Sequence variation observed in 27 Y-STR markers with U.S. population samples

Abstract

Sequencing short tandem repeat (STR) markers on the Y chromosome allows for characterization of repeat motif variations within the Y-STR marker that cannot be determined by length-based fragment analysis with capillary electrophoresis (CE). Two commercial sequence-based assays have been run at the U.S. National Institute of Standards and Technology (NIST) with U.S. population samples (Caucasian, Hispanic, African American and Asian). The ForenSeq DNA Signature Prep Kit and prototype PowerSeq 46GY System contain a total of 27 Y-STR markers between the two kits (DYF387S1, DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS460, DYS481, DYS505, DYS522, DYS533, DYS549, DYS570, DYS576, DYS612, DYS635, DYS643, and Y-GATA-H4). Data analysis was performed using an in-house pipeline based on open source software. The resulting data reveals the degree of information gained through sequencing Y-STR markers and will be illustrated per population for the 27 markers. Allele calls from corresponding CE data were compared to sequence data for concordance. Discordant allele calls were further investigated to assess underlying causes such as null alleles, imbalanced peaks in multi-copy markers, flanking region insertions/deletions (indels), copy number variations, high stutter, and artifacts.