variants generally have lar- ger effects on a trait than common ...of rare ...
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Evaluating methods for the analysis of rare variants in sequence data
... for rare variants. For common variants, of only minor importance in our analysis, the code represents the presumption of a dominant disease ...
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Statistical Properties of Single-Marker Tests for Rare Variants
... these rare variants on common, complex diseases, we must be able to accurately assess their statistical ...typical rare variant ( 1%) under the null hypothesis and tested the allelic 2 , ...
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Genetic mechanisms and age-related macular degeneration: common variants, rare variants, copy number variations, epigenetics, and mitochondrial genetics
... Common variants explain approximately 55% of the heritability of ...as rare variants, copy number variations, epigenetics, and mitochondrial inheritance may contribute to the missing ...
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New insights into old methods for identifying causal rare variants
... Because most of the SNPs are rare variants, many of them take identical values across all individuals in the data set; that is, statistically they are indistinguishable. In the preliminary data reduction ...
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Identification of multiple rare variants associated with a disease
... Identifying rare variants that are responsible for complex disease has been promoted by advances in sequencing ...these variants have ...exonic variants in the Genetic Analysis Workshop 17 ...
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Capability of common SNPs to tag rare variants
... genetic variants that may be asso- ciated with many common diseases ...causal variants. Under the common disease/rare variants hypothesis, which sug- gests that many rare ...
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