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Mitochondrial genomes gleaned from human whole-exome sequencing

Nature Methods volume 9, pages 523–524 (2012)Cite this article

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To the Editor:

Whole-exome sequencing (WES) is a cost-effective technology to explore variation in protein-coding genes. More than 30,000 WES data submissions have been made to the Sequence Read Archive (SRA) database in the last two years. Current library preparation platforms that enrich for DNA coding sequence show different capture efficiencies and yield variable numbers of off-target sequences. Here we demonstrate that off-target data from human WES can be used to assemble mitochondrial genomes—a precious source of information for many genomics and functional investigations. Although we were unable to identify specific probes for any human mitochondrial protein-coding gene in three commonly used, commercially available WES platforms (Supplementary Note), we devised an effective computational strategy for assembling complete mitochondrial genomes from off-target WES reads (Supplementary Fig.1, Supplementary Methods and Supplementary Software).

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Figure 1: Mitochondrial genomes assembled from whole-exome sequence data generated from peripheral blood of a human individual (SRA study SRP007499) using Illumina TruSeq, Agilent SureSelect and NimbleGen (Roche) SeqCap EZ-Exome platforms at a minimum one-fold-per-base coverage.

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Acknowledgements

This work was supported by the Ministero dell'Istruzione, Università e Ricerca (Italy): Laboratorio Internazionale di Bioinformatica, Laboratorio di Bioinformatica per la Biodiversità Molecolare (Project DM19410), PRIN2009, VIRTUALAB (PON01_01297), MICROMAP (PON01_02589); Consiglio Nazionale delle Ricerche (Italy): Invecchiamento: innovazioni tecnologiche e molecolari per un miglioramento della salute dell'anziano; and Center of Excellence in Comparative Genomics (Italy). We thank D.S. Horner, M. Chiara, M. Attimonelli and P. Cantatore for helpful discussions on the manuscript.

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Authors and Affiliations

  1. Dipartimento di Bioscienze, Biotecnologie e Scienze Farmacologiche, Università di Bari, Bari, Italy

    Ernesto Picardi & Graziano Pesole

  2. Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy

    Ernesto Picardi & Graziano Pesole

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  1. Ernesto Picardi
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  2. Graziano Pesole
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Correspondence to Graziano Pesole.

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Supplementary information

Supplementary Text and Figures

Supplementary Figure 1, Supplementary Tables 2 and 3, Supplementary Note and Supplementary Methods (PDF 529 kb)

Supplementary Table

Supplementary Table 1 (XLSX 18 kb)

Supplementary Software

Supplementary Software (ZIP 22 kb)

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Picardi, E., Pesole, G. Mitochondrial genomes gleaned from human whole-exome sequencing. Nat Methods 9, 523–524 (2012). https://doi.org/10.1038/nmeth.2029

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