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Human Chromosome Y and Haplogroups; introducing YDHS Database

BACKGROUND: As the high throughput sequencing efforts generate more biological information, scientists from different disciplines are interpreting the polymorphisms that make us unique. In addition, there is an increasing trend in general public to research their own genealogy, find distant relative...

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Autores principales: Tiirikka, Timo, Moilanen, Jukka S
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477006/
https://www.ncbi.nlm.nih.gov/pubmed/26061870
http://dx.doi.org/10.1186/s40169-015-0060-7
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author Tiirikka, Timo
Moilanen, Jukka S
author_facet Tiirikka, Timo
Moilanen, Jukka S
author_sort Tiirikka, Timo
collection PubMed
description BACKGROUND: As the high throughput sequencing efforts generate more biological information, scientists from different disciplines are interpreting the polymorphisms that make us unique. In addition, there is an increasing trend in general public to research their own genealogy, find distant relatives and to know more about their biological background. Commercial vendors are providing analyses of mitochondrial and Y-chromosomal markers for such purposes. Clearly, an easy-to-use free interface to the existing data on the identified variants would be in the interest of general public and professionals less familiar with the field. Here we introduce a novel metadatabase YDHS that aims to provide such an interface for Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants. METHODS: The database uses ISOGG Y-DNA tree as the source of mutations and haplogroups and by using genomic positions of the mutations the database links them to genes and other biological entities. YDHS contains analysis tools for deeper Y-SNP analysis. RESULTS: YDHS addresses the shortage of Y-DNA related databases. We have tested our database using a set of different cases from literature ranging from infertility to autism. The database is at http://www.semanticgen.net/ydhs CONCLUSIONS: Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants have not been in the scientific limelight, excluding certain specialized fields like forensics, mainly because there is not much freely available information or it is scattered in different sources. However, as we have demonstrated Y-SNPs do play a role in various cases on the haplogroup level and it is possible to create a free Y-DNA dedicated bioinformatics resource.
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spelling pubmed-44770062015-06-26 Human Chromosome Y and Haplogroups; introducing YDHS Database Tiirikka, Timo Moilanen, Jukka S Clin Transl Med Research BACKGROUND: As the high throughput sequencing efforts generate more biological information, scientists from different disciplines are interpreting the polymorphisms that make us unique. In addition, there is an increasing trend in general public to research their own genealogy, find distant relatives and to know more about their biological background. Commercial vendors are providing analyses of mitochondrial and Y-chromosomal markers for such purposes. Clearly, an easy-to-use free interface to the existing data on the identified variants would be in the interest of general public and professionals less familiar with the field. Here we introduce a novel metadatabase YDHS that aims to provide such an interface for Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants. METHODS: The database uses ISOGG Y-DNA tree as the source of mutations and haplogroups and by using genomic positions of the mutations the database links them to genes and other biological entities. YDHS contains analysis tools for deeper Y-SNP analysis. RESULTS: YDHS addresses the shortage of Y-DNA related databases. We have tested our database using a set of different cases from literature ranging from infertility to autism. The database is at http://www.semanticgen.net/ydhs CONCLUSIONS: Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants have not been in the scientific limelight, excluding certain specialized fields like forensics, mainly because there is not much freely available information or it is scattered in different sources. However, as we have demonstrated Y-SNPs do play a role in various cases on the haplogroup level and it is possible to create a free Y-DNA dedicated bioinformatics resource. Springer Berlin Heidelberg 2015-06-10 /pmc/articles/PMC4477006/ /pubmed/26061870 http://dx.doi.org/10.1186/s40169-015-0060-7 Text en © Tiirikka and Moilanen. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
spellingShingle Research
Tiirikka, Timo
Moilanen, Jukka S
Human Chromosome Y and Haplogroups; introducing YDHS Database
title Human Chromosome Y and Haplogroups; introducing YDHS Database
title_full Human Chromosome Y and Haplogroups; introducing YDHS Database
title_fullStr Human Chromosome Y and Haplogroups; introducing YDHS Database
title_full_unstemmed Human Chromosome Y and Haplogroups; introducing YDHS Database
title_short Human Chromosome Y and Haplogroups; introducing YDHS Database
title_sort human chromosome y and haplogroups; introducing ydhs database
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477006/
https://www.ncbi.nlm.nih.gov/pubmed/26061870
http://dx.doi.org/10.1186/s40169-015-0060-7
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