Human Mutation

Volume 34, Issue 9 p. 1189-1194

Informatic

HAPLOFIND: A New Method for High-Throughput mtDNA Haplogroup Assignment

Dario Vianello,

Corresponding Author

Dario Vianello

Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, 40126 Italy

C.I.G. – Interdepartmental Centre L. Galvani, University of Bologna, Bologna, 40126 Italy

Correspondence to: Dario Vianello, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna (BO), Italy. E-mail [email protected]Search for more papers by this author

Federica Sevini,

Federica Sevini

Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, 40126 Italy

C.I.G. – Interdepartmental Centre L. Galvani, University of Bologna, Bologna, 40126 Italy

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Gastone Castellani,

Gastone Castellani

C.I.G. – Interdepartmental Centre L. Galvani, University of Bologna, Bologna, 40126 Italy

Department of Physics, University of Bologna, Bologna, 40126 Italy

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Laura Lomartire,

Laura Lomartire

Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, 40126 Italy

C.I.G. – Interdepartmental Centre L. Galvani, University of Bologna, Bologna, 40126 Italy

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Miriam Capri,

Miriam Capri

Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, 40126 Italy

C.I.G. – Interdepartmental Centre L. Galvani, University of Bologna, Bologna, 40126 Italy

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Claudio Franceschi,

Claudio Franceschi

Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, 40126 Italy

C.I.G. – Interdepartmental Centre L. Galvani, University of Bologna, Bologna, 40126 Italy

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Dario Vianello,

Corresponding Author

Dario Vianello

Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, 40126 Italy

C.I.G. – Interdepartmental Centre L. Galvani, University of Bologna, Bologna, 40126 Italy

Correspondence to: Dario Vianello, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna (BO), Italy. E-mail [email protected]Search for more papers by this author

Federica Sevini,

Federica Sevini

Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, 40126 Italy

C.I.G. – Interdepartmental Centre L. Galvani, University of Bologna, Bologna, 40126 Italy

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Gastone Castellani,

Gastone Castellani

C.I.G. – Interdepartmental Centre L. Galvani, University of Bologna, Bologna, 40126 Italy

Department of Physics, University of Bologna, Bologna, 40126 Italy

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Laura Lomartire,

Laura Lomartire

Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, 40126 Italy

C.I.G. – Interdepartmental Centre L. Galvani, University of Bologna, Bologna, 40126 Italy

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Miriam Capri,

Miriam Capri

Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, 40126 Italy

C.I.G. – Interdepartmental Centre L. Galvani, University of Bologna, Bologna, 40126 Italy

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Claudio Franceschi,

Claudio Franceschi

Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, 40126 Italy

C.I.G. – Interdepartmental Centre L. Galvani, University of Bologna, Bologna, 40126 Italy

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First published: 20 May 2013

https://doi.org/10.1002/humu.22356

Citations: 113

Communicated by A. Jamie Cuticchia

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ABSTRACT

Deep sequencing technologies are completely revolutionizing the approach to DNA analysis. Mitochondrial DNA (mtDNA) studies entered in the “postgenomic era”: the burst in sequenced samples observed in nuclear genomics is expected also in mitochondria, a trend that can already be detected checking complete mtDNA sequences database submission rate. Tools for the analysis of these data are available, but they fail in throughput or in easiness of use. We present here a new pipeline based on previous algorithms, inherited from the “nuclear genomic toolbox,” combined with a newly developed algorithm capable of efficiently and easily classify new mtDNA sequences according to PhyloTree nomenclature. Detected mutations are also annotated using data collected from publicly available databases. Thanks to the analysis of all freely available sequences with known haplogroup obtained from GenBank, we were able to produce a PhyloTree-based weighted tree, taking into account each haplogroup pattern conservation. The combination of a highly efficient aligner, coupled with our algorithm and massive usage of asynchronous parallel processing, allowed us to build a high-throughput pipeline for the analysis of mtDNA sequences that can be quickly updated to follow the ever-changing nomenclature. HaploFind is freely accessible at the following Web address: https://haplofind.unibo.it.

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