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Y-STR analysis of degraded DNA using reduced-size amplicons


To increase the success rate of Y-STR genotyping for degraded DNA, we have developed two multiplex PCR sets for 21 Y-STR loci. Besides the 17 Y-STR loci of DYS19, DYS385, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and GATA H4.1 contained in a commercial Y-STR kit, AmpFlSTR® Yfiler™, the other four loci of DYS388, DYS446, DYS447, and DYS449 were also included in the multiplexes to increase the discrimination capacity. Among a total of 21 Y-STR loci, the primers for eight loci (DYS385, DYS390, DYS438, DYS446, DYS448, DYS449, and DYS635) were newly designed in the present study and nine loci (DYS385, DYS390, DYS391, DYS392, DYS438, DYS439, DYS448, and DYS635) have PCR amplicons smaller than those of the AmpFlSTR® Yfiler™ kit. A sensitivity test using serially diluted standard 9948 male DNA showed that all the values of Y-STR loci in the Y-miniplexes are reliable at template concentrations as low as 30 pg. We compared the effectiveness of the two multiplexes with the AmpFlSTR® Yfiler™ kit by using both enzymatically degraded DNA and 30 samples of 50-year-old skeletal remains. This comparison demonstrated that the new Y-miniplex sets can produce a better signal from degraded DNA than the AmpFlSTR® Yfiler™ kit.

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This work was supported by the Korea Research Foundation Grant funded by the Korean Government (MOEHRD, Basic Research Promotion Fund) (KRF-2004-003-E00004).

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Correspondence to Kyoung-Jin Shin.

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Table S1

Information on the 21 Y-STR loci of two multiplex PCR sets constructed in this study (PDF 89 kB)

Table S2

Primer sequences and concentrations of the optimized Y-miniplexes (PDF 68 kB)

Figure S1

Schematic of the PCR product size ranges produced with the known allele size ranges (see Table S1) for the loci in the two Y-miniplexes. Marker names were abbreviated (e.g. DYS391 is listed as 391)(PDF 77 kB)

Figure S2

Representative electropherograms of the allelic ladder and control 9948 male DNA amplified using the two Y-miniplexes.(PDF 150 kB)

Figure S3

Alignment of the top strands from DYS446 X and Y homologous sequences. The Y sequence comes from the GenBank accession number AC006152 while the X sequence comes from the GenBank accession number AL133512. Sequence difference between the X and Y homologs are boxed. The missing X sequence is indicated by dashes compared to the Y sequence. The primers indicated by dotted arrows are reported by Redd et al. [26] and these targeted a region containing four nucleotide differences between the X and Y sequences. The primers shown with solid arrows are the new ones described here that contains a single base difference in each of the forward and reverse primers (PDF 110 kB)

Figure S4

Sensitivity test for the two Y-miniplexes using control 9948 male DNAs in various concentrations: 1,000, 500, 250, 125, 62, 30 and 15 pg. The bar indicates the standard error from the average percent of alleles observed (PDF 109 kB)

Figure S5

Efficiency test using DNAs digested with DNase I for various time periods: 0, 2, 5, 10, 15, 20 and 30 min (PDF 606 kB)

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Park, M.J., Lee, H.Y., Chung, U. et al. Y-STR analysis of degraded DNA using reduced-size amplicons. Int J Legal Med 121, 152–157 (2007).

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  • Y chromosome
  • STR
  • AmpFlSTR Yfiler
  • Miniplex
  • Degraded DNA