Finding protein-coding genes through human polymorphisms.

Human gene catalogs are fundamental to the study of human biology and medicine. But they are all based on open reading frames (ORFs) in a reference genome sequence (with allowance for introns). Individual genomes, however, are polymorphic: their sequences are not identical. There has been much resea...

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Autores principales:	Edward Wijaya, Martin C Frith, Paul Horton, Kiyoshi Asai
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4b1f2a6ea84748a9a08c9946ab04f715
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id	oai:doaj.org-article:4b1f2a6ea84748a9a08c9946ab04f715
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spelling	oai:doaj.org-article:4b1f2a6ea84748a9a08c9946ab04f7152021-11-18T08:00:38ZFinding protein-coding genes through human polymorphisms.1932-620310.1371/journal.pone.0054210https://doaj.org/article/4b1f2a6ea84748a9a08c9946ab04f7152013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23349826/?tool=EBIhttps://doaj.org/toc/1932-6203Human gene catalogs are fundamental to the study of human biology and medicine. But they are all based on open reading frames (ORFs) in a reference genome sequence (with allowance for introns). Individual genomes, however, are polymorphic: their sequences are not identical. There has been much research on how polymorphism affects previously-identified genes, but no research has been done on how it affects gene identification itself. We computationally predict protein-coding genes in a straightforward manner, by finding long ORFs in mRNA sequences aligned to the reference genome. We systematically test the effect of known polymorphisms with this procedure. Polymorphisms can not only disrupt ORFs, they can also create long ORFs that do not exist in the reference sequence. We found 5,737 putative protein-coding genes that do not exist in the reference, whose protein-coding status is supported by homology to known proteins. On average 10% of these genes are located in the genomic regions devoid of annotated genes in 12 other catalogs. Our statistical analysis showed that these ORFs are unlikely to occur by chance.Edward WijayaMartin C FrithPaul HortonKiyoshi AsaiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 1, p e54210 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Edward Wijaya Martin C Frith Paul Horton Kiyoshi Asai Finding protein-coding genes through human polymorphisms.
description	Human gene catalogs are fundamental to the study of human biology and medicine. But they are all based on open reading frames (ORFs) in a reference genome sequence (with allowance for introns). Individual genomes, however, are polymorphic: their sequences are not identical. There has been much research on how polymorphism affects previously-identified genes, but no research has been done on how it affects gene identification itself. We computationally predict protein-coding genes in a straightforward manner, by finding long ORFs in mRNA sequences aligned to the reference genome. We systematically test the effect of known polymorphisms with this procedure. Polymorphisms can not only disrupt ORFs, they can also create long ORFs that do not exist in the reference sequence. We found 5,737 putative protein-coding genes that do not exist in the reference, whose protein-coding status is supported by homology to known proteins. On average 10% of these genes are located in the genomic regions devoid of annotated genes in 12 other catalogs. Our statistical analysis showed that these ORFs are unlikely to occur by chance.
format	article
author	Edward Wijaya Martin C Frith Paul Horton Kiyoshi Asai
author_facet	Edward Wijaya Martin C Frith Paul Horton Kiyoshi Asai
author_sort	Edward Wijaya
title	Finding protein-coding genes through human polymorphisms.
title_short	Finding protein-coding genes through human polymorphisms.
title_full	Finding protein-coding genes through human polymorphisms.
title_fullStr	Finding protein-coding genes through human polymorphisms.
title_full_unstemmed	Finding protein-coding genes through human polymorphisms.
title_sort	finding protein-coding genes through human polymorphisms.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/4b1f2a6ea84748a9a08c9946ab04f715
work_keys_str_mv	AT edwardwijaya findingproteincodinggenesthroughhumanpolymorphisms AT martincfrith findingproteincodinggenesthroughhumanpolymorphisms AT paulhorton findingproteincodinggenesthroughhumanpolymorphisms AT kiyoshiasai findingproteincodinggenesthroughhumanpolymorphisms
_version_	1718422662250758144

Finding protein-coding genes through human polymorphisms.

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