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Correction: Shelly Y. Shih; et al.; Applications of Probe Capture Enrichment Next Generation Sequencing for Whole Mitochondrial Genome and 426 Nuclear SNPs for Forensically Challenging Samples. Genes 2018, 9, 49
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Correction published on 14 February 2018, see Genes 2018, 9(2), 90.

Open AccessArticle
Genes 2018, 9(1), 49; https://doi.org/10.3390/genes9010049

Applications of Probe Capture Enrichment Next Generation Sequencing for Whole Mitochondrial Genome and 426 Nuclear SNPs for Forensically Challenging Samples

1
Children’s Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA
2
Forensic Science Graduate Program, University of California, Davis, 1909 Galileo Ct. Ste. B, Davis, CA 95618, USA
3
Laboratório de Diagnósticos por DNA (LDD), Universidade do Estado do Rio de Janeiro (UERJ), Instituto de Biologia Roberto Alcantara Gomes (IBRAG), Rua São Francisco Xavier, number 524, Pavilhão Haroldo Lisboa da Cunha, 20550-900 Rio de Janeiro, RJ, Brazil
*
Author to whom correspondence should be addressed.
Received: 20 December 2017 / Revised: 14 January 2018 / Accepted: 17 January 2018 / Published: 22 January 2018
(This article belongs to the Special Issue Forensic Genomics)
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Abstract

The application of next generation sequencing (NGS) for the analysis of mitochondrial (mt) DNA, short tandem repeats (STRs), and single nucleotide polymorphism (SNPs) has demonstrated great promise for challenging forensic specimens, such as degraded, limited, and mixed samples. Target enrichment using probe capture rather than PCR amplification offers advantages for analysis of degraded DNA since two intact PCR primer sites in the template DNA molecule are not required. Furthermore, NGS software programs can help remove PCR duplicates to determine initial template copy numbers of a shotgun library. Moreover, the same shotgun library prepared from a limited DNA source can be enriched for mtDNA as well as nuclear markers by hybrid capture with the relevant probe panels. Here, we demonstrate the use of this strategy in the analysis of limited and mock degraded samples using our custom probe capture panels for massively parallel sequencing of the whole mtgenome and 426 SNP markers. We also applied the mtgenome capture panel in a mixed sample and analyzed using both phylogenetic and variant frequency based bioinformatics tools to resolve the minor and major contributors. Finally, the results obtained on individual telogen hairs demonstrate the potential of probe capture NGS analysis for both mtDNA and nuclear SNPs for challenging forensic specimens. View Full-Text
Keywords: Next Generation Sequencing (NGS); Massively Parallel Sequencing (MPS); Probe Capture Target Enrichment; mitochondrial DNA (mtDNA); Single Nucleotide Polymorphism (SNP); Forensic Genetics; degraded DNA Next Generation Sequencing (NGS); Massively Parallel Sequencing (MPS); Probe Capture Target Enrichment; mitochondrial DNA (mtDNA); Single Nucleotide Polymorphism (SNP); Forensic Genetics; degraded DNA
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Shih, S.Y.; Bose, N.; Gonçalves, A.B.R.; Erlich, H.A.; Calloway, C.D. Applications of Probe Capture Enrichment Next Generation Sequencing for Whole Mitochondrial Genome and 426 Nuclear SNPs for Forensically Challenging Samples. Genes 2018, 9, 49.

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