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MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis
2013
Computer applications in the biosciences : CABIOS
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Results: MitoSeek is an open-source software tool that can reliably and easily extract mitochondrial genome information from exome and whole genome sequencing data. ...
These unintentionally sequenced mitochondrial reads provide unique opportunities to study the mitochondria genome. ...
, MitoSeek can extract mitochondrial genome information directly from a BAM file and also perform mitochondrial genome assembly. ...
doi:10.1093/bioinformatics/btt118
pmid:23471301
pmcid:PMC4492415
fatcat:2t3a4voyszeqnnqmpne6ddsr4a
MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing
2014
Computer applications in the biosciences : CABIOS
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To this purpose we developed MToolBox, a highly automated pipeline to reconstruct and analyze human mitochondrial DNA from high-throughput sequencing data. ...
Motivation: The increasing availability of mitochondria-targeted and off-targeted sequencing data in Whole Exome and Genome Sequencing studies (WXS and WGS) has risen the demand of effective pipelines ...
DISCUSSION A highly automated pipeline for mtDNA analysis from high throughput sequencing data is not available to date. ...
doi:10.1093/bioinformatics/btu483
pmid:25028726
pmcid:PMC4201154
fatcat:zaukpoou6rekpd3yjrlmmhvfm4
Mitochondria single nucleotide variation across six blood cell types
2016
Mitochondrion (Amsterdam. Print)
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Motivated by this question and using mitochondria sequences extracted from RNAseq data from six distinct blood cell types (neutrophil, monocyte, myeloid dendritic, natural killer, T and B), we thoroughly ...
Each cell type from each subject was sequenced at four time points used as biological replicates. We found that mitochondria content is low in neutrophil compared to the other five blood cell types. ...
The abundance of mitochondria in the cell insures the indirect sequencing of mtDNAin high throughput sequencing data. ...
doi:10.1016/j.mito.2016.03.001
pmid:26956645
pmcid:PMC5755964
fatcat:cb36yvzrqfbg7iurank2olpjry
High-throughput sequencing in mitochondrial DNA research
2014
Mitochondrion (Amsterdam. Print)
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To this end, we review how high-throughput sequencing has impacted mitochondrial research in the categories of SNPs, low level heteroplasmy, copy number, and structural variants. ...
Next-generation sequencing, also known as high-throughput sequencing, has greatly enhanced researchers' ability to conduct biomedical research on all levels. ...
Yan Guo, and ...
doi:10.1016/j.mito.2014.05.004
pmid:24859348
pmcid:PMC4149223
fatcat:oyygad2lz5bwja5pusosojftbq
MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing
2017
PeerJ
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To address this limitation, we developed MitoSuite, a user-friendly graphical tool for analysis of data from high-throughput sequencing of the human mitochondrial genome. ...
Recent rapid advances in high-throughput, next-generation sequencing (NGS) technologies have promoted mitochondrial genome studies in the fields of human evolution, medical genetics, and forensic casework ...
ACKNOWLEDGEMENTS The discussions with and cooperation of our lab members have greatly contributed to improving this tool. ...
doi:10.7717/peerj.3406
pmid:28584729
pmcid:PMC5452969
fatcat:atljcijldfhuvbvgicsrd7ha7e
Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data
2015
Briefings in Bioinformatics
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The rapid progress in high-throughput sequencing has significantly enriched our capacity for studying the mitochondrial DNA (mtDNA). ...
produced the best results, and that aligning to the nuclear genome first and afterwards to the mitochondrial genome performed poorly. ...
for Clinical and Translational Research (VR7875 towards sequencing of the two total RNA library samples). ...
doi:10.1093/bib/bbv057
pmid:26249222
pmcid:PMC5974936
fatcat:pwzfbvlw2vdebclt7btbywu4f4
Very Low-Level Heteroplasmy mtDNA Variations Are Inherited in Humans
2013
Journal of Genetics and Genomics
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In this study, we sequenced the mitochondrial genome of 44 individuals using Illumina highthroughput sequencing technology and obtained high-coverage mitochondria sequencing data. ...
Little is known about the inheritance of very low heteroplasmy mitochondria DNA variations. ...
We would also like to thank Peggy Schuyler and Margot Bjoring for their editing support. ...
doi:10.1016/j.jgg.2013.10.003
pmid:24377867
pmcid:PMC4149221
fatcat:xnx2idhnnfazxp7by5ve4sxgsq
Comprehensive mitochondrial DNA analysis and IVF outcome
2018
Human Reproduction Open
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A limitation may be the size of the sample and the high-throughput sequencing technology that might not have detected heteroplasmy levels below 2% which requires high sequence depth A clinical randomized ...
Sequencing reads mapping to the mtDNA genome were extracted from indexed bam files to identify copy number and heteroplasmy. ...
PARTICIPANTS/MATERIALS, SETTING, METHODS: Sequencing reads mapping to the mtDNA genome were extracted from indexed bam files to identify copy number and heteroplasmy. ...
doi:10.1093/hropen/hoy023
pmid:30895263
pmcid:PMC6396640
fatcat:e2d4gndykfbrvbi2ayj6tkfuha
Advancement in the diagnosis of mitochondrial diseases
2020
Journal of Translational Genetics and Genomics
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Here, in this review, we discuss these challenges and problems in mitochondrial disease diagnosis, focusing on the mutational profile of both primary and secondary mitochondrial diseases. ...
We also review the utilization of next-generation technology and multi-omics strategy to improve the diagnosis. ...
DNA; and (2) indirect analysis (the mtDNA mutations are obtained as byproducts of the high-throughput sequencing reads). ...
doi:10.20517/jtgg.2020.27
fatcat:ycfijgp56jap7oxhkbycvarxq4
Scalable Data Analysis of Mitochondrial DNA in the Era of High-Throughput Data Generation
2019
Figshare
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This work presents new algorithms and workflows to manage and analyze mtDNA data derived from high-throughput devices, like massive parallel sequencing data. ...
Subsequently all required computational steps from sequence alignment, mapping, mutation detection, annotation and quality control are presented. ...
Sebastian Schönherr and Lukas Forer PhD, thanks guys! ...
doi:10.6084/m9.figshare.8937899
fatcat:7g5oihrq2vekhb2d3apehiv4sm
Three-stage quality control strategies for DNA re-sequencing data
2013
Briefings in Bioinformatics
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In this review, we discuss the proper quality control procedures and parameters for Illumina technology^based human DNA re-sequencing at three different stages of sequencing: raw data, alignment and variant ...
One of the major challenges is quality control of the sequencing data. ...
Quality control should be performed for NGS DNA sequencing data at three different stages: Raw data, alignment and variant calling. ...
doi:10.1093/bib/bbt069
pmid:24067931
pmcid:PMC4492405
fatcat:4nnsvjgdmzewflenthmge7o4mi
Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms
2016
Nucleic Acids Research
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Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. ...
Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic ...
Such evaluations of mtDNA based on off-target data can be facilitated by dedicated bioinformatics tools such as MitoSeek, which extracts mitochondrial genome information from exome data and analyses associated ...
doi:10.1093/nar/gkw309
pmid:27105841
pmcid:PMC4889952
fatcat:ibzxckbn6zc5bdcspsmkubvxvu
Biodiversità ed Evoluzione Ciclo XXVII EVOLUTIONARY EPIGENETICS OF MODERN HUMAN POPULATIONS
unpublished
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Moreover a deepen analysis of three candidate genes (KRTCAP3, MAD1L and BRSK2) in a cohort of individuals of different countries (Morocco, Nigeria, China and Philippines) living in Bologna, was performed ...
Noteworthy, a mathematical model that considered methylation values of DNA extracted from cementum and pulp of living individuals can estimate chronological age with high accuracy (median absolute difference ...
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ...
fatcat:sfqscfgj3be7hod3q7dn5imuqa