Sanchez, J.J. et al. A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27, 1713-1724

Department of Forensic Genetics, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark.
Electrophoresis (Impact Factor: 3.03). 05/2006; 27(9):1713-24. DOI: 10.1002/elps.200500671
Source: PubMed


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

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Available from: Denise Syndercombe-Court
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    • "Recent advances in forensic genetics focused on the development of joint genotyping panels for multiple biallelic markers, such as single nucleotide polymorphisms [1] or the insertion/deletion (INDEL) of one or a few nucleotides [2] [3]. Unlike polymorphisms of a single nucleotide (SNP) analyses that are relatively complex from the laboratorial point of view, the analysis of INDEL markers can be carried out using the relatively simple and inexpensive methodologies that are commonly used in STR analysis [4]. "
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    ABSTRACT: The aim of this study was to estimate the diversity of 30 insertion/deletion (INDEL) markers (Investigator(®) DIPplex kit) in a sample of 519 individuals from six Brazilian states and to evaluate their applicability in forensic genetics. All INDEL markers were found to be highly polymorphic in the Brazilian population and were in Hardy-Weinberg equilibrium. To determine their forensic suitability in the Brazilian population, the markers were evaluated for discrimination power, match probability and exclusion power. The combined discrimination power (CDP), combined match power (CMP) and combined power of exclusion (CPE) were higher than 0.999999, 3.4×10(-13) and 0.9973, respectively. Further comparison of 29 worldwide populations revealed significant genetic differences between continental populations and a closer relationship between the Brazilian and European populations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
    Full-text · Article · Apr 2015 · Forensic Science International: Genetics
    • "In addition, Indels bring increased capability to detect mixed-source DNA, since they produce much more balanced peak patterns (within locus, the two alleles for a heterozygote show similar peak heights) than those of single base extension SNP tests. Of equal relevance to forensic analyses is the fact that SNP and Indel multiplexes used for identification purposes [13] [14] or ancestry analysis [2–4,12,15] have been developed specifically to analyze very short amplicons to enable increased sensitivity in the genotyping of highly degraded biological material. When dealing with challenging samples such as human skeletal remains, DNA degradation and/or the presence of PCR inhibitors from the soil may constrain the correct typing of the sample [16] [17]. "
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    ABSTRACT: Ancestry informative markers (AIMs) can be useful to infer ancestry proportions of the donors of forensic evidence. The probability of success typing degraded samples, such as human skeletal remains, is strongly influenced by the DNA fragment lengths that can be amplified and the presence of PCR inhibitors. Several AIM panels are available amongst the many forensic marker sets developed for genotyping degraded DNA. Using a 46 AIM Insertion Deletion (Indel) multiplex, we analyzed human skeletal remains of post mortem time ranging from 35 to 60 years from four different continents (Sub-Saharan Africa, South and Central America, East Asia and Europe) to ascertain the genetic ancestry components. Samples belonging to non-admixed individuals could be assigned to their corresponding continental group. For the remaining samples with admixed ancestry, it was possible to estimate the proportion of co-ancestry components from the four reference population groups. The 46 AIM Indel set was informative enough to efficiently estimate the proportion of ancestry even in samples yielding partial profiles, a frequent occurrence when analyzing inhibited and/or degraded DNA extracts. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
    No preview · Article · Dec 2014 · Forensic Science International: Genetics
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    • "The search for autosomal ancestry has also been a focus of attention in the forensic community [13, 20, 21]. Forensic geneticists have to deal with evidentiary samples containing little amounts of, and/or poorly preserved, DNA. "
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    ABSTRACT: Background There is a growing interest among geneticists in developing panels of Ancestry Informative Markers (AIMs) aimed at measuring the biogeographical ancestry of individual genomes. The efficiency of these panels is commonly tested empirically by contrasting self-reported ancestry with the ancestry estimated from these panels. Results Using SNP data from HapMap we carried out a simulation-based study aimed at measuring the effect of SNP coverage on the estimation of genome ancestry. For three of the main continental groups (Africans, East Asians, Europeans) ancestry was first estimated using the whole HapMap SNP database as a proxy for global genome ancestry; these estimates were subsequently compared to those obtained from pre-designed AIM panels. Panels that consider >400 AIMs capture genome ancestry reasonably well, while those containing a few dozen AIMs show a large variability in ancestry estimates. Curiously, 500-1,000 SNPs selected at random from the genome provide an unbiased estimate of genome ancestry and perform as well as any AIM panel of similar size. In simulated scenarios of population admixture, panels containing few AIMs also show important deficiencies to measure genome ancestry. Conclusions The results indicate that the ability to estimate genome ancestry is strongly dependent on the number of AIMs used, and not primarily on their individual informativeness. Caution should be taken when making individual (medical, forensic, or anthropological) inferences based on AIMs. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-543) contains supplementary material, which is available to authorized users.
    Full-text · Article · Jun 2014 · BMC Genomics
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