Technical note: developmental validation of a novel 6-dye typing system with 36 Y-STR loci

Abstract

Y-chromosomal short tandem repeats (Y-STRs) have proven to be very useful in investigating sexual assault cases and in paternity lineage differentiation. However, currently available commercial Y-STR multiplex amplification systems bear the limitations in the identification of related males from the same paternal lineage due to there being an insufficient number of loci in any single amplification kit. The aim of this study was to establish and validate a novel 6-dye, 36-plex Y-STR multiplex amplification system that incorporated all of the loci present in the Yfiler™ Plus kit (DYS19, DYS385a/b, DYF387S1, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, Y_GATA_H4) as well as a further nine highly polymorphic Y-STR loci (DYS388, DYS444, DYS447, DYS522, DYS527a/b, DYS549, DYS596, DYS643). The novel system was optimized and validated by a series of studies that tested the effect of different PCR-based conditions as well as the species specificity, sensitivity, stability, stutter precision, suitability for use on DNA mixtures, reproducibility, and parallel testing of the system, as well as its performance on casework samples and population analysis, according to the SWGDAM developmental validation guidelines. A total of 246 haplotypes were found for the 36 Y-STRs among 247 Guangdong Han unrelated males. Collectively, the results demonstrate that the developed 36-plex Y-STR system is sensitive, robust, reliable, and highly informative for use in forensic genetics.

Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs

“…We found 10 copy number variations (CNVs): DYS518 (37/38), DYS390 (23/24), DYS437 (15/16), DYS389 I (12/13), DYS576 (19/21), DYS456 (15/16 and 17/18), DYS385 (13/19/20), and DYF387S1 (34/35/36) in other 10 samples. After searching in the YHRD database and other referenced publications [ 29 , 34 , 35 , 36 , 37 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 ], DYS570 (19.2), DYS481 (23.2), DYF387S1 (35.3/35.3, 36.3/40, 35.3/37.3, 37.3/39 and 36.3/38.3), DYS385 (12.1,13.1), DYS576 (19,21), and DYS456 (15,16) were reported for the first time. All samples with variants are co-listed with their Y haplogroup affiliations in Table S2 .…”

“…Till now, a huge number of 27 Y-STR haplotypes have been published worldwide. First and foremost, in order to verify the population genetic backgrounds of the collected samples, a phylogenetic relationship analysis based on 27 Y-STR haplotypes in AmpFLSTR™ Yfiler™ PCR Amplification Kit (Thermo Fisher Scientific) [28] was performed by comparing Shandong and Yunnan Han populations with other 13 referenced populations, including Guangxi Zhuang (n = 2314) [29], Hulun Buir Mongolian (n = 282) [30], Xinjiang Uyghur (n = 161), Xinjiang Kazak (n = 130) [31], Yunnan Yi (n = 66) [32], Tibet Chamdo Tibetan (n = 172), Tibet Shigatse Tibetan populations (n = 230) [33], and Han groups from Guangdong (n = 247) [34], Shenzhen (n = 136) [35], Hainan (n = 473) [36], Shanghai (n = 843) [37], Changzhou, Jiangsu (n = 1550) [38], and Jining, Shandong (n = 877) [39]. Software Arlequin (version: 3.5.2.2) [40] was utilized to conduct an analysis of molecular variance (AMOVA, [41]).…”

Forensic DNA Analysis

“…Recently, a research group from China has developed and validated a typing system involving a multiplex amplification of 37 Y-STRs using capillary electrophoresis with 6 dye chemistry. The goal was to increase the power of discrimination between male individuals …”

A novel multiplex of 12 multicopy Y‐STRs for forensic application

“…We tested the specificity of the multiplex for human DNA template by making attempt to amplify primates and other organisms that are probable of being present at the crime scene. As expected, no Y‐STR profile was generated in microorganism and non‐primate animals, as other kits [33,38]. However, amplified products were obtained in Amelogenin for some primates (Figure 6).…”