Multiplex short tandem repeat typing in degraded samples using newly designed primers for the TH01, TPOX, CSF1PO, and vWA loci

Tsukada, K.; Takayanagi, Kayoko; Asamura, Hideki; Ôta, Masao; Fukushima, Hirofumi

doi:10.1016/s1344-6223(02)00049-4

Cited by 36 publications

(22 citation statements)

References 20 publications

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“…One approach for recovering information from degraded samples is to reduce the PCR amplicon sizes by moving primers as close as possible to the STR repeat region. The observation that smaller-sized amplicons from autosomal STR markers produce a higher success rate with degraded DNA was confirmed by a number of recent studies [12][13][14][15][16][17][18][19][20][21]. In this context, we expect that using reduced-size amplicons to type Y-STRs could also produce a high success rate with highly degraded forensic or anthropological samples.…”

Section: Introductionsupporting

confidence: 72%

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

et al. 2006

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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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Section: Introductionsupporting

confidence: 72%

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

et al. 2006

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“…Several previous studies have confirmed that smaller autosomal amplicons lead to more successful analysis of degraded DNA [16][17][18][19][20][21]. We attempted to apply this method to X-STR analyses.…”

Section: Resultsmentioning

confidence: 99%

“…On the other hand, certain forensic cases involving molecular postmortem identification sometimes require analysis of highly degraded samples, with DNA fragmentation and the presence of polymerase chain reaction (PCR) inhibitors. Several previous papers have discussed the usefulness of smaller PCR products for highly degraded samples [16][17][18][19][20][21]. In this study, we attempted to confirm a more effective system of X-STR analysis for highly degraded DNA.…”

Section: Introductionmentioning

confidence: 93%

MiniX-STR multiplex system population study in Japan and application to degraded DNA analysis

et al. 2006

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We sought to evaluate a more effective system for analyzing X-chromosomal short tandem repeats (X-STRs) in highly degraded DNA. To generate smaller amplicon lengths, we designed new polymerase chain reaction (PCR) primers for DXS7423, DXS6789, DXS101, GATA31E08, DXS8378, DXS7133, DXS7424, and GATA165B12 at X-linked short tandem repeat (STR) loci, devising two miniX-multiplex PCR systems. Among 333 Japanese individuals, these X-linked loci were detected in amplification products ranging in length from 76 to 169 bp, and statistical analyses of the eight loci indicated a high usefulness for the Japanese forensic practice. Results of tests on highly degraded DNA indicated the miniX-STR multiplex strategies to be an effective system for analyzing degraded DNA. We conclude that analysis by the current miniX-STR multiplex systems offers high effectiveness for personal identification from degraded DNA samples.

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“…These results showed that the miniSTR strategy was more successful for typing degraded samples than those of a commercial STR kit. Moreover, we previously designed new PCR primers for four STR loci linked with the CODIS markers and reported that the analysis of the PCR products was more efficient for typing degraded DNA samples than those of a commercial STR kit [4]. Consequently, it was concluded that a combination of analyses of the miniSTR loci, in addition to assays using commercially available STR kits, is highly beneficial in the context of Japanese forensics practice involving personal identification from degraded DNA samples.…”

Section: Resultsmentioning

confidence: 99%

“…However, for highly degraded samples, STR loci amplification is practically impossible due to DNA fragmentation and the presence of polymerase chain reaction (PCR) inhibitors. In recent years, several successful methods for analyses of degraded samples by means of smaller-sized PCR products have been reported [3,4]. Coble and Butler [5] conducted a literature-based research on 920 STR loci and reported new PCR primer designs for the STR loci D1S1677, D2S441, D4S2364, D10S1248, D14S1434, and D22S1045, which were not linked to the Combined DNA Index System (CODIS) markers.…”

Section: Introductionmentioning

confidence: 99%

Allele frequencies of the six miniSTR loci in a population from Japan

et al. 2005

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Allele frequencies and forensic parameters for the six miniSTR loci D1S1677, D2S441, D4S2364, D10S1248, D14S1434, and D22S1045 were investigated in a sample of 142 unrelated healthy Japanese individuals. The polymerase chain reaction (PCR) products contained within the six loci were less than 119 bp in size. The frequency distributions in the six short tandem repeat (STR) loci showed no deviations from Hardy-Weinberg equilibrium expectations. The accumulated powers of discrimination and power of exclusion for the six loci were 0.999998 and 0.98, respectively. It was thus considered that due to the small PCR products and the moderate degree of polymorphism, analysis with use of the six miniSTR loci was highly beneficial for the forensic analysis of degraded DNA.

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Multiplex short tandem repeat typing in degraded samples using newly designed primers for the TH01, TPOX, CSF1PO, and vWA loci

Cited by 36 publications

References 20 publications

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

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

MiniX-STR multiplex system population study in Japan and application to degraded DNA analysis

Allele frequencies of the six miniSTR loci in a population from Japan

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