Indexes genomic variants
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Genome-wide association studies have identified variants associated with obesity-related traits, such as the body mass index (BMI). We sought to determine how the combination of 31 validated, BMI-associated loci contributes to obesity- and diabetes-related traits in a French population sample.
5p vinarcissa 21-03-2023 4 1 Download
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There is growing interest in using genetic variants to augment the reference genome into a graph genome, with alternative sequences, to improve read alignment accuracy and reduce allelic bias. While adding a variant has the positive effect of removing an undesirable alignment score penalty, it also increases both the ambiguity of the reference genome and the cost of storing and querying the genome index.
16p vigalileogalilei 27-02-2022 10 1 Download
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Efficiently scaling genomic variant search indexes to thousands of samples is computationally challenging due to the presence of multiple coordinate systems to avoid reference biases. We present VariantStore, a system that indexes genomic variants from multiple samples using a variation graph and enables variant queries across any sample-specific coordinate system.
25p viarchimedes 26-01-2022 16 0 Download
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GWAS summary statistics are fundamental for a variety of research applications yet no common storage format has been widely adopted. Existing tabular formats ambiguously or incompletely store information about genetic variants and associations, lack essential metadata and are typically not indexed yielding poor query performance and increasing the possibility of errors in data interpretation and post-GWAS analyses.
10p viarchimedes 26-01-2022 12 0 Download
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Sample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigations, microbial detection in human samples, or circulating cell-free tumor DNA (ctDNA) variant detection. Therefore, the limit-of-detection of an MPS assay is directly related to the degree of index cross-talk.
10p vibeauty 23-10-2021 9 1 Download
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From genome-wide association studies, brain-derived neurotrophic factor (BDNF) locus on chromosome 11 was the only SNP associated with both smoking and body mass index (BMI) in European, African and Asian population.
16p vitzuyu2711 29-09-2021 13 1 Download
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Identifying genetic variants associated with complex human diseases is a great challenge in genome-wide association studies (GWAS). Single nucleotide polymorphisms (SNPs) arising from genetic background are often dependent. The existing methods, i.e., local index of significance (LIS) and pooled local index of significance (PLIS), were both proposed for modeling SNP dependence and assumed that the whole chromosome follows a hidden Markov model (HMM).
12p viwyoming2711 16-12-2020 20 1 Download
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It is clear that genetic variations in the fat mass and obesity-associated (FTO) gene affect body mass index and the risk of obesity. Given the mounting evidence showing a positive association between obesity and pancreatic cancer, this study aimed to investigate the relation between variants in the FTO gene, obesity and pancreatic cancer risk.
6p vijennie2711 29-09-2020 25 1 Download