Dataset Information

SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures.

ABSTRACT: The identification of structural variants using short-read data remains challenging. Most approaches that use discordant paired-end sequences ignore non-trivial signatures presented by variants containing 3 breakpoints, such as those generated by various copy-paste and cut-paste mechanisms. This can result in lower precision and sensitivity in the identification of the more common structural variants such as deletions and duplications. We present SVXplorer, which uses a graph-based clustering approach streamlined by the integration of non-trivial signatures from discordant paired-end alignments, split-reads and read depth information to improve upon existing methods. We show that SVXplorer is more sensitive and precise compared to several existing approaches on multiple real and simulated datasets. SVXplorer is available for download at https://github.com/kunalkathuria/SVXplorer.

SUBMITTER: Kathuria K

PROVIDER: S-EPMC7100977 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures.

Kathuria Kunal K Ratan Aakrosh A

PLoS computational biology 20200317 3

The identification of structural variants using short-read data remains challenging. Most approaches that use discordant paired-end sequences ignore non-trivial signatures presented by variants containing 3 breakpoints, such as those generated by various copy-paste and cut-paste mechanisms. This can result in lower precision and sensitivity in the identification of the more common structural variants such as deletions and duplications. We present SVXplorer, which uses a graph-based clustering ap ...[more]

PMID: 32182236

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Project description:BackgroundTo face the second wave of COVID-19, Italy implemented a tiered restriction system with different limitation levels (yellow = medium; orange = medium-high, red = high) at the beginning of November 2020. The restrictions systematically reduced the transmission of SARS-CoV-2 with increasing strength for increasing tier. However, it is unknown whether the effect of limitations was equal between provinces with different socioeconomic levels. Therefore, we investigated the association between the province's socioeconomic level and SARS-CoV-2 infection daily reproduction number in each restriction level.MethodsWe measured the province's socioeconomic level as the percentage of individuals whose 2019 total yearly income was lower than 10,000€, using the measure as a proxy of economic disadvantage. We estimated the daily reproduction number (Rt) at the province level using the SARS-CoV-2 daily incidence data from November 2020 to May 2021. We then used multilevel linear regression models with random intercepts stratified by restriction level to estimate the association between economic disadvantage and Rt. We also adjusted the analyses for potential confounders of the association between the province's economic disadvantage and the Rt: the percentage of people with 0-5 years, the quartiles of population density, and the geographical repartition.ResultsOverall, we found increasing Rt in yellow (+ 0.004 p < 0.01, from Rt = 0.99 to 1.08 in three weeks) and containing effects for the orange (-0.005 p < 0.01, from Rt = 1.03 to 0.93) and the red tier (-0.014 p < 0.01, from Rt = 1.05 to 0.76). More economically disadvantaged provinces had higher Rt levels in every tier, although non-significantly in the yellow level (yellow = 0.001 p = 0.19; orange = 0.002 p = 0.02; red = 0.004 p < 0.01). The results showed that the association between economic disadvantage and Rt differed by level of restriction. The number of days into the restriction and the economic disadvantage had statistically significant interactions in every adjusted model. Compared to better off, more economically disadvantaged provinces had slower increasing trends in yellow and steeper Rt reductions in orange, but they showed slower Rt reductions in the highest tier.ConclusionLower tiers were more effective in more economically disadvantaged provinces, while the highest restriction level had milder effects. These results underline the importance of accounting for socioeconomic level when implementing public health measures.

Dataset Information

SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures.

Publications

SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures.

Similar Datasets

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