Human Leukocyte Antigen alleles as an aid to STR in complex forensic DNA samples

Abstract

Human biological samples with multiple contributors remain one of the most challenging aspects of DNA typing within a forensic science context. With the increasing sensitivity of commercially available kits allowing detection of low template DNA, complex mixtures are now a standard component of forensic DNA evidence. Over the years, various methods and techniques have been developed to try to resolve the issue of mixed profiles. However, forensic DNA analysis has relied on the same markers to generate DNA profiles for the past 30 years causing considerable challenges in the deconvolution of complex mixed samples. The future of resolving complicated DNA mixtures may rely on utilising markers that have been previously applied to gene typing of nonforensic relevance. With Massively Parallel Sequencing (MPS), techniques becoming more popular and accessible even epigenetic markers have become a source of interest for forensic scientists.The aim of this review is to consider the potential of alleles from the Human Leukocyte Antigen (HLA) complex as effective forensic markers. While Massively Parallel Sequencing of HLA is routinely used in clinical laboratories in fields such as transplantation, pharmacology or population studies, there have not been any studies testing its suitability for forensic casework samples.

RETRACTED: Concordance and characterization of massively parallel sequencing at 58 STRs in a Tibetan population

“…In addition, MPS allows for the simultaneous analysis of significantly more loci than CE as it is not limited by restrictions in size‐based separation or fluorescence dye detection (Li et al, 2017). The smaller amplicon sizes in MPS may also improve the analysis of challenging or degraded DNA samples (Elwick et al, 2019; Fattorini et al, 2017; Kuffel et al, 2020). Given these advantages MPS is a promising supplementary method for forensic casework.…”

Utilizing Massively Parallel Sequencing (MPS) of Human Leukocyte Antigen (HLA) Gene Polymorphism to Assess Relatedness in Deficiency Parentage Testing

“…However, the incorporation of HLA alleles into the field of forensic identification should not be perceived as a substitution but rather as a supplementary tool to complement the well-established and extensively utilized markers already in place [53]. The integration of MPS for the analysis of HLA genes in paternity testing offers a complementary approach alongside conventional forensic kits, which primarily focus on STRs and SNPs.…”

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

“…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] ].…”