Forensic Science International: Genetics
Volume 6, Issue 1 , Pages e46-e47, January 2012

A genetic study of 12 X-STR loci in the Hungarian population☆

Institute of Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, 1536 Budapest, P.O. Box 216, Hungary

Received 23 November 2010 published online 06 April 2011.

Article Outline

 

Dear Editor,

Males carry one X-chromosome, thus they transmit their X-chromosome to daughters as haplotypes. Females carry two X-chromosomes which are liable to recombination during meiosis, thus this must be taken into consideration for interpretation and calculation of probabilities in kinship studies.

Analysis of X-chromosomal loci can be beneficial in deficient paternity cases, when offspring is female and the alleged father is missing, or in maternity cases [1], [2].

The commercially available Mentype Argus X-12 kit (Biotype AG) makes it possible to examine the DXS10148-DXS10135-DXS8378, DXS7132-DXS10079-DXS10074, DXS10103-HPRTB-DXS10101 and DXS10146-DXS10134-DXS7423 microsatellite markers, which belong to the four linkage groups of the X-chromosome [3]. The eight X-linked markers within four linkage groups (DXS10135-DXS8378, DXS7132-DXS10074, HPRTB-DXS10101 and DXS10134-DXS7423) have been previously studied in the Hungarian population [4], [5].

The purpose of this paper is to continue the process of establishing a suitable X-STR database in the Hungarian population for the twelve loci, mainly for deficiency paternity cases when the autosomal STR markers do not lead to desired results in relationship analysis [4], [5].

Peripheral blood was collected from 219 unrelated males and 188 females from different regions in Hungary. Each person gave their informed consent prior to their inclusion in the study.

The genomic DNA was extracted from whole blood samples using the QIAmp Blood Mini Kit. The genomic DNA was amplified using the Mentype Argus X-12 kit.

The PCR products were analyzed by using an ABI 3130 Genetic Analyzer. The fragment sizes and allele designations were determined by using the GeneMapper ID Versions 3.1. Software with the template files (Biotype_Panels_v2, BinSets Biotype_Bins_v2, Size Standard SST-BTO_60-500bp and Analysis_HID_3130) provided by the manufacturer (Biotype AG). The allele nomenclature follows the guidelines of the ISFG [6].

Polymorphism information content (PIC), expected heterozygosity (HETexp), observed heterozygosity (HETobs), and power of discrimination (PD) for males and females were calculated [7], [8], [9]. Mean exclusion chance (MEC) for deficiency cases (mother, daughter, putative grandmother) was determined using the formula of Krüger [10]. MEC values for normal trios (mother, daughter, putative father) were calculated according to Kishida et al. [11]. MEC for duo cases (daughter and putative father or son and putative mother) was estimated according to Desmarais et al. [8]. Arlequin 2.0 software [12] was used to perform the testing of the Hardy–Weinberg equilibrium for female samples. The G-tests were performed (p=0.05) for population comparisons.

Allele frequencies and forensic efficiency parameters (PIC, PDmale, PDfemale, HETexp, HETobs, MECKrüger, MECKishida, MECDesmarais duo, p-values for the HW equilibrium) of the twelve X-STR loci were determined in the Hungarian population based on the genotyping of 188 females and 219 males. The cumulative allele frequencies of the four, new loci (DXS10148, DXS10079, DXS10103 and DXS10146) and their forensic efficiency parameters are interpreted in Supplementary Table S1. The haplotype frequencies for three closely linked loci within four linkage groups for the 219 Hungarian males examined are presented in Supplementary Table S2. The allele frequencies of the four, new loci in the Hungarian population were compared with German [13], [14], [15], Italian [16], Algerian [17] and Korean [18] populations using the G-test as displayed in Supplementary Table S3. The haplotype frequency data on twelve X-STR loci observed in the 219 Hungarian males are shown in Supplementary Table S4.

No significant differences were observed between male and female allele frequencies using the G-test. There were no deviations from the Hardy–Weinberg equilibrium observed in the loci DXS10148 (p=0.444600) and DXS10146 (p=0.436480) at a 95% confidence interval. For the loci DXS10079 (p=0.048980) and DXS10103 (p=0.011410) significant differences could be detected (Table S1). The violation of HWE at DXS10079 and DXS10103 loci may be due to selection pressure on these loci.

Forensic efficiency parameters calculated for this set of markers proved to be especially useful in paternity testing showing high values of combined MEC in trios (99.999999%), and in duos (99.999956%). This value is lower (99.999876%) if the alleged grandmother is examined instead of the putative father. The lowest PD values in the locus DXS10103 and the highest ones in the DXS10146 locus were calculated for both female and male samples (Table S1). The combined PD values were also very high in both female and male samples (>0.99999999). These results indicate the application of the marker set in kinship analysis as well as human identification [1], [2].

The haplotype frequencies of three closely linked loci were counted within four linkage groups studying 219 males (Table S2). We have detected 181 haplotypes for linkage group 1, 125 for linkage group 2, 117 for linkage group 3 and 142 for linkage group 4. These cluster haplotype frequencies should be considered for PI calculation when half/full sisters and the alleged grandmother are examined.

The allele frequencies of the four, new loci were compared with other population data available from published sources. Statistically significant differences (p<0.05) were found between the Hungarian and Algerian populations in the loci DXS10079, DXS10146 and DXS10148 [17], and Hungarian and Korean populations at all four loci [18]. There were no significant differences detected between the Hungarian and three German and two Italian (Sardinia and Umbria) populations [13], [14], [15], [16]. Additionally, we have expanded the population comparisons published before [5] with new data for the earlier eight X-STR loci (Table S3).

Haplotype frequency data for twelve X-STR loci in the Hungarian population (219 males) are presented for external evaluation (Table S4).

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Conflict of interest 

The authors state that they have no interests which might be perceived as posing a conflict or bias.

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Acknowledgement 

We would like to say special thanks to Dr. Eva Susa (General Director of the Network of Forensic Science Institutes) for her support, and Betty-Jean Sigethy for English editing. We also thank all the sample donors and the laboratory assistants.

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Appendix A. Supplementary data 

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References 

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☆ The laboratory participated in the GEDNAP and ISFG ESWG PTW 2001–2010 proficiency testing programs. The paper meets the editorial requirements of the FSI Genetics [19].

PII: S1872-4973(11)00052-4

doi:10.1016/j.fsigen.2011.03.007

Forensic Science International: Genetics
Volume 6, Issue 1 , Pages e46-e47, January 2012

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