A multipurpose panel of microhaplotypes for use with STR markers in casework

Kenneth K Kidd; Andrew J Pakstis; Neeru Gandotra; Curt Scharfe; Daniele Podini

doi:10.1016/j.fsigen.2022.102729

A multipurpose panel of microhaplotypes for use with STR markers in casework

Forensic Sci Int Genet. 2022 Sep:60:102729. doi: 10.1016/j.fsigen.2022.102729. Epub 2022 Jun 3.

Authors

Kenneth K Kidd¹, Andrew J Pakstis², Neeru Gandotra², Curt Scharfe², Daniele Podini³

Affiliations

¹ Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States. Electronic address: Kenneth.Kidd@yale.edu.
² Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States.
³ The George Washington University, Department of Forensic Science, 2100 Foxhall Road, NW, Washington, DC 20007, United States.

PMID: 35696960
DOI: 10.1016/j.fsigen.2022.102729

Abstract

A small panel of highly informative loci that can be genotyped on the same equipment as the standard CODIS short tandem repeat (STR) markers has strong potential for application in forensic casework. Single nucleotide polymorphisms (SNPs) can be typed by a couple of methods on capillary electrophoresis (CE) machines and on sequencers, but the amount of information relative to the laboratory effort has hindered use of SNPs in actual casework. Insertion-deletion markers (InDels) suffer from similar problems. Microhaplotypes (MHs) are much more informative per locus but have similar technical difficulties unless they are typed by massively parallel sequencing (MPS). As forensic labs are acquiring sequencing machines, MHs become more likely to be used in casework, especially if multiplexed with STRs. Here we present the details of a multipurpose panel of 24 MHs with the highest effective number of alleles (A_e) from previous work. An augmented STR panel of 24 loci (20 CODIS markers plus four commonly typed STRs) is also considered. The A_e and ancestry informativeness (I_n) distributions of these two datasets are compared. The MH panel is shown to have better individualization and population distinction than the augmented CODIS STRs. We note that the 24 MHs should be better for mixture analyses than the STRs. Finally, we suggest that a commercial kit including both the standard CODIS markers and this set of 24 MH would greatly improve the discrimination power over that of current commercial assays.

Keywords: Ancestry; CODIS; Microhaplotype; Population genetics; SNP; STR.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Alleles
DNA Fingerprinting* / methods
High-Throughput Nucleotide Sequencing / methods
Humans
Microsatellite Repeats*
Polymorphism, Single Nucleotide
Sequence Analysis, DNA / methods