Human Y-STR profiling using fully automated electrospray ionization time of flight mass spectrometry

Abstract

Polymorphic Y-chromosomal markers are useful for studying the male-specific complement of human DNA. In forensic analyses, Y-chromosomal short tandem repeats (Y-STRs) are typed to produce a haplotype profile that is shared among male members of a lineage and can be useful in parentage and relationship testing of male family members. Y-STRs can also be valuable in cases involving a male suspect's DNA with an excess of female DNA, such as rape cases. An automated Y-STR profiling assay has been developed for the Ibis Biosciences PLEX-ID™ mass spectrometry platform that reveals sequence polymorphisms within Y-STR alleles and requires only DNA template is added to a pre-fabricated plate prior to thermal cycling. The assay analyzes sixteen loci: DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4. Samples from Caucasian, African American and Hispanic population groups were analyzed via PCR followed by direct ESI-MS. Correct allele assignments were confirmed for a subset of samples by comparison to truth data produced using standard Y-STR typing techniques. Allelic variants differing by sequence polymorphisms were revealed, expanding the allele base for several loci. Preliminary validation has shown sensitivity to approximately 125–250 pg of DNA per reaction. The assay has been characterized for sensitivity, reproducibility, species specificity, and specificity to male DNA in the presence of a 100- to 1000-fold excess of female DNA. The ESI-MS platform is capable of running Y-STR, autosomal STR, mitochondrial DNA, and SNP analyses on a single instrument within the same automated run.