Massively parallel sequencing of human skeletal remains in Vietnam using the precision ID mtDNA control region panel on the Ion S5™ system

Ta, May Thi Anh; Nguyen, Nam Ngoc; Tran, Duc Minh; Nguyen, Trang Hong; Vu, Tuan A.; Le, Dung Thi; Le, Phuong Thi; Hong, Thu Thi; Hoang, Ha; Chu, Ha Hoang

doi:10.1007/s00414-021-02649-1

Cited by 9 publications

(5 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This makes the procedure very demanding and time-consuming. In recent years, next-generation sequencing (NGS) or massively parallel sequencing has emerged as highly robust techniques for typing mtDNA sequences in forensics and ancient DNA [8][9][10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Mitochondrial DNA control region typing from highly degraded skeletal remains by single‐multiplex next‐generation sequencing

Vinueza‐Espinosa,

Cuesta‐Aguirre,

Malgosa

et al. 2023

Electrophoresis

View full text Add to dashboard Cite

Poor nuclear DNA preservation from highly degraded skeletal remains is the most limiting factor for the genetic identification of individuals. Mitochondrial DNA (mtDNA) typing, and especially of the control region (CR), using next‐generation sequencing (NGS), enables retrieval of valuable genetic information in forensic contexts where highly degraded human skeletal remains are the only source of genetic material. Currently, NGS commercial kits can type all mtDNA‐CR in fewer steps than the conventional Sanger technique. The PowerSeq CRM Nested System kit (Promega Corporation) employs a nested multiplex‐polymerase chain reaction (PCR) strategy to amplify and index all mtDNA‐CR in a single reaction. Our study analyzes the success of mtDNA‐CR typing of highly degraded human skeletons using the PowerSeq CRM Nested System kit. We used samples from 41 individuals from different time periods to test three protocols (M1, M2, and M3) based on modifications of PCR conditions. To analyze the detected variants, two bioinformatic procedures were compared: an in‐house pipeline and the GeneMarker HTS software. The results showed that many samples were not analyzed when the standard protocol (M1) was used. In contrast, the M3 protocol, which includes 35 PCR cycles and longer denaturation and extension steps, successfully recovered the mtDNA‐CR from highly degraded skeletal samples. Mixed base profiles and the percentage of damaged reads were both indicators of possible contamination and can provide better results if used together. Furthermore, our freely available in‐house pipeline can provide variants concordant with the forensic software.

show abstract

Section: Introductionmentioning

confidence: 99%

“…NGS has yet to be widely adopted in forensic laboratories. Several commercial NGS kits are available for mtDNA-CR analysis and have been used successfully in highly degraded skeletal remains [12]. The ForenSeq mtDNA-CR Kit (Verogen) [16] can recover 18 overlapping amplicons of 60-150 bp using 18 primer pairs distributed in 2 multiplexes.…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial DNA control region typing from highly degraded skeletal remains by single‐multiplex next‐generation sequencing

Vinueza‐Espinosa,

Cuesta‐Aguirre,

Malgosa

et al. 2023

Electrophoresis

View full text Add to dashboard Cite

show abstract

“…In particular, with the development of next-generation sequencing (NGS) techniques and efforts to apply these techniques in forensic practices, several commercial kits are available, especially multiplex panels covering the entire or control region of the mitochondrial genome. 1 2 3 4 5 They have been validated in various populations 6 7 8 using a variety of sample types including blood, bones, hair shafts, frozen tissues, and formalin-fixed tissues. 6 7 8 9 10 11 Additionally, with increasing interest in the role of mitochondria and their DNAs in the development and progression of several medical conditions such as various types of cancers and neuromuscular diseases, a few attempts have been made to apply these techniques to medical research.…”

Section: Introductionmentioning

confidence: 99%

“… 1 2 3 4 5 They have been validated in various populations 6 7 8 using a variety of sample types including blood, bones, hair shafts, frozen tissues, and formalin-fixed tissues. 6 7 8 9 10 11 Additionally, with increasing interest in the role of mitochondria and their DNAs in the development and progression of several medical conditions such as various types of cancers and neuromuscular diseases, a few attempts have been made to apply these techniques to medical research. 3 4 5 12 13 14 …”

Section: Introductionmentioning

confidence: 99%

Comparison of Two Variant Analysis Programs for Next-Generation Sequencing Data of Whole Mitochondrial Genome

Lee,

Kim,

Kim

et al. 2023

J Korean Med Sci

View full text Add to dashboard Cite

Background With advance of next-generation sequencing (NGS) techniques, the need for mitochondrial DNA analysis is increasing not only in the forensic area, but also in medical fields. Methods Two commercial programs, Converge Software (CS) and Torrent Variant Caller for variant calling of NGS data, were compared with a considerable amount of sequence data of 50 samples with a homogeneous ethnicity. Results About 2,300 variants were identified and the two programs showed about 90% of consistency. CS, a dedicated analysis program for mitochondrial DNA, showed some advantages for forensic use. By additional visual inspection, several causes of discrepancy in variant calling results were identified. Application of different notation rules for mitochondrial sequence and the minor allele frequency close to detection threshold were the two most significant reasons. Conclusion With prospective improvement of each program, researchers and practitioners should be aware of characteristics of the analysis program they use and prepare their own strategies to determine variants.

show abstract

“…The high mutation rates of mtDNA sequences make that the sequences are high polymorphisms especially in the control region. And the highly polymorphic mtDNA control region sequences have the potential to distinguish unrelated individuals ( Strobl et al, 2019 ; Ta et al, 2021 ). The characteristics of the mtDNA maternal inheritance can be used to track the maternal family ( Bandelt and Dür, 2007 ; Parson et al, 2014 ), and can also be used to track the genetic relationships among the Kirgiz group and other reference populations.…”

Section: Introductionmentioning

confidence: 99%

Genetic Background of Kirgiz Ethnic Group From Northwest China Revealed by Mitochondrial DNA Control Region Sequences on Massively Parallel Sequencing

Wang

Chen

et al. 2022

Front. Genet.

View full text Add to dashboard Cite

The mitochondrial DNA (mtDNA) has been used to trace population evolution and apply to forensic identification due to the characteristics including lack of recombination, higher copy number and matrilineal inheritance comparing with nuclear genome DNA. In this study, mtDNA control region sequences of 91 Kirgiz individuals from the Northwest region of China were sequenced to identify genetic polymorphisms and gain insight into the genetic background of the Kirgiz ethnic group. MtDNA control region sequences of Kirgiz individuals presented relatively high genetic polymorphisms. The 1,122 bp sequences of mtDNA control region could differ among unrelated Kirgiz individuals, which suggested the mtDNA control region sequences have a good maternal pedigree tracing capability among different Kirgiz individuals. The neutrality test, mismatch distribution, Bayesian phylogenetic inference, Bayesian skyline analysis, and the median network analyses showed that the Kirgiz group might occurred population expansion, and the expansion could be observed at about ∼53.41 kilo years ago (kya) when ancestries of modern humans began to thrive in Eurasia. The pairwise population comparisons, principal component analyses, and median network analyses were performed based on haplogroup frequencies or mtDNA control region sequences of 5,886 individuals from the Kirgiz group and the 48 reference populations all over the world. And the most homologous haplotypes were found between Kirgiz individuals and the East Asian individuals, which indicated that the Kirgiz group might have gene exchanges with the East Asian populations.

show abstract

Massively parallel sequencing of human skeletal remains in Vietnam using the precision ID mtDNA control region panel on the Ion S5™ system

Cited by 9 publications

References 55 publications

Mitochondrial DNA control region typing from highly degraded skeletal remains by single‐multiplex next‐generation sequencing

Mitochondrial DNA control region typing from highly degraded skeletal remains by single‐multiplex next‐generation sequencing

Comparison of Two Variant Analysis Programs for Next-Generation Sequencing Data of Whole Mitochondrial Genome

Genetic Background of Kirgiz Ethnic Group From Northwest China Revealed by Mitochondrial DNA Control Region Sequences on Massively Parallel Sequencing

Contact Info

Product

Resources

About