Comparison of the optimal and suboptimal quantity of mitotype libraries using next-generation sequencing.
Haplotype
Library input
Mitogenome
Next-generation sequencing
Second World War
Journal
International journal of legal medicine
ISSN: 1437-1596
Titre abrégé: Int J Legal Med
Pays: Germany
ID NLM: 9101456
Informations de publication
Date de publication:
30 Sep 2023
30 Sep 2023
Historique:
received:
25
08
2023
accepted:
20
09
2023
medline:
1
10
2023
pubmed:
1
10
2023
entrez:
30
9
2023
Statut:
aheadofprint
Résumé
Optimizing analysis parameters and sample input is crucial in forensic genetics methods to generate reliable results, and even more so when working with muti-copy mitochondrial DNA (mtDNA) and low-quality samples. This study compared mitotypes based on next-generation sequencing (NGS) results derived from the same samples at two different sequencing library concentrations-30 pM and 0.3 pM. Thirty femur samples from the Second World War were used as a model for poorly preserved DNA. Quantitative PCR (qPCR) method targeting 113 bp long fragment was employed to assess the quantity of mitogenomes. HID Ion Chef™ Instrument with Precision ID mtDNA Control Region Panel was used for library preparation and templating. Sequencing was performed with Ion GeneStudio™ S5 System. Reference haplotypes were determined from sequencing samples at 30 pM library input. Haplotypes were compared between optimal (30 pM) and suboptimal (0.3 pM) library inputs. Often the difference in haplotypes was length heteroplasmy, which in line with other studies shows that this type of variant is not reliable for interpretation in forensics. Excluding length variants at positions 573, 309, and 16,193, 56.7% of the samples matched, and in two samples, no sequence was obtained at suboptimal library input. The rest of the samples differed between optimal and suboptimal library input. To conclude, genotyping and analyzing low-quantity libraries derived from low-quality aged skeletonized human remains therefore must be done with caution in forensic genetics casework.
Identifiants
pubmed: 37776378
doi: 10.1007/s00414-023-03099-7
pii: 10.1007/s00414-023-03099-7
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Javna Agencija za Raziskovalno Dejavnost RS
ID : J3-3080
Informations de copyright
© 2023. The Author(s).
Références
Goodwin WH (2016) DNA: mitochondrial DNA. In: Payne-James J, Byard W (eds) Encyclopedia of Forensic and Legal Medicine, 2nd edn. Elsevier, pp 351–358
doi: 10.1016/B978-0-12-800034-2.00155-5
Cuenca D, Battaglia J, Halsing M, Sheehan S (2020) Mitochondrial sequencing of missing persons DNA casework by implementing thermo Fisher’s precision ID mtDNA whole genome assay. genes 11:1303. https://doi.org/10.3390/genes11111303
doi: 10.3390/genes11111303
pubmed: 33158032
pmcid: 7692767
Pipek O, Medgyes-Horváth A, Dobos L, Steger J, Szalai-Gindl J, Visontai D et al (2019) Worldwide human mitochondrial haplogroup distribution from urban sewage. Sci Rep 9:11624. https://doi.org/10.1038/s41598-019-48093-5
doi: 10.1038/s41598-019-48093-5
pubmed: 31406241
pmcid: 6690936
Översti S, Majander K, Salmela E, Salo K, Arppe L, Belskiy S et al (2019) Human mitochondrial DNA lineages in iron-age Fennoscandia suggest incipient admixture and eastern introduction of farming-related maternal ancestry. Sci Rep 9:16883. https://doi.org/10.1038/s41598-019-51045-8
doi: 10.1038/s41598-019-51045-8
pubmed: 31729399
pmcid: 6858343
Ivanov P, Wadhams M, Roby R, Holland MM, Weedn VW, Parsons TJ (1996) Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II. Nat Genet 12:417–420. https://doi.org/10.1038/ng0496-417
doi: 10.1038/ng0496-417
pubmed: 8630496
Wurst C, Maixner F, Castella V, Cipollini G, Hotz G, Zink A (2022) The lady from Basel’s Barfüsserkirche–molecular confirmation of the mummy’s identity through mitochondrial DNA of living relatives spanning 22 generations. Forensic Sci Int Genetics 56:102604. https://doi.org/10.1016/j.fsigen.2021.102604
doi: 10.1016/j.fsigen.2021.102604
Marshall C, Taylor R, Sturk-Andreaggi K, Barritt-Ross S, Berg GE, McMahon TP (2020) Mitochondrial DNA haplogrouping to assist with the identification of unknown service members from the World War II Battle of Tarawa. Forensic Sci Int Genetics 47:102291. https://doi.org/10.1016/j.fsigen.2020.102291
doi: 10.1016/j.fsigen.2020.102291
Slatko BE, Gardner AF, Ausubel FM (2018) Overview of next-generation sequencing technologies. Curr Protoc Mol Biol 122:e59. https://doi.org/10.1002/cpmb.59
doi: 10.1002/cpmb.59
pubmed: 29851291
pmcid: 6020069
Bruijns B, Tiggelaar R, Gardeniers H (2018) Massively parallel sequencing techniques for forensics: a review. Electrophoresis 39:2642–2654. https://doi.org/10.1002/elps.201800082
doi: 10.1002/elps.201800082
pubmed: 30101986
pmcid: 6282972
Wachsmuth M, Hübner A, Li M, Madea B (2016) Stoneking M. Age-related and heteroplasmy-related variation in human mtDNA copy number. PLOS Genetics. https://doi.org/10.1371/journal.pgen.1005939
doi: 10.1371/journal.pgen.1005939
pubmed: 26978189
pmcid: 4792396
Hussing C, Kampmann ML, Smidt Mogensen H, Børsting C, Morling N (2018) Quantification of massively parallel sequencing libraries–a comparative study of eight methods. Sci Rep 8:1110. https://doi.org/10.1038/s41598-018-19574-w
doi: 10.1038/s41598-018-19574-w
pubmed: 29348673
pmcid: 5773690
Inkret J, Podovšovnik E, Zupanc T, Haring G, Zupanič Pajnič I (2021) Intra-bone nuclear DNA variability in Second World War metatarsal and metacarpal bones. Int J Legal Med 135(4):1245–1256. https://doi.org/10.1007/s00414-021-02528-9
doi: 10.1007/s00414-021-02528-9
pubmed: 33624158
Zupanič Pajnič I, (2016) Extraction of DNA from human skeletal material. In: Goodwin W (ed) Forensic DNA Typing Protocols, Methods in Molecular Biology, vol 1420. Springer Science&Business Media. LLC, New York, pp 89–108
doi: 10.1007/978-1-4939-3597-0_7
Alonso A, Martín P, Albarrán C, García P, García O, Fernández de Simón L, García-Hirschfeld J, Sancho M, DelaRúa C, Fernández-Piqueras J (2004) Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies. Forensic Sci Int 139(2–3):141–149
doi: 10.1016/j.forsciint.2003.10.008
pubmed: 15040907
Thermo Fisher Scientific (2021) Precision ID mtDNA panels with the HID ion S5TM/HID ion GeneStudioTM S5 system application guide, Revision C.0. https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0017770_PrecisionID_mtDNA_Panels_S5_UG.pdf . Accessed 25 Aug 2023
Yasmin M, Rakha A, Noreen S, Salahuddin Z (2017) Mitochondrial control region diversity in Sindhi ethnic group of Pakistan. Leg Med 26:11–13. https://doi.org/10.1016/j.legalmed.2017.02
doi: 10.1016/j.legalmed.2017.02
Just RS, Scheible MK, Fast SA, Sturk-Andreaggi K, Röck AW, Bush JM, Higginbotham JL, Peck MA, Ring JD, Huber GE, Xavier C, Strobl C, Lyons EA, Diegoli TM, Bodner M, Fendt L, Kralj P, Nagl S, Niederwieser D, Zimmermann B, Parson W, Irwin JA (2015) Full mtGenome reference data: development and characterization of 588 forensic-quality haplotypes representing three U.S. populations. Forensic Sci Int: Genetics 14:141–155. https://doi.org/10.1016/j.fsigen.2014.09.021
doi: 10.1016/j.fsigen.2014.09.021
Parson W, Strobl C, Huber G, Zimmermann B, Gomes MS, Souto L et al (2013) Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM). Forensic Sci Int Genetics 7:543–549. https://doi.org/10.1016/j.fsigen.2013.06.003
doi: 10.1016/j.fsigen.2013.06.003
Sturk-Andreaggi K, Parson W, Allen M, Marshall C (2020) Impact of the sequencing method on the detection and interpretation of mitochondrial DNA length heteroplasmy. Forensic Sci Int Genetics 44:102205. https://doi.org/10.1016/j.fsigen.2019.102205
doi: 10.1016/j.fsigen.2019.102205