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Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples.
Forensic Sci Int Genet. 2013 May; 7(3):345-52.FS

Abstract

Heterozygote imbalances leading to allele drop-outs and disproportionally large stutters leading to allele drop-ins are known stochastic phenomena related to STR typing of low-template DNA (LtDNA). The large stutters and the many drop-ins in typical STR stutter positions are artifacts from the PCR amplification of tandem repeats. These artifacts may be avoided by typing bi-allelic markers instead of STRs. In this work, the SNPforID multiplex assay was used to type LtDNA. A sensitized SNP typing protocol was introduced, that increased signal strengths without increasing noise and without affecting the heterozygote balance. Allele drop-ins were only observed in experiments with 25 pg of DNA and not in experiments with 50 and 100 pg of DNA. The allele drop-in rate in the 25 pg experiments was 0.06% or 100 times lower than what was previously reported for STR typing of LtDNA. A composite model and two different consensus models were used to interpret the SNP data. Correct profiles with 42-49 SNPs were generated from the 50 and 100 pg experiments, whereas a few incorrect genotypes were included in the generated profiles from the 25 pg experiments. With the strict consensus model, between 35 and 48 SNPs were correctly typed in the 25 pg experiments and only one allele drop-out (error rate: 0.07%) was observed in the consensus profiles. A total of 28 crime case samples were selected for typing with the sensitized SNPforID protocol. The samples were previously typed with old STR kits during the crime case investigation and only partial profiles (0-6 STRs) were obtained. Eleven of the samples could not be quantified with the Quantifiler™ Human DNA Quantification kit because of partial or complete inhibition of the PCR. For eight of these samples, SNP typing was only possible when the buffer and DNA polymerase used in the original protocol was replaced with the AmpFℓSTR(®) SEfiler Plus™ Master Mix, which was developed specifically for challenging forensic samples. All the crime case samples were successfully typed with the SNPforID multiplex assay and the match probabilities ranged from 1.1×10(-15) to 7.9×10(-23). In comparison, four of the samples could not be typed with the AmpFℓSTR(®) SEfiler Plus™ kit and the match probabilities were higher than 10(-7) for another six samples.

Authors+Show Affiliations

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100, Copenhagen, Denmark. claus.boersting@forensic.ku.dkNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

23523365

Citation

Børsting, Claus, et al. "Forensic Genetic SNP Typing of Low-template DNA and Highly Degraded DNA From Crime Case Samples." Forensic Science International. Genetics, vol. 7, no. 3, 2013, pp. 345-52.
Børsting C, Mogensen HS, Morling N. Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples. Forensic Sci Int Genet. 2013;7(3):345-52.
Børsting, C., Mogensen, H. S., & Morling, N. (2013). Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples. Forensic Science International. Genetics, 7(3), 345-52. https://doi.org/10.1016/j.fsigen.2013.02.004
Børsting C, Mogensen HS, Morling N. Forensic Genetic SNP Typing of Low-template DNA and Highly Degraded DNA From Crime Case Samples. Forensic Sci Int Genet. 2013;7(3):345-52. PubMed PMID: 23523365.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples. AU - Børsting,Claus, AU - Mogensen,Helle Smidt, AU - Morling,Niels, Y1 - 2013/03/19/ PY - 2012/08/09/received PY - 2012/11/08/revised PY - 2013/02/12/accepted PY - 2013/3/26/entrez PY - 2013/3/26/pubmed PY - 2013/10/29/medline SP - 345 EP - 52 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 7 IS - 3 N2 - Heterozygote imbalances leading to allele drop-outs and disproportionally large stutters leading to allele drop-ins are known stochastic phenomena related to STR typing of low-template DNA (LtDNA). The large stutters and the many drop-ins in typical STR stutter positions are artifacts from the PCR amplification of tandem repeats. These artifacts may be avoided by typing bi-allelic markers instead of STRs. In this work, the SNPforID multiplex assay was used to type LtDNA. A sensitized SNP typing protocol was introduced, that increased signal strengths without increasing noise and without affecting the heterozygote balance. Allele drop-ins were only observed in experiments with 25 pg of DNA and not in experiments with 50 and 100 pg of DNA. The allele drop-in rate in the 25 pg experiments was 0.06% or 100 times lower than what was previously reported for STR typing of LtDNA. A composite model and two different consensus models were used to interpret the SNP data. Correct profiles with 42-49 SNPs were generated from the 50 and 100 pg experiments, whereas a few incorrect genotypes were included in the generated profiles from the 25 pg experiments. With the strict consensus model, between 35 and 48 SNPs were correctly typed in the 25 pg experiments and only one allele drop-out (error rate: 0.07%) was observed in the consensus profiles. A total of 28 crime case samples were selected for typing with the sensitized SNPforID protocol. The samples were previously typed with old STR kits during the crime case investigation and only partial profiles (0-6 STRs) were obtained. Eleven of the samples could not be quantified with the Quantifiler™ Human DNA Quantification kit because of partial or complete inhibition of the PCR. For eight of these samples, SNP typing was only possible when the buffer and DNA polymerase used in the original protocol was replaced with the AmpFℓSTR(®) SEfiler Plus™ Master Mix, which was developed specifically for challenging forensic samples. All the crime case samples were successfully typed with the SNPforID multiplex assay and the match probabilities ranged from 1.1×10(-15) to 7.9×10(-23). In comparison, four of the samples could not be typed with the AmpFℓSTR(®) SEfiler Plus™ kit and the match probabilities were higher than 10(-7) for another six samples. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/23523365/Forensic_genetic_SNP_typing_of_low_template_DNA_and_highly_degraded_DNA_from_crime_case_samples_ DB - PRIME DP - Unbound Medicine ER -