The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser

BMC Genomics

Research Article

Domenico Simone¹  Marcella Attimonelli¹  Francesco Maria Calabrese¹  Giuseppe Gasparre²  Martin Lang³ 

[1] Dipartimento di Biochimica e Biologia Molecolare 'E. Quagliariello', Università di Bari, 70126, Bari, Italy;Dipartimento di Biochimica e Biologia Molecolare 'E. Quagliariello', Università di Bari, 70126, Bari, Italy;Dipartimento di Scienze Ginecologiche, Ostetriche e Pediatriche, U.O. Genetica Medica, Università di Bologna, 40138, Bologna, Italy;Dipartimento di Scienze Ginecologiche, Ostetriche e Pediatriche, U.O. Genetica Medica, Università di Bologna, 40138, Bologna, Italy;

关键词: Mitochondrial Genome;    Nuclear Genome;    UCSC Genome Browser;    CYTB Gene;    HapMap Sample;   

DOI  :  10.1186/1471-2164-12-517

 received in 2011-04-13, accepted in 2011-10-20,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundEukaryotic nuclear genomes contain fragments of mitochondrial DNA called NumtS (Nuclear mitochondrial Sequences), whose mode and time of insertion, as well as their functional/structural role within the genome are debated issues. Insertion sites match with chromosomal breaks, revealing that micro-deletions usually occurring at non-homologous end joining loci become reduced in presence of NumtS. Some NumtS are involved in recombination events leading to fragment duplication. Moreover, NumtS are polymorphic, a feature that renders them candidates as population markers. Finally, they are a cause of contamination during human mtDNA sequencing, leading to the generation of false heteroplasmies.ResultsHere we present RHNumtS.2, the most exhaustive human NumtSome catalogue annotating 585 NumtS, 97% of which were here validated in a European individual and in HapMap samples. The NumtS complete dataset and related features have been made available at the UCSC Genome Browser. The produced sequences have been submitted to INSDC databases. The implementation of the RHNumtS.2 tracks within the UCSC Genome Browser has been carried out with the aim to facilitate browsing of the NumtS tracks to be exploited in a wide range of research applications.ConclusionsWe aimed at providing the scientific community with the most exhaustive overview on the human NumtSome, a resource whose aim is to support several research applications, such as studies concerning human structural variation, diversity, and disease, as well as the detection of false heteroplasmic mtDNA variants. Upon implementation of the NumtS tracks, the application of the BLAT program on the UCSC Genome Browser has now become an additional tool to check for heteroplasmic artefacts, supported by data available through the NumtS tracks.

【 授权许可】

Unknown   
© Simone et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.