Massively parallel sequencing of complete mitochondrial genomes from hair shaft samples

Parson, Walther; Huber, Gabriela; Moreno, Lilliana I.; Madel, Maria‐Bernadette; Brandhagen, Michael D.; Nagl, Simone; Xavier, Catarina; Eduardoff, Mayra; Callaghan, Thomas; Irwin, Jodi A.

doi:10.1016/j.fsigen.2014.11.009

Cited by 84 publications

(74 citation statements)

References 41 publications

(54 reference statements)

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“…Coverage did not seem to be affected by a specific haplotype or haplogroup, as 90 unique haplotypes and 81 different haplogroups were included in this study [9], and coverage patterns were consistent across all of them ( Figure 2). Instead, the observed pattern of coverage was consistent with what has been described in previous studies, in which coverage was reduced at the HVII polycytosine stretch and around np 3500 when using Nextera XT library preparation [13,14,16,35]. The dip at HVII is likely a result of a combination of sequencing difficulty in this region and complex alignment of homopolymeric regions resulting in fewer aligned reads.…”

Section: Coveragesupporting

confidence: 89%

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Concordance and reproducibility of a next generation mtGenome sequencing method for high-quality samples using the Illumina MiSeq

Peck

Brandhagen

Marshall

et al. 2016

Forensic Science International: Genetics

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Section: Coveragesupporting

confidence: 89%

“…Of the approximately 1.5 million bases (16,479 (Tables 2 and 3). The vast majority of these variants were reproduced in Set 2 ( Table 3).…”

Section: Concordance and Reproducibilitymentioning

confidence: 99%

Concordance and reproducibility of a next generation mtGenome sequencing method for high-quality samples using the Illumina MiSeq

Peck

Brandhagen

Marshall

et al. 2016

Forensic Science International: Genetics

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“…Massively parallel sequencing (MPS) is adding a new dimension to the field of forensic genetics, providing distinct advantages over CE systems in terms of captured information, multiplex sizes, and analyzing highly degraded samples [12][13][14]. In recent years, MPS has been applied to the generation of STR sequence data [15][16][17][18][19] with the general outcome that STRs can be successfully typed producing genotypes compatible with those of CE analyses, even from compromised forensic samples [20].…”

Section: Introductionmentioning

confidence: 99%

Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements

Parson

Ballard

Budowle

et al. 2016

Forensic Science International: Genetics

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The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that provide a precise description of the repeat allele structure of a STR marker and variants that may reside in the flanking areas of the repeat region. When a STR contains a complex arrangement of repeat motifs, the level of genetic polymorphism revealed by the sequence data can increase substantially. As repeat structures can be complex and include substitutions, insertions, deletions, variable tandem repeat arrangements of multiple nucleotide motifs, and flanking region SNPs, established capillary electrophoresis (CE) allele descriptions must be supplemented by a new system of STR allele nomenclature, which retains backward compatibility with the CE data that currently populate national DNA databases and that will continue to be produced for the coming years. Thus, there is a pressing need to produce a standardized framework for describing complex sequences that enable comparison with currently used repeat allele nomenclature derived from conventional CE systems. It is important to discern three levels of information in hierarchical order (i) the sequence, (ii) the alignment, and (iii) the nomenclature of STR sequence data. We propose a sequence (text) string format the minimal requirement of data storage that laboratories should follow when adopting MPS of STRs. We further discuss the variant annotation and sequence comparison framework necessary to maintain compatibility among established and future data. This system must be easy to use and interpret by the DNA specialist, based on a universally accessible genome assembly, and in place before the uptake of MPS by the general forensic community starts to generate sequence data on a large scale. While the established nomenclature for CE-based STR analysis will remain unchanged in the future, the nomenclature of sequence-based STR genotypes will need to follow updated rules and be generated by expert systems that translate MPS sequences to match CE conventions in order to guarantee compatibility between the different generations of STR data.

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“…However, the most established currently available MPS protocols for whole mtDNA genome sequencing are based on PCR amplification of large mtDNA fragments, typically several kilobases in size [Sosa et al., ; Parson et al., ], which fail when applied to degraded DNA as encountered in many mtDNA applications. A very recent publication [Parson et al., ] described a midi‐sized amplicon approach for whole mtDNA MPS analysis using 62 PCR amplicons of 300–500 bp (average about 380 bp) in two multiplex assays, which proved useful for human hair analysis. However, many DNA samples encountered in mtDNA testing, especially for forensic and anthropological purposes are more severely degraded resulting in smaller‐sized fragments.…”

Section: Introductionmentioning

confidence: 99%

Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine

et al. 2015

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Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long‐range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications.

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Massively parallel sequencing of complete mitochondrial genomes from hair shaft samples

Cited by 84 publications

References 41 publications

Concordance and reproducibility of a next generation mtGenome sequencing method for high-quality samples using the Illumina MiSeq

Concordance and reproducibility of a next generation mtGenome sequencing method for high-quality samples using the Illumina MiSeq

Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements

Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine

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