Autosomal SNP typing of forensic samples with the GenPlex™ HID System: Results of a collaborative study

Tomàs, Carmen; Axler-DiPerte, Grace L.; Budimlija, Zoran; Børsting, Claus; Coble, Michael D.; Decker, Amy E.; Eisenberg, Arthur J.; Fang, Rixun; Fondevila, M.; Fredslund, Stine Frisk; Gonzalez, Suzanne; Hansen, Anders J.; Hoff-Olsen, P.; Haas, Cordula; Kohler, Priscila; Kriegel, A.K.; Lindblom, Bertil; Manohar, F.; Maroñas, Olalla; Mogensen, Helle Smidt; Neureuther, Katharina; Nilsson, Helena; Scheible, Melissa; Schneider, Peter M.; Sonntag, Marie Luise; Stangegaard, Michael; Syndercombe‐Court, Denise; Thacker, C.R.; Vallone, Peter M.; Westen, Antoinette A.; Morling, Niels

doi:10.1016/j.fsigen.2010.06.007

Cited by 17 publications

(11 citation statements)

References 15 publications

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“…SNPs are mainly used as supplementary markers, but there are situations where SNPs may be the best choice of markers. If the DNA is highly degraded, there is a much higher chance of obtaining results with SNP markers than with short tandem repeat (STR) markers, because SNPs may be amplified on very short amplicons (<100 bp) [1][2][3][4][5]. Furthermore, the commonly used STR kits amplify 15-17 STRs, and one mutation is expected to occur in one of the loci typed with these kits in approximately 3% of all meioses.…”

Section: Introductionmentioning

confidence: 99%

Kinship Analysis with Diallelic SNPs Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory

Børsting

Mikkelsen²,

Morling³

2012

Transfus Med Hemother

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Background: The mutation rate of single nucleotide polymorphisms (SNPs) is estimated to be 100,000 times lower than that of short tandem repeats (STRs), which makes SNPs very suitable for relationship testing. The SNPforID multiplex assay was the first SNP typing assay that was a real alternative to the commonly used STR kits in kinship and crime case work and the first SNP assay to be validated in a forensic laboratory accredited according to the ISO17025 standard. Methods: A total of 54 crime case samples were typed with the SNPforID multiplex assay. 30 samples from relationship cases were sequenced in selected SNP loci. Results: It was demonstrated that mixtures were easily detected with the SNPforID assay by analyzing the signal strengths of the detected alleles. Unusual imbalances in signal strengths that were observed in a few individuals could be explained by unexpected SNPs in one of the primer binding sites. A complicated relationship case with four closely related individuals is presented. Conclusion: Mixtures can be detected with bi-allelic SNPs. The SNPforID assay is a very useful supplement to the STR kits in relationship testing.

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Section: Introductionmentioning

confidence: 99%

Kinship Analysis with Diallelic SNPs Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory

Børsting

Mikkelsen²,

Morling³

2012

Transfus Med Hemother

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“…However, some drawbacks exist in these IISNP sets that will greatly hamper their universal application. For example, SNPforID (11) recommends using rs1335873, which has uneven allele distributions in Africans (0.947/0.053, n = 226) and may lead to low discriminative power in African populations. Additionally, the LD of six SNPs in the panel recommended by Pakstis et al.…”

Section: Discussionmentioning

confidence: 99%

“…The pool of 1881 SNPs was used for our final selection of 96 SNPs. To avoid linkage, we chose SNPs with at least 5 Mb between‐marker distance between SNPs and at least 1 Mb distance from other promising markers, including the 20 frequently used forensic STRs (3–5), the 52 SNPforID’s SNPs (11), and the 92 SNPs determined by Pakstis et al. (12).…”

Section: Methodsmentioning

confidence: 99%

“…In 2001, Gill (9) suggested that relatively small arrays of c. 50 SNPs could be comparable to STR multiplexes. To date, many researchers have suggested a variety of IISNP panels, each containing 50-100 SNPs, for human identification (10)(11)(12).…”

mentioning

confidence: 99%

“…There are currently two major panels of SNPs, and both of these have attracted significant attention. One was developed as part of the high-throughput analysis of SNPs for the forensic Identification of Persons (SNPforID) project (10,11), and it includes 52 SNPs. The other panel was developed by Pakstis et al (12), and it includes 92 SNPs.…”

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Evaluation of 96 SNPs in 14 Populations for Worldwide Individual Identification*

Zeng

Wang

Feng

et al. 2012

Journal of Forensic Sciences

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Great advances have been made recently in searching for individual identification single-nucleotide polymorphisms (IISNPs or IDSNPs). Such SNPs as suggested by SNPforID scientists and by Pakstis et al., are promising, although they were selected from older or smaller databases rather than the most recent database. Here, we describe a new computational strategy for developing IDSNPs based on HapMap. We searched through HapMap r27 for SNPs having minor allele frequencies ≥0.30 in all its 11 populations and found more than 1881 qualified SNPs. We examined 96 of them with 183 DNA samples from three Chinese populations using Illumina arrays. The average allele frequency for these 96 SNPs among the three populations was 0.495/0.505, the average number of identical SNP genotypes shared by two individuals among the 14 populations (three Chinese and 11 HapMap) was 37.9, and the random matching probability for two unrelated Hans to match in all 96 genotypes was 9.793 × 10(-39). Thus, most of these 96 SNPs are universally applicable.

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A 48-plex Autosomal SNP GenPlex™ Assay for Human Individualization and Relationship Testing

Tomàs¹,

Børsting²,

Morling³

2011

Methods in Molecular Biology

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SNPs are being increasingly used by forensic laboratories. Different platforms have been developed for SNP typing. We describe the GenPlex™ HID system protocol, a new SNP-typing platform developed by Applied Biosystems where 48 of the 52 SNPforID SNPs and amelogenin are included. The GenPlex™ HID system protocol has been successfully tested by a number of forensic laboratories using both ordinary and forensic samples.

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Autosomal SNP typing of forensic samples with the GenPlex™ HID System: Results of a collaborative study

Cited by 17 publications

References 15 publications

Kinship Analysis with Diallelic SNPs Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory

Kinship Analysis with Diallelic SNPs Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory

Evaluation of 96 SNPs in 14 Populations for Worldwide Individual Identification*

A 48-plex Autosomal SNP GenPlex™ Assay for Human Individualization and Relationship Testing

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Autosomal SNP typing of forensic samples with the GenPlex™ HID System: Results of a collaborative study

Cited by 17 publications

References 15 publications

Kinship Analysis with Diallelic SNPs  Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory

Kinship Analysis with Diallelic SNPs  Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory

Evaluation of 96 SNPs in 14 Populations for Worldwide Individual Identification*

A 48-plex Autosomal SNP GenPlex™ Assay for Human Individualization and Relationship Testing

Contact Info

Product

Resources

About

Kinship Analysis with Diallelic SNPs Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory

Kinship Analysis with Diallelic SNPs Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory