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Individual Genome of the Russian Male: SNP Calling and a de novo Assembly of Unmapped Reads.

ABSTRACT: A somatic cell genome was recently resequenced for a patient with renal cancer. The data were submitted to the NCBI Sequence Read Archive under the accession number SRA012240. Here, we have performed SNP calling for the genome and compared it with several published genomes. We have found 2, 921, 724 SNPs, including 1, 472, 679 newly described ones. Among them, 63, 462 SNPs have been mapped to the Y chromosome and, based on 18 markers, the genome has been ascribed to the R1a1a haplogroup predominant in Russian males. The mitochondrial haplogroup has been determined as U5a, which is also common in the European part of Russia. Short reads unmapped to the human genome were used for thede novoassembly of DNA sequences. This resulted in genome-specific contigs (more than 100 bp in length) with an overall length of 154 kbp (for GAII) and 4.7 kbp (for SOLiD).

SUBMITTER: Chekanov NN

PROVIDER: S-EPMC3347568 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature

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Individual Genome of the Russian Male: SNP Calling and a de novo Assembly of Unmapped Reads.

Chekanov N N NN Boulygina E S ES Beletskiy A V AV Prokhortchouk E B EB Skryabin K G KG

Acta naturae 20100701 3

A somatic cell genome was recently resequenced for a patient with renal cancer. The data were submitted to the NCBI Sequence Read Archive under the accession number SRA012240. Here, we have performed SNP calling for the genome and compared it with several published genomes. We have found 2, 921, 724 SNPs, including 1, 472, 679 newly described ones. Among them, 63, 462 SNPs have been mapped to the Y chromosome and, based on 18 markers, the genome has been ascribed to the R1a1a haplogroup predomin ...[more]

PMID: 22649659

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