MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing

被引：162

作者：

Calabrese, Claudia ^{[1
]}

Simone, Domenico ^{[2
]}

Diroma, Maria Angela ^{[3
]}

Santorsola, Mariangela ^{[4
]}

Gutta, Cristiano ^{[3
]}

Gasparre, Giuseppe

Picardi, Ernesto ^{[1
,3
,5
,6
]}

Pesole, Graziano ^{[3
,5
,7
]}

Attimonelli, Marcella ^{[3
]}

机构：

[1] Univ Bologna, Dept Med & Surg Sci, I-40138 Bologna, Italy

[2] Univ Milan, Dept Biosci, I-20133 Milan, Italy

[3] Univ Bari, Dept Biosci Biotechnol & Biopharmaceut, I-70126 Bari, Italy

[4] Univ Sannio, Dept Sci & Technol, Benevento 82100, BN, Italy

[5] CNR, Inst Biomembranes & Bioenerget, I-70126 Bari, Italy

[6] Natl Inst Biostruct & Biosyst, I-00136 Rome, Italy

[7] Univ Bari, CEGBA, I-70126 Bari, Italy

来源：

BIOINFORMATICS | 2014年 / 30卷 / 21期

关键词：

GENOMES; TREE;

D O I：

10.1093/bioinformatics/btu483

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

Motivation: The increasing availability of mitochondria-targeted and off-target sequencing data in whole-exome and whole-genome sequencing studies (WXS and WGS) has risen the demand of effective pipelines to accurately measure heteroplasmy and to easily recognize the most functionally important mitochondrial variants among a huge number of candidates. To this purpose, we developed MToolBox, a highly automated pipeline to reconstruct and analyze human mitochondrial DNA from high-throughput sequencing data. Results: MToolBox implements an effective computational strategy for mitochondrial genomes assembling and haplogroup assignment also including a prioritization analysis of detected variants. MToolBox provides a Variant Call Format file featuring, for the first time, allele-specific heteroplasmy and annotation files with prioritized variants. MToolBox was tested on simulated samples and applied on 1000 Genomes WXS datasets.

引用

页码：3115 / 3117

页数：3

共 13 条

[1]

An integrated map of genetic variation from 1,092 human genomes [J].

Altshuler, David M. ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Donnelly, Peter ;

Eichler, Evan E. ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Green, Eric D. ;

Hurles, Matthew E. ;

Knoppers, Bartha M. ;

Korbel, Jan O. ;

Lander, Eric S. ;

Lee, Charles ;

Lehrach, Hans ;

Mardis, Elaine R. ;

Marth, Gabor T. ;

McVean, Gil A. ;

Nickerson, Deborah A. ;

Schmidt, Jeanette P. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Dinh, Huyen ;

Kovar, Christie ;

Lee, Sandra ;

Lewis, Lora ;

Muzny, Donna ;

Reid, Jeff ;

Wang, Min ;

Wang, Jun ;

Fang, Xiaodong ;

Guo, Xiaosen ;

Jian, Min ;

Jiang, Hui ;

Jin, Xin ;

Li, Guoqing ;

Li, Jingxiang ;

Li, Yingrui ;

Li, Zhuo ;

Liu, Xiao ;

Lu, Yao ;

Ma, Xuedi ;

Su, Zhe ;

Tai, Shuaishuai ;

Tang, Meifang .

NATURE, 2012, 491 (7422) :56-65

[2]

Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA [J].

Andrews, RM ;

Kubacka, I ;

Chinnery, PF ;

Lightowlers, RN ;

Turnbull, DM ;

Howell, N .

NATURE GENETICS, 1999, 23 (02) :147-147

[3]

The case for the continuing use of the revised Cambridge Reference Sequence (rCRS) and the standardization of notation in human mitochondrial DNA studies [J].

Bandelt, Hans-Juergen ;

Kloss-Brandstaetter, Anita ;

Richards, Martin B. ;

Yao, Yong-Gang ;

Logan, Ian .

JOURNAL OF HUMAN GENETICS, 2014, 59 (02) :66-77

[4]

A "Copernican" Reassessment of the Human Mitochondrial DNA Tree from its Root [J].

Behar, Doron M. ;

van Oven, Mannis ;

Rosset, Saharon ;

Metspalu, Malt ;

Loogvali, Eva-Liis ;

Silva, Nuno M. ;

Kivisild, Toomas ;

Torroni, Antonio ;

Villems, Richard .

AMERICAN JOURNAL OF HUMAN GENETICS, 2012, 90 (04) :675-684

[5]

Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data [J].

Diroma, Maria Angela ;

Calabrese, Claudia ;

Simone, Domenico ;

Santorsola, Mariangela ;

Calabrese, Francesco Maria ;

Gasparre, Giuseppe ;

Attimonelli, Marcella .

BMC GENOMICS, 2014, 15

[6]

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis [J].

Guo, Yan ;

Li, Jiang ;

Li, Chung-I ;

Shyr, Yu ;

Samuels, David C. .

BIOINFORMATICS, 2013, 29 (09) :1210-1211

[7]

Heteroplasmic mitochondrial DNA mutations in normal and tumour cells [J].

He, Yiping ;

Wu, Jian ;

Dressman, Devin C. ;

Iacobuzio-Donahue, Christine ;

Markowitz, Sanford D. ;

Velculescu, Victor E. ;

Diaz, Luis A., Jr. ;

Kinzler, Kenneth W. ;

Vogelstein, Bert ;

Papadopoulos, Nickolas .

NATURE, 2010, 464 (7288) :610-U175

[8]

Universal heteroplasmy of human mitochondrial DNA [J].

Payne, Brendan A. I. ;

Wilson, Ian J. ;

Yu-Wai-Man, Patrick ;

Coxhead, Jonathan ;

Deehan, David ;

Horvath, Rita ;

Taylor, Robert W. ;

Samuels, David C. ;

Santibanez-Koref, Mauro ;

Chinnery, Patrick F. .

HUMAN MOLECULAR GENETICS, 2013, 22 (02) :384-390

[9]

Mitochondrial genomes gleaned from human whole-exome sequencing [J].

Picardi, Ernesto ;

Pesole, Graziano .

NATURE METHODS, 2012, 9 (06) :523-524

[10]

HmtDB, a genomic resource for mitochondrion-based human variability studies [J].

Rubino, Francesco ;

Piredda, Roberta ;

Calabrese, Francesco Maria ;

Simone, Domenico ;

Lang, Martin ;

Calabrese, Claudia ;

Petruzzella, Vittoria ;

Tommaseo-Ponzetta, Mila ;

Gasparre, Giuseppe ;

Attimonelli, Marcella .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D1150-D1159

← 1 2 →