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Whole genome mapping and identification of single nucleotide polymorphisms of four Bangladeshi individuals and their functional significance
OBJECTIVE: The major objective of the study was to sequence the whole genome of four Bangladeshi individuals and identify variants that are known to be associated with functional changes or disease states. We also carried out an ontology analysis to identify the functions and pathways most likely to...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7981821/ https://www.ncbi.nlm.nih.gov/pubmed/33743798 http://dx.doi.org/10.1186/s13104-021-05514-x |
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author | Khan, Salim Akter, Shahina Goswami, Barna Habib, Ahashan Banu, Tanjina Akhtar Barton, Carl Osman, Eshrar Samir, Samiruzzaman Arjuman, Farida Hasan, Saam Hossain, Maqsud |
author_facet | Khan, Salim Akter, Shahina Goswami, Barna Habib, Ahashan Banu, Tanjina Akhtar Barton, Carl Osman, Eshrar Samir, Samiruzzaman Arjuman, Farida Hasan, Saam Hossain, Maqsud |
author_sort | Khan, Salim |
collection | PubMed |
description | OBJECTIVE: The major objective of the study was to sequence the whole genome of four Bangladeshi individuals and identify variants that are known to be associated with functional changes or disease states. We also carried out an ontology analysis to identify the functions and pathways most likely to be affected by these variants. RESULTS: We identified around 900,000 common variants and close to 5 million unique ones in all four of the individuals. This included over 11,500 variants that caused nonsynonymous changes in proteins. Heart function associated pathways were heavily implicated by the ontology analysis; corroborating previous studies that claimed the Bangladeshi population as highly susceptible to heart disorders. Two variants were found that have been previously identified as pathogenic factors in familial hypercholesteremia and structural disorders of the heart. Other pathogenic variants we found were associated with pseudoxanthoma elasticum, cancer progression, polyagglutinable erythrocyte syndrome, preeclampsia, and others. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13104-021-05514-x. |
format | Online Article Text |
id | pubmed-7981821 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-79818212021-03-22 Whole genome mapping and identification of single nucleotide polymorphisms of four Bangladeshi individuals and their functional significance Khan, Salim Akter, Shahina Goswami, Barna Habib, Ahashan Banu, Tanjina Akhtar Barton, Carl Osman, Eshrar Samir, Samiruzzaman Arjuman, Farida Hasan, Saam Hossain, Maqsud BMC Res Notes Research Note OBJECTIVE: The major objective of the study was to sequence the whole genome of four Bangladeshi individuals and identify variants that are known to be associated with functional changes or disease states. We also carried out an ontology analysis to identify the functions and pathways most likely to be affected by these variants. RESULTS: We identified around 900,000 common variants and close to 5 million unique ones in all four of the individuals. This included over 11,500 variants that caused nonsynonymous changes in proteins. Heart function associated pathways were heavily implicated by the ontology analysis; corroborating previous studies that claimed the Bangladeshi population as highly susceptible to heart disorders. Two variants were found that have been previously identified as pathogenic factors in familial hypercholesteremia and structural disorders of the heart. Other pathogenic variants we found were associated with pseudoxanthoma elasticum, cancer progression, polyagglutinable erythrocyte syndrome, preeclampsia, and others. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13104-021-05514-x. BioMed Central 2021-03-20 /pmc/articles/PMC7981821/ /pubmed/33743798 http://dx.doi.org/10.1186/s13104-021-05514-x Text en © The Author(s) 2021 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Note Khan, Salim Akter, Shahina Goswami, Barna Habib, Ahashan Banu, Tanjina Akhtar Barton, Carl Osman, Eshrar Samir, Samiruzzaman Arjuman, Farida Hasan, Saam Hossain, Maqsud Whole genome mapping and identification of single nucleotide polymorphisms of four Bangladeshi individuals and their functional significance |
title | Whole genome mapping and identification of single nucleotide polymorphisms of four Bangladeshi individuals and their functional significance |
title_full | Whole genome mapping and identification of single nucleotide polymorphisms of four Bangladeshi individuals and their functional significance |
title_fullStr | Whole genome mapping and identification of single nucleotide polymorphisms of four Bangladeshi individuals and their functional significance |
title_full_unstemmed | Whole genome mapping and identification of single nucleotide polymorphisms of four Bangladeshi individuals and their functional significance |
title_short | Whole genome mapping and identification of single nucleotide polymorphisms of four Bangladeshi individuals and their functional significance |
title_sort | whole genome mapping and identification of single nucleotide polymorphisms of four bangladeshi individuals and their functional significance |
topic | Research Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7981821/ https://www.ncbi.nlm.nih.gov/pubmed/33743798 http://dx.doi.org/10.1186/s13104-021-05514-x |
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