MicroHapDB: a portable and extensible database of all published microhaplotype marker and frequency data

Abstract

2Microhaplotypes are the subject of significant interest in the forensics community as a promising 3 multi-purpose forensic DNA marker for human identification. Microhaplotype markers are 4 composed of multiple SNPs in close proximity, such that a single NGS read can simultaneously 5 genotype the individual SNPs and phase them in aggregate to determine the associated donor 6 haplotype. Abundant throughout the human genome, numerous recent studies have sought 7 to discover and rank microhaplotype markers according to allelic diversity within and among 8 populations. Microhaplotypes provide an appealing alternative to STR markers for human 9 identification and mixture deconvolution, but can also be optimized for ancestry inference or 10 combined with phenotype SNPs for prediction of externally visible characteristics in a multiplex 11 NGS assay. Designing and evaluating panels of microhaplotypes is complicated by the lack of a 12 convenient database of all published data, as well as the lack of population allele frequency data 13 spanning disparate marker collections. We present MicroHapDB, a comprehensive database of 14 published microhaplotype marker and frequency data, as a tool to advance the development of 15 microhaplotype-based human forensics capabilities. We also present population allele frequencies 16 derived from 26 global population samples for all microhaplotype markers published to date, 17 facilitating the design and interpretation of custom multi-source panels. We submit MicroHapDB 18 as a resource for community members engaged in marker discovery, population studies, assay 19 development, and panel and kit design. 20 Well-studied short tandem repeat (STR) markers have formed the basis of forensic human identification 22 methods since the 1990s. The most common strategy in practice today utilizes several fluorescent dyes 23 to type 20 or more STR markers in a single polymerase chain reaction (PCR) followed by capillary 24 electrophoresis (CE) detection (Butler, 2010). The resulting DNA profiles, combined with STR allele 25 frequency estimates, can then be used to calculate match statistics or evaluate the relative weight of evidence 26 1 Standage & Mitchell MicroHapDB v0.5for competing propositions in a likelihood ratio framework (Butler, 2015; Cowell et al., 2015; Bleka et al., 27 2016a,b). Statistics obtained via STR typing can provide high confidence given the number of independent 28 markers in an assay and the multiallelic nature of each marker. 29 Despite impressive recent improvements in DNA sequencing technologies, next-generation sequencing 30 (NGS) assays of single nucleotide polymorphism (SNP) markers have seen slow adoption for forensic 31 human identification. The ability to genotype sufficient numbers of SNPs to achieve suitable statistical 32 power remains beyond the scope of many forensics laboratories. A relevant factor is the forensics 33 community's strong disinclination, on ethical and privacy grounds, to use DNA markers associated 34 with human disease...

Evolution of single‐nucleotide polymorphism use in forensic genetics

“…In addition, MicroHapDB reports the effective number of alleles (Ae) and informativeness for assignment (In) values for ranking MHs for different forensic purposes. The genomic coordinates of each marker are also stored in MicroHapDB, enabling convenient calculation of physical distances between markers residing on the same chromosome (for linkage and recombination calculations) so that correct interpretation of DNA profiles can be achieved (Standage & Mitchell, 2020).…”

“…In 2020, Standage and Mitchell described MicroHapDB, a comprehensive database of published microhaplotype marker and frequency data, with a goal of advancing the development and capabilities of microhaplotype-based forensic technologies and assays. Within the database, population allele frequencies derived from a minimum of 26 global populations have been published for 412 microhaplotype markers, which has served as a valuable template for the design and interpretation of custom multi-source panels (Standage & Mitchell, 2020). MicroHapDB is a portable database that, once installed, can be accessed by the user without an Internet connection (via: https://github.com/ bioforensics/MicroHapDB/tree/0.6/dbbuild).…”

Applications of massively parallel sequencing in forensic genetics

“…When talking about reliability and exclusion or discrimination power, the first markers that come to mind are STRs, due to their multi-allelic nature and high variability. While the same power could be achieved with larger panels of SNPs, forensic human identification still faces difficulties implementing large-scale SNP assays to their labs (Cheung et al, 2019;Standage and Mitchell, 2020;Pang et al, 2020).…”

“…SNP microhaplotypes represent an outstanding alternative to both SNPs and STRs in the contexts of a missing person, relationship and human identification, non-human DNA analysis, sample mixtures, and biogeographical ancestry since a thorough selection of those markers could establish a single MPS assay to deal with all those elements. These markers also avoid problems commonly seen in STR assays, such as stutters peaks/reads, which sometimes complicate the identification and deconvolution of mixtures when the difference between the major and minor DNA donors is high Standage and Mitchell, 2020).…”