Abstract
BackgroundAs 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.MethodsThe 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.ResultsYDHS 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/ydhsConclusionsY-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.
Highlights
As the high throughput sequencing efforts generate more biological information, scientists from different disciplines are interpreting the polymorphisms that make us unique
Since there are altogether 3896 SNPs in the International Society of Genetic Genealogy (ISOGG) Y-chromosomal DNA (Y-DNA) tree (December 2013) and many more unsubstantiated ones, we decided to show the use of YDHS database using case examples
Mutations on the Y chromosome should be preserved in male offspring that these men do produce, it is unclear whether specific haplotypes are associated with such microdeletions
Summary
As the high throughput sequencing efforts generate more biological information, scientists from different disciplines are interpreting the polymorphisms that make us unique. There is an increasing trend in general public to research their own genealogy, find distant relatives and to know more about their biological background. 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. We introduce a novel metadatabase YDHS that aims to provide such an interface for Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants. The human Y chromosome has unique characteristics which make it the subject of intense research. It has been 10 years since the Y chromosome was initially sequenced in 2003. The uniparental inheritance of mutations results in different “at risk” haplotypes among different paternal lineages [1], which are frequently dependent on ethnicity and the
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