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

Bioinformatics

Volumn 30, Issue 21, 2014, Pages 3115-3117

  Calabrese, Claudia ^a   Simone, Domenico ^b   Diroma, Maria Angela ^c   Santorsola, Mariangela ^d   Gutta, Cristiano ^c   Gasparre, Giuseppe ^a   Picardi, Ernesto ^c,e,f   Pesole, Graziano ^c,e   Attimonelli, Marcella ^c  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b UNIVERSITY OF MILAN   (Italy)

^c UNIVERSITY OF BARI   (Italy)

^d UNIVERSITY OF SANNIO   (Italy)

^e CNR   (Italy)

^f NATIONAL INSTITUTE OF BIOSTRUCTURES AND BIOSYSTEMS   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

CHEMISTRY; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; MITOCHONDRIAL GENOME; MOLECULAR GENETICS; PROCEDURES;

DNA, MITOCHONDRIAL; GENETIC VARIATION; GENOME, MITOCHONDRIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84911428521     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu483     Document Type: Article

References (13)

1. Andrews, R.M. et al. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet., 23, 147.
2. Bandelt, H.J. et al. (2014) The case of the continuing use of the revised Cambridge Reference Sequence (rCRS) and the standardization of notation in human mitochondrial DNA studies. J. Hum. Genet., 59, 66-77.
3. Behar, D.M. et al. (2012) A "Copernican" reassessment of the human mitochondrial DNA tree from its root. Am. J. Hum. Genet., 90, 675-684.
4. Diroma, M.A. et al. (2014) Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data. BMC Genomics., 15 (Suppl. 3), S2.
5. Genomes Project, C. et al. (2012) An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65.
6. Guo, Y. et al. (2013) MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis. Bioinformatics, 29, 1210-1211.
7. He, Y. et al. (2010) Heteroplasmic mitochondrial DNA mutations in normal and tumour cells. Nature, 464, 610-614.
8. Payne, B.A. et al. (2013) Universal heteroplasmy of human mitochondrial DNA. Hum. Mol. Genet., 22, 384-390.
9. Picardi, E. and Pesole, G. (2012) Mitochondrial genomes gleaned from human whole-exome sequencing. Nat. Methods., 9, 523-524.
10. Rubino, F. et al. (2012) HmtDB, a genomic resource for mitochondrion-based human variability studies. Nucleic Acids Res., 40, D1150-D1159.
11. Ruiz-Pesini, E. et al. (2007) An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res., 35, D823-D828.
12. Simone, D. et al. (2011) The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics, 12, 517.
13. van Oven, M. and Kayser, M. (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum. Mutat., 30, E386-E394.