title: Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data.
abstract: BACKGROUND
  Whole Exome Sequencing (WES) is one of the most used and cost-effective next generation technologies that allows sequencing of all nuclear exons. Off-target regions may be captured if they present high sequence similarity with baits. Bioinformatics tools have been optimized to retrieve a large amount of WES off-target mitochondrial DNA (mtDNA), by exploiting the aspecificity of probes, partially overlapping to Nuclear mitochondrial Sequences (NumtS). The 1000 Genomes project represents one of the widest resources to extract mtDNA sequences from WES data, considering the large effort the scientific community is undertaking to reconstruct human population history using mtDNA as marker, and the involvement of mtDNA in pathology.
  
  
  RESULTS
  A previously published pipeline aimed at assembling mitochondrial genomes from off-target WES reads and further improved to detect insertions and deletions (indels) and heteroplasmy in a dataset of 1242 samples from the 1000 Genomes project, enabled to obtain a nearly complete mitochondrial genome from 943 samples (76% analyzed exomes). The robustness of our computational strategy was highlighted by the reduction of reads amount recognized as mitochondrial in the original annotation produced by the Consortium, due to NumtS filtering.
  
  
  CONCLUSIONS
  To the best of our knowledge, this is likely the most extended population-scale mitochondrial genotyping in humans enriched with the estimation of heteroplasmies.
authors: Maria Angela
authors: MA
authors: Diroma
authors: Claudia
authors: C
authors: Calabrese
authors: Domenico
authors: D
authors: Simone
authors: Mariangela
authors: M
authors: Santorsola
authors: Francesco Maria
authors: FM
authors: Calabrese
authors: Giuseppe
authors: G
authors: Gasparre
authors: Marcella
authors: M
authors: Attimonelli
mesh_terms: D002460:Cell Line; D002874:Chromosome Mapping; D016000:Cluster Analysis; D019295:Computational Biology; D066264:Datasets as Topic; D059472:Exome; D005260:Female; D005787:Gene Frequency; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D023281:Genomics; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D008297:Male; D058977:Molecular Sequence Annotation; D044382:Population Groups / Q000235:genetics; D015203:Reproducibility of Results