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Assessment of impact of DNA extraction methods on analysis of human remain samples on massively parallel sequencing success.
Int J Legal Med. 2019 Jan; 133(1):51-58.IJ

Abstract

Skeletal remains recovered from missing persons' cases are often exposed to harsh environmental conditions resulting in the DNA being damaged, degraded, and/or the samples containing PCR inhibitors. In this study, the efficacy of common extraction methods was evaluated to remove high levels of PCR inhibitors commonly encountered with human remains, and their downstream compatibility with the two leading sequencing chemistries and platforms for human identification purposes. Blood, hair, and bone samples were spiked with high levels of inhibitors commonly identified in each particular substrate in order to test the efficiency of various DNA extraction methods prior to sequencing. Samples were extracted using three commercial extraction kits (DNA IQ™, DNA Investigator, and PrepFiler® BTA), organic (blood and hair only), and two total demineralization protocols (bone only)). Massively parallel sequencing (MPS) was performed using two different systems: Precision ID chemistry and a custom AmpliSeq™ STR and iiSNP panel on the Ion S5™ System and the ForenSeq DNA Signature Prep Kit on the MiSeq FGx™. The overall results showed that all DNA extraction methods were efficient and are fully compatible with both MPS systems. Key performance indicators such as STR and SNP reportable alleles, read depth, and heterozygote balance were comparable for each extraction method. In samples where CE-based STRs yielded partial profiles (bone), MPS-based STRs generated more complete or full profiles. Moreover, MPS panels contain more STR loci than current CE-based STR kits and also include SNPs, which can further increase the power of discrimination obtained from these samples, making MPS a desirable choice for the forensic analysis of such challenging samples.

Authors+Show Affiliations

Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA.Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA. kee019@shsu.edu.Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA.Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA.Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA.Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA.Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA.Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30341454

Citation

Zeng, Xiangpei, et al. "Assessment of Impact of DNA Extraction Methods On Analysis of Human Remain Samples On Massively Parallel Sequencing Success." International Journal of Legal Medicine, vol. 133, no. 1, 2019, pp. 51-58.
Zeng X, Elwick K, Mayes C, et al. Assessment of impact of DNA extraction methods on analysis of human remain samples on massively parallel sequencing success. Int J Legal Med. 2019;133(1):51-58.
Zeng, X., Elwick, K., Mayes, C., Takahashi, M., King, J. L., Gangitano, D., Budowle, B., & Hughes-Stamm, S. (2019). Assessment of impact of DNA extraction methods on analysis of human remain samples on massively parallel sequencing success. International Journal of Legal Medicine, 133(1), 51-58. https://doi.org/10.1007/s00414-018-1955-9
Zeng X, et al. Assessment of Impact of DNA Extraction Methods On Analysis of Human Remain Samples On Massively Parallel Sequencing Success. Int J Legal Med. 2019;133(1):51-58. PubMed PMID: 30341454.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Assessment of impact of DNA extraction methods on analysis of human remain samples on massively parallel sequencing success. AU - Zeng,Xiangpei, AU - Elwick,Kyleen, AU - Mayes,Carrie, AU - Takahashi,Maiko, AU - King,Jonathan L, AU - Gangitano,David, AU - Budowle,Bruce, AU - Hughes-Stamm,Sheree, Y1 - 2018/10/19/ PY - 2018/08/27/received PY - 2018/10/12/accepted PY - 2018/10/21/pubmed PY - 2019/4/4/medline PY - 2018/10/21/entrez KW - DNA extraction KW - Ion S5™ KW - Massively parallel sequencing KW - MiSeq FGx™ KW - Missing persons KW - PCR inhibitors SP - 51 EP - 58 JF - International journal of legal medicine JO - Int J Legal Med VL - 133 IS - 1 N2 - Skeletal remains recovered from missing persons' cases are often exposed to harsh environmental conditions resulting in the DNA being damaged, degraded, and/or the samples containing PCR inhibitors. In this study, the efficacy of common extraction methods was evaluated to remove high levels of PCR inhibitors commonly encountered with human remains, and their downstream compatibility with the two leading sequencing chemistries and platforms for human identification purposes. Blood, hair, and bone samples were spiked with high levels of inhibitors commonly identified in each particular substrate in order to test the efficiency of various DNA extraction methods prior to sequencing. Samples were extracted using three commercial extraction kits (DNA IQ™, DNA Investigator, and PrepFiler® BTA), organic (blood and hair only), and two total demineralization protocols (bone only)). Massively parallel sequencing (MPS) was performed using two different systems: Precision ID chemistry and a custom AmpliSeq™ STR and iiSNP panel on the Ion S5™ System and the ForenSeq DNA Signature Prep Kit on the MiSeq FGx™. The overall results showed that all DNA extraction methods were efficient and are fully compatible with both MPS systems. Key performance indicators such as STR and SNP reportable alleles, read depth, and heterozygote balance were comparable for each extraction method. In samples where CE-based STRs yielded partial profiles (bone), MPS-based STRs generated more complete or full profiles. Moreover, MPS panels contain more STR loci than current CE-based STR kits and also include SNPs, which can further increase the power of discrimination obtained from these samples, making MPS a desirable choice for the forensic analysis of such challenging samples. SN - 1437-1596 UR - https://www.unboundmedicine.com/medline/citation/30341454/Assessment_of_impact_of_DNA_extraction_methods_on_analysis_of_human_remain_samples_on_massively_parallel_sequencing_success_ L2 - https://dx.doi.org/10.1007/s00414-018-1955-9 DB - PRIME DP - Unbound Medicine ER -