Academic Journal
ATAV: a comprehensive platform for population-scale genomic analyses
| Title: | ATAV: a comprehensive platform for population-scale genomic analyses |
|---|---|
| Authors: | Ren, Zhong, Povysil, Gundula, Hostyk, Joseph A., Cui, Hongzhu, Bhardwaj, Nitin, Goldstein, David B. |
| Publication Year: | 2021 |
| Collection: | Columbia University: Academic Commons |
| Subject Terms: | Genomics, Nucleotide sequence--Computer programs, Nucleotide sequence--Computer network resources |
| Description: | Background A common approach for sequencing studies is to do joint-calling and store variants of all samples in a single file. If new samples are continually added or controls are re-used for several studies, the cost and time required to perform joint-calling for each analysis can become prohibitive. Results We present ATAV, an analysis platform for large-scale whole-exome and whole-genome sequencing projects. ATAV stores variant and per site coverage data for all samples in a centralized database, which is efficiently queried by ATAV to support diagnostic analyses for trios and singletons, as well as rare-variant collapsing analyses for finding disease associations in complex diseases. Runtime logs ensure full reproducibility and the modularized ATAV framework makes it extensible to continuous development. Besides helping with the identification of disease-causing variants for a range of diseases, ATAV has also enabled the discovery of disease-genes by rare-variant collapsing on datasets containing more than 20,000 samples. Analyses to date have been performed on data of more than 110,000 individuals demonstrating the scalability of the framework. To allow users to easily access variant-level data directly from the database, we provide a web-based interface, the ATAV data browser ( http://atavdb.org/ ). Through this browser, summary-level data for more than 40,000 samples can be queried by the general public representing a mix of cases and controls of diverse ancestries. Users have access to phenotype categories of variant carriers, as well as predicted ancestry, gender, and quality metrics. In contrast to many other platforms, the data browser is able to show data of newly-added samples in real-time and therefore evolves rapidly as more and more samples are sequenced. Conclusions Through ATAV, users have public access to one of the largest variant databases for patients sequenced at a tertiary care center and can look up any genes or variants of interest. Additionally, since the entire code is freely ... |
| Document Type: | article in journal/newspaper |
| Language: | English |
| DOI: | 10.7916/yaa2-qy53 |
| Availability: | https://doi.org/10.7916/yaa2-qy53 |
| Accession Number: | edsbas.E8C1FB9B |
| Database: | BASE |
| FullText | Text: Availability: 0 CustomLinks: – Url: https://doi.org/10.7916/yaa2-qy53# Name: EDS - BASE (ns324271) Category: fullText Text: View record from BASE |
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| Items | – Name: Title Label: Title Group: Ti Data: ATAV: a comprehensive platform for population-scale genomic analyses – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Ren%2C+Zhong%22">Ren, Zhong</searchLink><br /><searchLink fieldCode="AR" term="%22Povysil%2C+Gundula%22">Povysil, Gundula</searchLink><br /><searchLink fieldCode="AR" term="%22Hostyk%2C+Joseph+A%2E%22">Hostyk, Joseph A.</searchLink><br /><searchLink fieldCode="AR" term="%22Cui%2C+Hongzhu%22">Cui, Hongzhu</searchLink><br /><searchLink fieldCode="AR" term="%22Bhardwaj%2C+Nitin%22">Bhardwaj, Nitin</searchLink><br /><searchLink fieldCode="AR" term="%22Goldstein%2C+David+B%2E%22">Goldstein, David B.</searchLink> – Name: DatePubCY Label: Publication Year Group: Date Data: 2021 – Name: Subset Label: Collection Group: HoldingsInfo Data: Columbia University: Academic Commons – Name: Subject Label: Subject Terms Group: Su Data: <searchLink fieldCode="DE" term="%22Genomics%22">Genomics</searchLink><br /><searchLink fieldCode="DE" term="%22Nucleotide+sequence--Computer+programs%22">Nucleotide sequence--Computer programs</searchLink><br /><searchLink fieldCode="DE" term="%22Nucleotide+sequence--Computer+network+resources%22">Nucleotide sequence--Computer network resources</searchLink> – Name: Abstract Label: Description Group: Ab Data: Background A common approach for sequencing studies is to do joint-calling and store variants of all samples in a single file. If new samples are continually added or controls are re-used for several studies, the cost and time required to perform joint-calling for each analysis can become prohibitive. Results We present ATAV, an analysis platform for large-scale whole-exome and whole-genome sequencing projects. ATAV stores variant and per site coverage data for all samples in a centralized database, which is efficiently queried by ATAV to support diagnostic analyses for trios and singletons, as well as rare-variant collapsing analyses for finding disease associations in complex diseases. Runtime logs ensure full reproducibility and the modularized ATAV framework makes it extensible to continuous development. Besides helping with the identification of disease-causing variants for a range of diseases, ATAV has also enabled the discovery of disease-genes by rare-variant collapsing on datasets containing more than 20,000 samples. Analyses to date have been performed on data of more than 110,000 individuals demonstrating the scalability of the framework. To allow users to easily access variant-level data directly from the database, we provide a web-based interface, the ATAV data browser ( http://atavdb.org/ ). Through this browser, summary-level data for more than 40,000 samples can be queried by the general public representing a mix of cases and controls of diverse ancestries. Users have access to phenotype categories of variant carriers, as well as predicted ancestry, gender, and quality metrics. In contrast to many other platforms, the data browser is able to show data of newly-added samples in real-time and therefore evolves rapidly as more and more samples are sequenced. Conclusions Through ATAV, users have public access to one of the largest variant databases for patients sequenced at a tertiary care center and can look up any genes or variants of interest. Additionally, since the entire code is freely ... – Name: TypeDocument Label: Document Type Group: TypDoc Data: article in journal/newspaper – Name: Language Label: Language Group: Lang Data: English – Name: DOI Label: DOI Group: ID Data: 10.7916/yaa2-qy53 – Name: URL Label: Availability Group: URL Data: https://doi.org/10.7916/yaa2-qy53 – Name: AN Label: Accession Number Group: ID Data: edsbas.E8C1FB9B |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.7916/yaa2-qy53 Languages: – Text: English Subjects: – SubjectFull: Genomics Type: general – SubjectFull: Nucleotide sequence--Computer programs Type: general – SubjectFull: Nucleotide sequence--Computer network resources Type: general Titles: – TitleFull: ATAV: a comprehensive platform for population-scale genomic analyses Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Ren, Zhong – PersonEntity: Name: NameFull: Povysil, Gundula – PersonEntity: Name: NameFull: Hostyk, Joseph A. – PersonEntity: Name: NameFull: Cui, Hongzhu – PersonEntity: Name: NameFull: Bhardwaj, Nitin – PersonEntity: Name: NameFull: Goldstein, David B. IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Type: published Y: 2021 Identifiers: – Type: issn-locals Value: edsbas – Type: issn-locals Value: edsbas.oa |
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