A multiplex assay with 52 single nucleotide polymorphisms for human identification

Abstract

A total of 52 SNPs reported to be polymorphic in European, Asian and African populations were selected. Of these, 42 were from the distal regions of each autosome (except chromosome 19). Nearly all selected SNPs were located at least 100 kb distant from known genes and commonly used STRs. We established a highly sensitive and reproducible SNP-typing method with amplification of all 52 DNA fragments in one PCR reaction followed by detection of the SNPs with two single base extension reactions analysed using CE. The amplicons ranged from 59 to 115 bp in length. Complete SNP profiles were obtained from 500 pg DNA. The 52 loci were efficiently amplified from degraded samples where previously only partial STR profiles had been obtained. A total of 700 individuals from Denmark, Greenland, Somalia, Turkey, China, Germany, Taiwan, Thailand and Japan were typed, and the allele frequencies estimated. All 52 SNPs were polymorphic in the three major population groups. The mean match probability was at least 5.0 x 10(-19) in the populations studied. Typical paternity indices ranged from 336 000 in Asians to 549 000 in Europeans. Details of the 52 SNP loci and population data generated in this work are freely available at http://www.snpforid.org.

Exploration of 19 serotoninergic candidate genes in adults and children with attention-deficit/hyperactivity disorder identifies association for 5HT2A, DDC and MAOB

“…To detect population stratification, 48 unlinked anonymous SNPs located at least 100 kb distant from known genes were also genotyped. 58 All SNPs were genotyped using the SNPlex platform (Applied Biosystems, Foster City, CA, USA) as described. 59 Briefly, DNA was fragmented by heating at 99 1C for 10 min.…”

A new set of markers for human identification based on 32 polymorphic Alu insertions

“…4,7 Similar to SNPs, polymorphic REs are distributed differently among human populations, some of them being restricted to a particular human group(s), whereas the others are distributed evenly among many populations. 13,20,21 Evenly distributed polymorphic RE insertions are suitable for human genetic identification.…”

“…3,7,8 The use of fluorescence-based approaches allows performing large-scale human genetic tests and significantly reduces contamination because of keeping laboratory microtubes closed after PCR amplification. Accordingly, we checked the possibility of polymorphic Alu allelic discrimination by means of real-time PCR with Sybr Green dye and dissociation curves analysis using two primer pairs from our set.…”

“…3 SNP-based MGMs are mostly biallelic and have therefore less discriminative power compared to STRs. An increasing number of well-characterized SNPs and some unique characteristics of this MGM type made them a useful tool for human identification [4][5][6][7] Both SNP and STR assays include two steps: (i) PCR amplification of multiple loci containing MGM and (ii) identification of the number of tandem repeats or SNP allele in each amplified locus. The application of PCR at the first stage allows to use small amounts of genomic DNA to be analyzed and permits to analyze highly degraded samples.…”

SNP Miniplexes for Individual Identification of Random‐Bred Domestic Cats

“…Peak height ratios were used to support allele calls as previously described 36. The instrument detection limits were set with a minimum peak threshold of 120 Relative Fluorescent Units (RFUs) (dR110 – blue), 60 RFUs (dR6 – green), 30 RFUs (dTamara – yellow, dROX – red, and LIZ – orange).…”