MitoVariome: a variome database of human mitochondrial DNA

Lee, Yong Seok; Kim, Woo-Yeon; Ji, Mihyun; Kim, Ji Han; Bhak, Jong

doi:10.1186/1471-2164-10-s3-s12

Cited by 12 publications

(7 citation statements)

References 14 publications

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“…MitoVariome is another database application that provides limited query functionalities to determine haplogroups using mutation motifs [Lee et al, 2009]. Unfortunately, it is only possible to classify one sample at a time and the classification process takes about 30 sec for a single sample.…”

Section: Resultsmentioning

confidence: 99%

HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups

et al. 2010

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An ongoing source of controversy in mitochondrial DNA (mtDNA) research is based on the detection of numerous errors in mtDNA profiles that led to erroneous conclusions and false disease associations. Most of these controversies could be avoided if the samples' haplogroup status would be taken into consideration. Knowing the mtDNA haplogroup affiliation is a critical prerequisite for studying mechanisms of human evolution and discovering genes involved in complex diseases, and validating phylogenetic consistency using haplogroup classification is an important step in quality control. However, despite the availability of Phylotree, a regularly updated classification tree of global mtDNA variation, the process of haplogroup classification is still time-consuming and error-prone, as researchers have to manually compare the polymorphisms found in a population sample to those summarized in Phylotree, polymorphism by polymorphism, sample by sample. We present HaploGrep, a fast, reliable and straight-forward algorithm implemented in a Web application to determine the haplogroup affiliation of thousands of mtDNA profiles genotyped for the entire mtDNA or any part of it. HaploGrep uses the latest version of Phylotree and offers an all-in-one solution for quality assessment of mtDNA profiles in clinical genetics, population genetics and forensics. HaploGrep can be accessed freely at http:// haplogrep.uibk.ac.at.

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Section: Resultsmentioning

confidence: 99%

HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups

et al. 2010

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“…Furthermore, there appears to be a class of slightly deleterious mutations that modify the risks of developing certain complex diseases or traits [14]. Besides, heteroplasmic and homoplasmic mtDNA have also been observed along with large number of basal polymorphisms in the mitochondrial genome across databases like OMIM [http://www.ncbi.nlm.nih.gov/omim] [15], MitoMap [16], Mitovariome [17]and mtDB [18]. These facts highlight the challenges in assessing the role of mtDNA variants in diseases or phenotypes.…”

Section: Introductionmentioning

confidence: 99%

MitoLSDB: A Comprehensive Resource to Study Genotype to Phenotype Correlations in Human Mitochondrial DNA Variations

et al. 2013

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Human mitochondrial DNA (mtDNA) encodes a set of 37 genes which are essential structural and functional components of the electron transport chain. Variations in these genes have been implicated in a broad spectrum of diseases and are extensively reported in literature and various databases. In this study, we describe MitoLSDB, an integrated platform to catalogue disease association studies on mtDNA (http://mitolsdb.igib.res.in). The main goal of MitoLSDB is to provide a central platform for direct submissions of novel variants that can be curated by the Mitochondrial Research Community. MitoLSDB provides access to standardized and annotated data from literature and databases encompassing information from 5231 individuals, 675 populations and 27 phenotypes. This platform is developed using the Leiden Open (source) Variation Database (LOVD) software. MitoLSDB houses information on all 37 genes in each population amounting to 132397 variants, 5147 unique variants. For each variant its genomic location as per the Revised Cambridge Reference Sequence, codon and amino acid change for variations in protein-coding regions, frequency, disease/phenotype, population, reference and remarks are also listed. MitoLSDB curators have also reported errors documented in literature which includes 94 phantom mutations, 10 NUMTs, six documentation errors and one artefactual recombination. MitoLSDB is the largest repository of mtDNA variants systematically standardized and presented using the LOVD platform. We believe that this is a good starting resource to curate mtDNA variants and will facilitate direct submissions enhancing data coverage, annotation in context of pathogenesis and quality control by ensuring non-redundancy in reporting novel disease associated variants.

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“…A total of 57 SNVs were found in the Pathan mitochondrial genome, 13 of which had not been previously reported. The variants were then mapped with MitoVariome [ 46 ] to identify the mitochondrial haplogroup of our Pathan individual. A total of 14 SNVs were diagnostic of the H2 haplogroup (Additional file 10 : Table S9), which has been argued to be of exclusive Caucasian origin, and its marginal occurrence in Pathans reflects admixture [ 47 ].…”

Section: Resultsmentioning

confidence: 99%

Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan

et al. 2015

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BackgroundPakistan covers a key geographic area in human history, being both part of the Indus River region that acted as one of the cradles of civilization and as a link between Western Eurasia and Eastern Asia. This region is inhabited by a number of distinct ethnic groups, the largest being the Punjabi, Pathan (Pakhtuns), Sindhi, and Baloch.ResultsWe analyzed the first ethnic male Pathan genome by sequencing it to 29.7-fold coverage using the Illumina HiSeq2000 platform. A total of 3.8 million single nucleotide variations (SNVs) and 0.5 million small indels were identified by comparing with the human reference genome. Among the SNVs, 129,441 were novel, and 10,315 nonsynonymous SNVs were found in 5,344 genes. SNVs were annotated for health consequences and high risk diseases, as well as possible influences on drug efficacy. We confirmed that the Pathan genome presented here is representative of this ethnic group by comparing it to a panel of Central Asians from the HGDP-CEPH panels typed for ~650 k SNPs. The mtDNA (H2) and Y haplogroup (L1) of this individual were also typical of his geographic region of origin. Finally, we reconstruct the demographic history by PSMC, which highlights a recent increase in effective population size compatible with admixture between European and Asian lineages expected in this geographic region.ConclusionsWe present a whole-genome sequence and analyses of an ethnic Pathan from the north-west province of Pakistan. It is a useful resource to understand genetic variation and human migration across the whole Asian continent.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1290-1) contains supplementary material, which is available to authorized users.

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MitoVariome: a variome database of human mitochondrial DNA

Cited by 12 publications

References 14 publications

HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups

HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups

MitoLSDB: A Comprehensive Resource to Study Genotype to Phenotype Correlations in Human Mitochondrial DNA Variations

Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan

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