Targeted capture and sequencing of 1245 SNPs for forensic applications

Wu, Liangjun; Chu, Xufeng; Zheng, Jing; Xiao, Changfu; Zhang, Zhe; Huang, Guiyang; Li, Dan; Zhan, Jinbang; Huang, Daixin; Hu, Ping; Xiong, Bo

doi:10.1016/j.fsigen.2019.07.006

Cited by 14 publications

(7 citation statements)

References 44 publications

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“…In the field of DNA genetic marker detection, the CE platform is the most widely used detection platform currently. Along with the invention and development of next‐generation sequencing (NGS) platform, challenge coexists with opportunity for the CE platform to keep its dominance in genetic marker detection [33–35]. More and more AIMs panels with large quantities of markers have been established for ancestry inference and achieved target populations distinction [36–38].…”

Section: Discussionmentioning

confidence: 99%

A targeted ancestry informative InDels panel on capillary electrophoresis for ancestry inference in Asian populations

et al. 2021

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CE is the primary methodology used in forensic DNA typing. Alleles of commonly used types of genetic markers could be separated and detected via CE based on dye color and migration time. Insertion/deletion (InDel) is an ideal genetic marker for forensic DNA analysis due to their abundance in the human genome, low mutation rate, availability of their allele types via CE, and elimination of stutter peaks. Moreover, InDels could be used as ancestry informative markers since allele frequencies of InDels is different among geographically separated populations. Several ancestry informative insertion/deletion panels have been established based on CE platform to achieve the intercontinental populations distinction. However, improvements to differentiate intracontinental populations is few. In this study, 21 InDels with fixation index (FST) > 0.15 were selected and assembled into one ancestry informative insertion/deletion panel. Using well‐designed primers, those 21 InDels could be amplified successfully and genotyped on the CE platform accurately and completely. The panel showed a large FST distance distinction among the ten Asian populations. Using clustering analysis, ten Asian populations were classified into three subgroups: East Asian, Southeast Asian, and South Asian subgroups. To evaluate the panel's capability in ancestry inference, a validation experiment was undertaken with 319 individuals from four geographically separated populations in China. Four Chinese populations were classified into different ancestry subgroups and 81.8% test individuals’ ancestry could be inferred correctly. Our result showed that development of high ancestry informative InDels panel based on CE platform is a potential for individual ancestry inference among intracontinental populations.

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Section: Discussionmentioning

confidence: 99%

A targeted ancestry informative InDels panel on capillary electrophoresis for ancestry inference in Asian populations

et al. 2021

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“…Novel MPS STR and SNP panels developed in recent years include IdPrism [ 366 ], a QIAGEN 140-locus SNP panel [ 367 ], the 21plex monSTR identity panel [ 368 ], a 42plex STR NGS panel to assist with kinship analysis [ 369 ], the 5422 marker FORCE (FORensic Capture Enrichment) panel [ 370 ], a forensic panel with 186 SNPs and 123 STRs [ 371 ], the SifaMPS panel for targeting 87 STRs and 294 SNPs [ 372 ], a 1245 SNP panel [ 373 ], 90 STRs and 100 SNPs for application with kinship cases [ 374 ], an adaption of the SNPforID 52plex panel to MPS [ 375 ], 448plex SNP panel [ 376 ], a 133plex panel with 52 autosomal and 81 Y-chromosome STRs [ 377 ], and a forensic identification multiplex with 1270 tri-allelic SNPs involving 1241 autosomal and 29 X-chromosome markers [ 378 ]. The 124 SNPs in the Precision ID Identity Panel were examined in a central Indian population [ 379 ] and human leukocyte antigen (HLA) alleles used in the early 1990s were revisited with MPS capability [ [380] , [381] , [382] ].…”

Section: Emerging Technologies Research Studies and Other Topicsmentioning

confidence: 99%

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

Butler

2023

Forensic Science International: Synergy

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“…This involves tagging each sample with a unique combination of fingerprint variant genotypes. Currently, many panels of fingerprint variants have been proposed for sample tagging of DNA genomic data by comparing genotypes of the fingerprint variants generated using WGS and other methods [12][13][14]. In contrast, very few panels have been proposed to check sample identities of multi-omics data, such as epigenomics data.…”

Section: Introductionmentioning

confidence: 99%

A pipeline for sample tagging of whole genome bisulfite sequencing data using genotypes of whole genome sequencing

Cheng

Qiu

et al. 2023

BMC Genomics

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Background In large-scale high-throughput sequencing projects and biobank construction, sample tagging is essential to prevent sample mix-ups. Despite the availability of fingerprint panels for DNA data, little research has been conducted on sample tagging of whole genome bisulfite sequencing (WGBS) data. This study aims to construct a pipeline and identify applicable fingerprint panels to address this problem. Results Using autosome-wide A/T polymorphic single nucleotide variants (SNVs) obtained from whole genome sequencing (WGS) and WGBS of individuals from the Third China National Stroke Registry, we designed a fingerprint panel and constructed an optimized pipeline for tagging WGBS data. This pipeline used Bis-SNP to call genotypes from the WGBS data, and optimized genotype comparison by eliminating wildtype homozygous and missing genotypes, and retaining variants with identical genomic coordinates and reference/alternative alleles. WGS-based and WGBS-based genotypes called from identical or different samples were extensively compared using hap.py. In the first batch of 94 samples, the genotype consistency rates were between 71.01%-84.23% and 51.43%-60.50% for the matched and mismatched WGS and WGBS data using the autosome-wide A/T polymorphic SNV panel. This capability to tag WGBS data was validated among the second batch of 240 samples, with genotype consistency rates ranging from 70.61%-84.65% to 49.58%-61.42% for the matched and mismatched data, respectively. We also determined that the number of genetic variants required to correctly tag WGBS data was on the order of thousands through testing six fingerprint panels with different orders for the number of variants. Additionally, we affirmed this result with two self-designed panels of 1351 and 1278 SNVs, respectively. Furthermore, this study confirmed that using the number of genetic variants with identical coordinates and ref/alt alleles, or identical genotypes could not correctly tag WGBS data. Conclusion This study proposed an optimized pipeline, applicable fingerprint panels, and a lower boundary for the number of fingerprint genetic variants needed for correct sample tagging of WGBS data, which are valuable for tagging WGBS data and integrating multi-omics data for biobanks.

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Targeted capture and sequencing of 1245 SNPs for forensic applications

Cited by 14 publications

References 44 publications

A targeted ancestry informative InDels panel on capillary electrophoresis for ancestry inference in Asian populations

A targeted ancestry informative InDels panel on capillary electrophoresis for ancestry inference in Asian populations

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

A pipeline for sample tagging of whole genome bisulfite sequencing data using genotypes of whole genome sequencing

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