Application of the new insertion–deletion polymorphism kit for forensic identification and parentage testing on the Czech population

Abstract

Insertion-deletion polymorphisms (INDELs) are diallelic markers derived from a single mutation event. Their low mutation frequency makes them suitable for forensic and parentage testing. The examination of INDELs thus combines advantages of both short tandem repeats (STR) and single nucleotide polymorphisms (SNP). This type of polymorphisms may be examined using as small amplicon size as SNP (about 100 bp) but could be analyzed by techniques used for routine STR analysis. For our population study, we genotyped 55 unrelated Czech individuals. We also genotyped 11 trios to analyze DIPplex Kit (QIAGEN, Germany) suitability for parentage testing. DIPplex Kit contains 30 diallelic autosomal markers. INDELs in DIPplex Kit were tested with linkage disequilibrium test, which showed that they could be treated as independent markers. All 30 loci fulfill Hardy–Weinberg equilibrium. There were several significant differences between Czech and African populations, but no significant ones within European population. Probability of a match in the Czech population was 1 in 6.8 × 1012; combined power of discrimination was 99.9999999999%. Average paternity index was 1.13–1.77 for each locus; combined paternity index reached about 27,000 for a set of 30 loci. We can conclude that DIPplex kit is useful as an additional panel of markers in paternity cases when mutations in STR polymorphisms are present. For application on degraded or inhibited samples, further optimization of buffer and primer concentrations is needed.Electronic supplementary materialThe online version of this article (doi:10.1007/s00414-011-0649-3) contains supplementary material, which is available to authorized users.

Population data of 30 insertion–deletion markers in four Chinese populations

“…This study also revealed no significant difference in allele frequencies at most loci in Korean [3] and US Asian population [8] except for HLD118, HLD111, HLD81, and HLD39. However, statistically significant differences (after Bonferroni's correction; p<0.0026) were found with the populations of various ethnicities including Portuguese [4], Danes [5], Czechs [6], Germans [6], Spanish from central Spain [7], Basques [7], US Caucasians [8], US Afro-Americans [8], and US Hispanics [8]. For all 19 populations combined, Fst values arranged from 0.0093 to 0.2310.…”

“…In this study, we analyzed 30 Indels in 952 Chinese individuals using the Investigator DIPplex® kit (Qiagen, Hilden, Germany). To test forensic efficiency and genetic relationship, we compared the data with other published population studies using the Investigator DIPplex® kit [2][3][4][5][6][7][8].…”

“…Fst was calculated for the allele frequencies using the formula of Wright with no modification for sample size variation among the population samples [11]. Multidimensional scaling (MDS) was used to illustrate the genetic distance on the allelic frequencies of published populations [2][3][4][5][6][7][8], by using XLSTAT (version 2009.4.07; Addinsoft SARL, http://www.xlstat.com/ en/company/). The Indel types and some forensic parameters for the 30 Indel loci in the four studied Chinese populations are shown in Supplementary Table 1 and Table 2.…”

Study of InDel genetic markers with forensic and ancestry informative interest in PALOP’s immigrant populations in Lisboa

“…They are characterized by the presence or absence of a specific sequence of nucleotides [9][10][11][12]. Significative differences in allele frequencies of InDel markers, between different groups or populations, can be used as ancestry and eventually, evolutionary indicators [13].…”

Population genetics of 30 INDELs in populations of Poland and Taiwan

“…They are relatively common throughout the human genome representing 15–20 % of all polymorphisms [1] with the total number estimated at about 2 million [2]. Short amplicon size (50–150 bp), low mutation rate (<2 × 10 −8 ), and capacity to multiplex (30–40 markers) and type using a single multiplexed PCR with fluorescently labeled primers followed by capillary electrophoresis (a current technology for human identification) [3–5] are the main advantages that make INDELs useful in forensic genetics applications including individual identification, kinship testing, population studies and ancient DNA analysis [6–8]. The Investigator DIPplex ® kit (Qiagen) contain components for the simultaneous amplification and analysis of 30 biallelic autosomal INDELs and amelogenin.…”