The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing
Open accessAbstract
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. Availability and implementation: MToolBox package is available at https://sourceforge.net/projects/mtoolbox/ . Contact: marcella.attimonelli@uniba.it Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA
Andrews, R. M., Kubacka, I., Chinnery, P. F., Lightowlers, R. N., Turnbull, D. M., & Howell, N. (1999) · Nature Genetics · doi:10.1038/13779 · Cited by 3,337
Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation
van Oven, M., & Kayser, M. (2009) · Human Mutation · doi:10.1002/humu.20921 · Cited by 1,810
Cited by
The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
Ricketts, C. J., De Cubas, A. A., Fan, H., Smith, C. C., Lang, M., Reznik, E., Bowlby, R., Gibb, E. A., Akbani, R., Beroukhim, R., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.06.032 · Cited by 734
Mitochondrial DNA variation and cancer
Kopinski, P. K., Singh, L. N., Zhang, S., Lott, M. T., & Wallace, D. C. (2021) · Nature reviews. Cancer · doi:10.1038/s41568-021-00358-w · Cited by 301
mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud
Weissensteiner, H., Forer, L., Fuchsberger, C., Schöpf, B., Kloss-Brandstätter, A., Specht, G., Kronenberg, F., & Schönherr, S. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw247 · Cited by 188
Cai, N., Gomez-Duran, A., Yonova-Doing, E., Kundu, K., Burgess, A. I., Golder, Z. J., Calabrese, C., Bonder, M. J., Camacho, M., Lawson, R. A., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01441-3 · Cited by 73
Self-citationCell reprogramming shapes the mitochondrial DNA landscape
Wei, W., Gaffney, D. J., & Chinnery, P. F. (2021) · Nature Communications · doi:10.1038/s41467-021-25482-x · Cited by 47
Metadata
- Authors
- Calabrese, C., Simone, D., Diroma, M. A., Santorsola, M., Guttà, C., Gasparre, G., Picardi, E., Pesole, G., & Attimonelli, M.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-07-14
- Volume
- 30
- Issue
- 21
- Pages
- 3115-3117
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2146112039
- Cited by
- 214
- References
- 3
- FWCI
- 5.23
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Calabrese, C., Simone, D., Diroma, M. A., Santorsola, M., Guttà, C., Gasparre, G., Picardi, E., Pesole, G., & Attimonelli, M. (2014). MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. Bioinformatics. https://doi.org/10.1093/bioinformatics/btu483
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