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MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

Yan Guo, Jiang Li, Chung-I Li, Yu Shyr, David C. Samuels
2013 Computer applications in the biosciences : CABIOS  
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

Claudia Calabrese, Domenico Simone, Maria Angela Diroma, Mariangela Santorsola, Cristiano Guttà, Giuseppe Gasparre, Ernesto Picardi, Graziano Pesole, Marcella Attimonelli
2014 Computer applications in the biosciences : CABIOS  
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

Pan Zhang, David C. Samuels, Jing Wang, Shilin Zhao, Yu Shyr, Yan Guo
2016 Mitochondrion (Amsterdam. Print)  
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

Fei Ye, David C. Samuels, Travis Clark, Yan Guo
2014 Mitochondrion (Amsterdam. Print)  
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

Koji Ishiya, Shintaroh Ueda
2017 PeerJ  
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

Pan Zhang, David C. Samuels, Brian Lehmann, Thomas Stricker, Jennifer Pietenpol, Yu Shyr, Yan Guo
2015 Briefings in Bioinformatics  
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

Yan Guo, Chung-I Li, Quanhu Sheng, Jeanette F. Winther, Qiuyin Cai, John D. Boice, Yu Shyr
2013 Journal of Genetics and Genomics  
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

B Lledo, J A Ortiz, R Morales, E García-Hernández, J Ten, A Bernabeu, J Llácer, R Bernabeu
2018 Human Reproduction Open  
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

Siti Aishah Sulaiman, Zamzureena Mohd Rani, Fara Zela Mohd Radin, Nor Azian Abdul Murad
2020 Journal of Translational Genetics and Genomics  
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

Hansi Weissensteiner
2019 Figshare  
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

Y. Guo, F. Ye, Q. Sheng, T. Clark, D. C. Samuels
2013 Briefings in Bioinformatics  
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

Cyrielle Gasc, Eric Peyretaillade, Pierre Peyret
2016 Nucleic Acids Research  
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

Cristina Giuliani
unpublished
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