An integrative computational approach for prioritization of genomic variants
Abstract
An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidate genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. This study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest.
- Authors:
- more »
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Institutes of Health (NIH)
- OSTI Identifier:
- 1212419
- Alternate Identifier(s):
- OSTI ID: 1222963
- Grant/Contract Number:
- AC02-06CH11357; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 12; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 96 KNOWLEDGE MANAGEMENT AND PRESERVATION; genomic databases; genome analysis; spina bifida; protein structure prediction; genomic medicine; phenotypes; bioinformatics; genome evolution
Citation Formats
Dubchak, Inna, Balasubramanian, Sandhya, Wang, Sheng, Meydan, Cem, Sulakhe, Dinanath, Poliakov, Alexander, Börnigen, Daniela, Xie, Bingqing, Taylor, Andrew, Ma, Jianzhu, Paciorkowski, Alex R., Mirzaa, Ghayda M., Dave, Paul, Agam, Gady, Xu, Jinbo, Al-Gazali, Lihadh, Mason, Christopher E., Ross, M. Elizabeth, Maltsev, Natalia, Gilliam, T. Conrad, and Huang, Qingyang. An integrative computational approach for prioritization of genomic variants. United States: N. p., 2014.
Web. doi:10.1371/journal.pone.0114903.
Dubchak, Inna, Balasubramanian, Sandhya, Wang, Sheng, Meydan, Cem, Sulakhe, Dinanath, Poliakov, Alexander, Börnigen, Daniela, Xie, Bingqing, Taylor, Andrew, Ma, Jianzhu, Paciorkowski, Alex R., Mirzaa, Ghayda M., Dave, Paul, Agam, Gady, Xu, Jinbo, Al-Gazali, Lihadh, Mason, Christopher E., Ross, M. Elizabeth, Maltsev, Natalia, Gilliam, T. Conrad, & Huang, Qingyang. An integrative computational approach for prioritization of genomic variants. United States. https://doi.org/10.1371/journal.pone.0114903
Dubchak, Inna, Balasubramanian, Sandhya, Wang, Sheng, Meydan, Cem, Sulakhe, Dinanath, Poliakov, Alexander, Börnigen, Daniela, Xie, Bingqing, Taylor, Andrew, Ma, Jianzhu, Paciorkowski, Alex R., Mirzaa, Ghayda M., Dave, Paul, Agam, Gady, Xu, Jinbo, Al-Gazali, Lihadh, Mason, Christopher E., Ross, M. Elizabeth, Maltsev, Natalia, Gilliam, T. Conrad, and Huang, Qingyang. Mon .
"An integrative computational approach for prioritization of genomic variants". United States. https://doi.org/10.1371/journal.pone.0114903. https://www.osti.gov/servlets/purl/1212419.
@article{osti_1212419,
title = {An integrative computational approach for prioritization of genomic variants},
author = {Dubchak, Inna and Balasubramanian, Sandhya and Wang, Sheng and Meydan, Cem and Sulakhe, Dinanath and Poliakov, Alexander and Börnigen, Daniela and Xie, Bingqing and Taylor, Andrew and Ma, Jianzhu and Paciorkowski, Alex R. and Mirzaa, Ghayda M. and Dave, Paul and Agam, Gady and Xu, Jinbo and Al-Gazali, Lihadh and Mason, Christopher E. and Ross, M. Elizabeth and Maltsev, Natalia and Gilliam, T. Conrad and Huang, Qingyang},
abstractNote = {An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidate genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. This study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest.},
doi = {10.1371/journal.pone.0114903},
journal = {PLoS ONE},
number = 12,
volume = 9,
place = {United States},
year = {Mon Dec 15 00:00:00 EST 2014},
month = {Mon Dec 15 00:00:00 EST 2014}
}
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VISTA Enhancer Browser--a database of tissue-specific human enhancers
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Genome-wide discovery of human heart enhancers
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The Developmental Brain Disorders Database (DBDB): A curated neurogenetics knowledge base with clinical and research applications
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McKusick's Online Mendelian Inheritance in Man (OMIM(R))
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AutDB: a gene reference resource for autism research
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The Genetic Association Database
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A searchable database of genetic evidence for psychiatric disorders
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A conditional neural fields model for protein threading
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A multiple-template approach to protein threading
journal, April 2011
- Peng, Jian; Xu, Jinbo
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Protein structure alignment beyond spatial proximity
journal, March 2013
- Wang, Sheng; Ma, Jianzhu; Peng, Jian
- Scientific Reports, Vol. 3, Issue 1
Etiology, pathogenesis and prevention of neural tube defects
journal, June 2006
- Padmanabhan, Rengasamy
- Congenital Anomalies, Vol. 46, Issue 2
Gene–environment interactions, folate metabolism and the embryonic nervous system
journal, June 2010
- Ross, M. Elizabeth
- WIREs Systems Biology and Medicine, Vol. 2, Issue 4
The Continuing Challenge of Understanding, Preventing, and Treating Neural Tube Defects
journal, March 2013
- Wallingford, John B.; Niswander, Lee A.; Shaw, Gary M.
- Science, Vol. 339, Issue 6123
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
journal, July 2010
- Wang, K.; Li, M.; Hakonarson, H.
- Nucleic Acids Research, Vol. 38, Issue 16
Neural tube defects-disorders of neurulation and related embryonic processes
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- Copp, Andrew J.; Greene, Nicholas D. E.
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Neural Tube Defects and Folate Pathway Genes: Family-Based Association Tests of Gene–Gene and Gene–Environment Interactions
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- Boyles, Abee L.; Billups, Ashley V.; Deak, Kristen L.
- Environmental Health Perspectives, Vol. 114, Issue 10
A Genetic Signature of Spina Bifida Risk from Pathway-Informed Comprehensive Gene-Variant Analysis
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- PLoS ONE, Vol. 6, Issue 11
Neural tube defects and maternal intake of micronutrients related to one-carbon metabolism or antioxidant activity
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- Chandler, Angela L.; Hobbs, Charlotte A.; Mosley, Bridget S.
- Birth Defects Research Part A: Clinical and Molecular Teratology, Vol. 94, Issue 11
Folate-related gene variants in Irish families affected by neural tube defects
journal, January 2013
- Fisk Green, Ridgely; Byrne, Julianne; Crider, Krista S.
- Frontiers in Genetics, Vol. 4
Investigations of single nucleotide polymorphisms in folate pathway genes in Chinese families with neural tube defects
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Maternal Genetic Effects, Exerted by Genes Involved in Homocysteine Remethylation, Influence the Risk of Spina Bifida
journal, November 2002
- Doolin, Marie-Therese; Barbaux, Sandrine; McDonnell, Maeve
- The American Journal of Human Genetics, Vol. 71, Issue 5
Mutations in CUBN, encoding the intrinsic factor-vitamin B12 receptor, cubilin, cause hereditary megaloblastic anaemia 1
journal, March 1999
- Aminoff, Maria; Carter, Jo Ellen; Chadwick, Robert B.
- Nature Genetics, Vol. 21, Issue 3
An association study of 45 folate-related genes in spina bifida: Involvement ofcubilin(CUBN) andtRNA aspartic acid methyltransferase 1(TRDMT1)
journal, March 2009
- Franke, Barbara; Vermeulen, Sita H. H. M.; Steegers-Theunissen, Regine P. M.
- Birth Defects Research Part A: Clinical and Molecular Teratology, Vol. 85, Issue 3
Acquired and inherited disorders of cobalamin and folate in children
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