Evaluation of miniY-STR multiplex PCR systems for extended 16 Y-STR loci

Abstract

We developed three short amplicon Y-chromosomal short tandem repeat (miniY-STR) polymerase chain reaction multiplex systems for 16 Y-STR loci (DYS441, DYS446, DYS462, DYS481, DYS485, DYS495, DYS505, DYS510, DYS511, DYS549, DYS 575, DYS578, DYS593, DYS618, DYS638, and DYS643), using newly designed primer sets. In an assay of 238 Japanese males using the three miniY-STR systems, amplification product lengths ranged from 91 to 151 bp for all 16 Y-STR loci. We identified 212 different haplotypes among the 238 individuals, finding haplotype diversity and discrimination capacity of 0.9974 and 0.8908, respectively. An assay of degraded DNA samples using the three miniY-STR multiplex systems, including artificially degraded samples and degraded forensic casework samples, proved remarkably effective. In conclusion, analyses of miniY-STR multiplex systems will play an important role in forensic applications involving degraded DNA samples for which genotyping using only commercial kits is ill-suited.

Bone DNA typing using a new miniYSTR multiplex

“…Although such kits are not developed specifically to analyze degraded samples of DNA, they are commonly used for this purpose. However, the results are not so satisfactory, as the products' amplification varies between 100 and 450 bp and in general, amplification of this type of DNA is hampered with STRs that amplify fragments over 200bp [8]. In this study, results obtained from amplifications using AmpFLSTR ® Identifiler™ and AmpFlSTR ® Yfiler™ commercial kits, both with STR Kits confirm that.…”

“…In this study, results obtained from amplifications using AmpFLSTR ® Identifiler™ and AmpFlSTR ® Yfiler™ commercial kits, both with STR Kits confirm that. It has been demonstrated that miniSTRs are a better method for analyzing degraded DNA [1,2,7,8]. Results obtained here were more efficient when using the AmpFLSTR ® Minifiler™ commercial kit and the multiplex Mini YSTR09, both containing mini-YSTR.…”

Development of Multiple Assays using 46 SNPs for Comprehensive mtDNA Haplogrouping and Application to Highly Degraded DNA

“…To improve the usefulness of the systems for analyzing degraded DNA samples, we designed primers to render amplicons of 150 bp or shorter. This stems from the fact that past research has already shown that DNA fragmentation is a major obstacle in analyzing degraded DNA samples, and because in STR analysis, we obtained extremely useful results with amplicons 150 bp or smaller . In the assay of the Jomon skeleton, c .260 bp region in the HVS1 failed to be amplified.…”

Y-short tandem repeat haplotype and paternal lineage of the Ezhava population of Kerala, south India

“…To our knowledge, there are no published data about the genetic structure of Y-chromosome in Kerala population, although data on various other ethnic groups have been reported in the last decade (12-19). Y-STR haplotypes are useful for investigating and reconstructing the phylogeny of the more recently diverged paternal lineages (5,6), as well as for forensic/paternity testing (20-24).…”