D5S2500 is an ambiguously characterized STR: Identification and description of forensic microsatellites in the genomics age. (July 2016) - Phillips, C.
Highlights: An STR named D5S2500 is part of two established forensic multiplexes: Qiagen's HDplex and AGCU ScienTech's non-CODIS STR 21plex. The AGCU D5S2500 marker, originally developed as a miniSTR, does not match the details of D5S2500 in NCBI's Probe microsatellite database. Genomic characteristics are outlined for both loci, confirming the HDplex D5S2500 STR is correctly identified. To avoid future ambiguities, a recommended minimum genomic data framework for novel forensic markers is proposed, plus the name D5S2800 for the component STR of the AGCU 21plex. Abstract: In the process of establishing short tandem repeat (STR) sequence variant nomenclature guidelines in anticipation of expanded forensic multiplexes for massively parallel sequencing (MPS), it was discovered that the STR D5S2500 has multiple positions and genomic characteristics reported. This ambiguity is because the marker named D5S2500 consists of two different microsatellites forming separate components in the capillary electrophoresis multiplexes of Qiagen's HDplex (Hilden, Germany) and AGCU ScienTech's non-CODIS STR 21plex (Wuxi, Jiangsu, China). This study outlines the genomic details used to identify each microsatellite and reveals the D5S2500 marker in HDplex has the correctly assigned STR name, while the D5S2500 marker in the AGCU 21plex, closely positioned a further 1643 nucleotides in the human reference sequence, is an unnamed microsatellite. The fact that the D5S2500 marker has existed as two distinct STR loci undetected for almost ten years, even with reported discordant genotypes for the standard control DNA, underlines the need for careful scrutiny of the genomic properties of forensic STRs, as they become adapted for sequence analysis with MPS systems. We make the recommendation that precise chromosome location data must be reported for any forensic marker under development but not in common use, so that the genomic characteristics of the locus are validated to the same level of accuracy as its allelic variation and forensic performance. To clearly differentiate each microsatellite, we propose the name D5S2800 be used to identify the Chromosome-5 STR in the AGCU 21plex.