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References from An easy-to-use pipeline to analyze amplicon-based Next Generation Sequencing results of human mitochondrial DNA from degraded samples. Local targets link to admitted publications; unresolved targets remain external evidence.
High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq.
10.1016/j.fsigen.2014.06.001 · 2014 · External reference
2006 GEP-ISFG collaborative exercise on mtDNA: reflections about interpretation, artefacts, and DNA mixtures.
10.1016/j.fsigen.2007.10.010 · 2008 · External reference
Developmental validation of a Nextera XT mitogenome Illumina MiSeq sequencing method for high-quality samples
10.1016/j.fsigen.2018.01.004 · 2018 · External reference
10.1016/b978-0-12-815499-1.00013-2
10.1016/b978-0-12-815499-1.00013-2 · 2020 · External reference
Validation of mitochondrial DNA sequencing for forensic casework analysis
10.1007/bf01369907 · 1995 · External reference
Improved MtDNA sequence analysis of forensic remains using a “mini-primer set” amplification strategy.
10.1520/jfs14957j · 2001 · External reference
Next-generation DNA sequencing methods
10.1146/annurev.genom.9.081307.164359 · 2008 · External reference
Application of next-generation sequencing technology in forensic science.
10.1016/j.gpb.2014.09.001 · 2014 · External reference
Mitochondrial DNA analysis of the putative skeletal remains of Sieur de Marle: Genetic support for anthropological assessment of biogeographic ancestry
10.1016/j.forsciint.2021.110682 · 2021 · External reference
Validation of NGS for mitochondrial DNA casework at the FBI Laboratory
10.1016/j.fsigen.2019.102151 · 2020 · External reference
Mitochondrial DNA analysis of a Viking age mass grave in Sweden. Forensic Science International
2019 · External reference
Mitochondrial sequencing of missing persons dna casework by implementing thermo fisher’s precision id mtdna whole genome assay
10.3390/genes11111303 · 2020 · External reference
Assessment of the ForenSeq mtDNA control region kit and comparison of orthogonal technologies
2022 · External reference
Evaluation of GeneMarker® HTS for improved alignment of mtDNA MPS data, haplotype determination, and heteroplasmy assessment.
10.1016/j.fsigen.2017.01.016 · 2017 · External reference
Human mitochondrial control region and mtgenome: Design and forensic validation of ngs multiplexes, sequencing and analytical software.
2021 · External reference
Evaluation of the precision ID whole MtDNA genome panel for forensic analyses.
10.1016/j.fsigen.2018.03.013 · 2018 · External reference
Sequencing of mitochondrial genomes using the Precision ID mtDNA Whole Genome Panel
10.1002/elps.201800088 · 2018 · External reference
Ancient DNA: Using molecular biology to explore the past
10.1002/bies.950161006 · 1994 · External reference
Genetic analyses from ancient DNA
10.1146/annurev.genet.37.110801.143214 · 2004 · External reference
Ancient DNA: Extraction, characterization, molecular cloning, and enzymatic amplification
10.1073/pnas.86.6.1939 · 1989 · External reference
Instability and decay of the primary structure of DNA.
10.1038/362709a0 · 1993 · External reference
Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA
10.1371/journal.pone.0034131 · 2012 · External reference
Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments
10.1534/genetics.106.057349 · 2006 · External reference
Patterns of damage in genomic DNA sequences from a Neandertal
10.1073/pnas.0704665104 · 2007 · External reference
mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters
10.1093/bioinformatics/btt193 · 2013 · External reference
Schmutzi: Estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA
10.1186/s13059-015-0776-0 · 2015 · External reference
Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal
10.1073/pnas.1318934111 · 2014 · External reference
Progress in forensic bone DNA analysis: Lessons learned from ancient DNA.
10.1016/j.fsigen.2021.102538 · 2021 · External reference
Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches
10.1186/s12859-016-1097-3 · 2016 · External reference
Twelve years of SAMtools and BCFtools.
10.1093/gigascience/giab008 · 2021 · External reference
EAGER: efficient ancient genome reconstruction
10.1186/s13059-016-0918-z · 2016 · External reference
Unresolved reference
2019 · External reference
fastp: an ultra-fast all-in-one FASTQ preprocessor
10.1093/bioinformatics/bty560 · 2018 · External reference
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
10.7717/peerj.10947 · 2021 · External reference
New Insights Into Mitochondrial DNA Reconstruction and Variant Detection in Ancient Samples.
2021 · External reference
Human DNA extraction from highly degraded skeletal remains: How to find a suitable method?
10.1002/elps.202000171 · 2020 · External reference
Mitochondrial DNA control region typing from highly degraded skeletal remains by single‐multiplex next‐generation sequencing
10.1002/elps.202200052 · 2023 · External reference
Integrative genomics viewer
10.1038/nbt.1754 · 2011 · External reference
R: A Language and environment for statistical computing.
2021 · External reference
Unresolved reference
2022 · External reference
Unresolved reference
2010 · External reference
Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA
10.1038/13779 · 1999 · External reference
Fast and accurate short read alignment with Burrows–Wheeler transform
10.1093/bioinformatics/btp324 · 2009 · External reference
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data
10.1093/bioinformatics/btv566 · 2016 · External reference
Unresolved reference
2012 · External reference
A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar
10.1371/journal.pcbi.1009123 · 2022 · External reference
HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing
10.1093/nar/gkw233 · 2016 · External reference
Distribution patterns of postmortem damage in human mitochondrial DNA
10.1086/345378 · 2003 · External reference
Damage patterns observed in mtDNA control region MPS data for a range of template concentrations and when using different amplification approaches
10.1007/s00414-020-02410-0 · 2021 · External reference
Postmortem miscoding lesions in sequence analysis of human ancient mitochondrial DNA
10.1007/s00239-008-9184-3 · 2009 · External reference
Considering DNA damage when interpreting mtDNA heteroplasmy in deep sequencing data.
10.1016/j.fsigen.2016.09.008 · 2017 · External reference
Tissue specificity of DNA damage response and tumorigenesis.
10.20892/j.issn.2095-3941.2019.0097 · 2019 · External reference
Improved methods of DNA extraction from human spermatozoa that mitigate experimentally-induced oxidative DNA damage
10.1371/journal.pone.0195003 · 2018 · External reference
Sequencing error profiles of Illumina sequencing instruments
10.1093/nargab/lqab019 · 2021 · External reference
Evidence for frequent and tissue-specific sequence heteroplasmy in human mitochondrial DNA
10.1016/j.mito.2014.12.002 · 2015 · External reference
Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations
10.1073/pnas.1419651112 · 2015 · External reference
Investigation of Heteroplasmy in the Human Mitochondrial DNA Control Region: A Synthesis of Observations from More Than 5000 Global Population Samples
10.1007/s00239-009-9227-4 · 2009 · External reference
MARS: improving multiple circular sequence alignment using refined sequences
10.1186/s12864-016-3477-5 · 2017 · External reference
Unresolved reference
2016 · External reference
Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment
10.1002/ece3.8297 · 2021 · External reference
Frequency and Pattern of Heteroplasmy in the Complete Human Mitochondrial Genome
10.1371/journal.pone.0074636 · 2013 · External reference
Frequency and Pattern of Heteroplasmy in the Control Region of Human Mitochondrial DNA
10.1007/s00239-008-9138-9 · 2008 · External reference
