Tags

Type your tag names separated by a space and hit enter

Comparison of Two Massively Parallel Sequencing Platforms using 83 Single Nucleotide Polymorphisms for Human Identification.
Sci Rep. 2017 03 24; 7(1):398.SR

Abstract

The potential of Massively Parallel Sequencing (MPS) technology to vastly expand the capabilities of human identification led to the emergence of different MPS platforms that use forensically relevant genetic markers. Two of the MPS platforms that are currently available are the MiSeq® FGx™ Forensic Genomics System (Illumina) and the HID-Ion Personal Genome Machine (PGM)™ (Thermo Fisher Scientific). These are coupled with the ForenSeq™ DNA Signature Prep kit (Illumina) and the HID-Ion AmpliSeq™ Identity Panel (Thermo Fisher Scientific), respectively. In this study, we compared the genotyping performance of the two MPS systems based on 83 SNP markers that are present in both MPS marker panels. Results show that MiSeq® FGx™ has greater sample-to-sample variation than the HID-Ion PGM™ in terms of read counts for all the 83 SNP markers. Allele coverage ratio (ACR) values show generally balanced heterozygous reads for both platforms. Two and four SNP markers from the MiSeq® FGx™ and HID-Ion PGM™, respectively, have average ACR values lower than the recommended value of 0.67. Comparison of genotype calls showed 99.7% concordance between the two platforms.

Authors+Show Affiliations

Program on Forensics and Ethnicity, Philippine Genome Center, University of the Philippines, Diliman, Quezon City, 1101, Philippines. DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines.Program on Forensics and Ethnicity, Philippine Genome Center, University of the Philippines, Diliman, Quezon City, 1101, Philippines. DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines. Philippine Council for Industry, Energy and Emerging Technology Research and Development Department of Science and Technology, Bicutan, Taguig City, 1631, Philippines.Program on Forensics and Ethnicity, Philippine Genome Center, University of the Philippines, Diliman, Quezon City, 1101, Philippines. DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines.Program on Forensics and Ethnicity, Philippine Genome Center, University of the Philippines, Diliman, Quezon City, 1101, Philippines. DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines.Program on Forensics and Ethnicity, Philippine Genome Center, University of the Philippines, Diliman, Quezon City, 1101, Philippines. madeungria@up.edu.ph. DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines. madeungria@up.edu.ph.

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

28341840

Citation

Apaga, Dame Loveliness T., et al. "Comparison of Two Massively Parallel Sequencing Platforms Using 83 Single Nucleotide Polymorphisms for Human Identification." Scientific Reports, vol. 7, no. 1, 2017, p. 398.
Apaga DL, Dennis SE, Salvador JM, et al. Comparison of Two Massively Parallel Sequencing Platforms using 83 Single Nucleotide Polymorphisms for Human Identification. Sci Rep. 2017;7(1):398.
Apaga, D. L., Dennis, S. E., Salvador, J. M., Calacal, G. C., & De Ungria, M. C. (2017). Comparison of Two Massively Parallel Sequencing Platforms using 83 Single Nucleotide Polymorphisms for Human Identification. Scientific Reports, 7(1), 398. https://doi.org/10.1038/s41598-017-00510-3
Apaga DL, et al. Comparison of Two Massively Parallel Sequencing Platforms Using 83 Single Nucleotide Polymorphisms for Human Identification. Sci Rep. 2017 03 24;7(1):398. PubMed PMID: 28341840.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comparison of Two Massively Parallel Sequencing Platforms using 83 Single Nucleotide Polymorphisms for Human Identification. AU - Apaga,Dame Loveliness T, AU - Dennis,Sheila E, AU - Salvador,Jazelyn M, AU - Calacal,Gayvelline C, AU - De Ungria,Maria Corazon A, Y1 - 2017/03/24/ PY - 2016/10/04/received PY - 2017/02/28/accepted PY - 2017/3/26/entrez PY - 2017/3/28/pubmed PY - 2018/8/29/medline SP - 398 EP - 398 JF - Scientific reports JO - Sci Rep VL - 7 IS - 1 N2 - The potential of Massively Parallel Sequencing (MPS) technology to vastly expand the capabilities of human identification led to the emergence of different MPS platforms that use forensically relevant genetic markers. Two of the MPS platforms that are currently available are the MiSeq® FGx™ Forensic Genomics System (Illumina) and the HID-Ion Personal Genome Machine (PGM)™ (Thermo Fisher Scientific). These are coupled with the ForenSeq™ DNA Signature Prep kit (Illumina) and the HID-Ion AmpliSeq™ Identity Panel (Thermo Fisher Scientific), respectively. In this study, we compared the genotyping performance of the two MPS systems based on 83 SNP markers that are present in both MPS marker panels. Results show that MiSeq® FGx™ has greater sample-to-sample variation than the HID-Ion PGM™ in terms of read counts for all the 83 SNP markers. Allele coverage ratio (ACR) values show generally balanced heterozygous reads for both platforms. Two and four SNP markers from the MiSeq® FGx™ and HID-Ion PGM™, respectively, have average ACR values lower than the recommended value of 0.67. Comparison of genotype calls showed 99.7% concordance between the two platforms. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/28341840/Comparison_of_Two_Massively_Parallel_Sequencing_Platforms_using_83_Single_Nucleotide_Polymorphisms_for_Human_Identification_ L2 - https://doi.org/10.1038/s41598-017-00510-3 DB - PRIME DP - Unbound Medicine ER -