Design, installation, and performance evaluation of a custom dye matrix standard for automated capillary electrophoresis

Automated detection and removal of capillary electrophoresis artifacts due to spectral overlap

While DNA detection using capillary electrophoresis has enabled improvements in both resolution and throughput, the use of CE - particularly with multiple dye channels - can introduce artifacts that can complicate analyses. Undetected pull-up artifacts can pose a challenge to investigators, especially in low-level samples, while partial pull-up peaks can distort peak height balance within a locus and impact the downstream likelihood ratio. Current methods for addressing pull-up are typically manually implemented. This study presents an effective alternative: a series of mathematical models, created using symbolic regression achieved through genetic programming. The models estimate the amount of pull-up expected in a peak from a true allele for a given dye-dye relationship and instrument type. This leads to the removal of artifactual pull-up peaks and peak height corrections when pull-up is present within true alleles. When models are used in conjunction with a dynamic threshold, pull-up peaks were automatically detected and removed with an accuracy rate of 96.1%. The removal of partial pull-up from true allele peaks led to a more accurate heterozygote balance for the affected locus. These models have been optimized for use with any analytical threshold and can be implemented by any lab using a 3100 or 3500 instrument series.

Novel Y-chromosome short tandem repeat sequence variation for loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449

In forensic casework, Y-chromosome short tandem repeats (Y-STRs) are essential for differentiating between unrelated males and resolving the male component of admixed biological evidence. While the majority of Y-STRs are adequate for discriminating between different paternal lineages, rapidly mutating Y-STRs are necessary for improving discrimination between males within populations of low Y-chromosome diversity and between paternal relatives. Alternatively, sequencing of Y-STRs may also improve the discrimination between isometric Y-STR alleles by identifying variation in the repeat unit pattern arrangements and by identifying SNPs in the flanking region or within the STR repeat unit itself. In this report, a total of 153 DNA sequences are presented across the Y-STR loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449. A total of 94 Y-STR sequences provided herein are reported for the first time, of which 37 sequences represent alleles showing size homoplasy, 34 sequences of known alleles for which sequence data has been unavailable and a total of 23 novel allele sequences across loci DYS644, DS447, DYS710 and DYS504. This study further encountered a rare sequence variant in the 5' flanking region of DYS385 and a total of two SNPs in the repeat structure at DYS481 and DYS449.