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Analysis of patrilineal relationship in Russian Federation using several commercial Y-STR multiplex panels

Published:September 25, 2017DOI:https://doi.org/10.1016/j.fsigss.2017.09.203

      Abstract

      We have analysed 285 cases of patrilineal relationship between individuals from various regions of the Russian Federation. Y-STR analysis was performed using Yfiler®, Yfiler® Plus (both Applied Biosystems, USA), and COrDYS-Y (GORDIZ Ltd, Russia) genotyping systems. The number of meioses between the individuals varied from 1 to 3 (based on self-declaration by the study participants). In 235 cases either a complete match of Y-STR profiles between alleged relatives (86.0%) or mismatches at no more than 3 loci (14.0%) were observed. In 50 cases, more than 3 mismatches between participants were detected and these samples where not taken for further analysis. When using Yfiler® (n = 119) a complete match between participants was observed in 91.6% cases, 1 mismatch – in 7.6% cases, and 3 mismatches – in 0.8% cases. When using Yfiler® Plus (n = 58) a complete match between participants was observed in 79.3% cases, 1 mismatch – in 20.7% cases, and 2 mismatches – in 3.4% cases. In cases analysed by COrDYS-Y (n = 58) a complete match between participants was observed in 81.0% cases, 1 mismatch – in 13.8% cases, 2 mismatches – in 3.5% cases, and 3 mismatches – in 1.7% cases. All mismatches detected during the present study were by one STR repeat with a single exception of locus DYS627 (Yfiler® Plus) where a mismatch of two repeats was found in one case. Overall, mismatches were present at all loci studied with exception of DYS392, DYS437, DYS438, DYS447, DYS448, DYS481 and DYS533. The highest mutation frequency was observed for locus DYS570 (0.0256).

      Keywords

      1. Introduction

      Isolated mismatches at STR loci are commonly observed between participants of kinship testing, including patrilineal kinship. These inconsistences can be due either to mutations or to absence of the expected relationship between the alleged relatives. The purpose of the present study was to investigate how widespread are single inconsistencies in cases of non-exclusion of patrilineal relationship in a Russian population using three commercial Y-STR marker systems.

      2. Materials and methods

      2.1 Population

      We have analysed 285 cases of patrilineal relationship between individuals from various regions of the Russian Federation. The number of meioses between the individuals varied from 1 to 3 (based on self-declaration by the study participants). For all cases, prior consent for DNA analysis was obtained from the participants.

      2.2 Genotyping

      DNA from buccal swabs was extracted using Buccal Swabs DNA Extraction Kit (Lytech, Russia). Y-STR genotyping was performed with AmpFℓSTR® Yfiler® PCR Amplification Kit, AmpFℓSTR® Yfiler® Plus PCR Amplification Kit (Applied Biosystems, USA) and COrDYS-Y (Gordiz Ltd, Russia) kits. PCR was performed using Applied Biosystems® 2720 and SureCycler 8800 (Agilent Technologies, USA) thermal cyclers. The products of amplification were analysed on a 3500 Genetic Analyzer (Applied Biosystems) instrument. Genotypes were assigned using GeneMapper® ID-X 1.4 (Applied Biosystems) software.

      3. Results and discussion

      In 50 cases, more than 3 mismatches between participants were identified and these samples where not taken for further analysis. In 235 cases either a complete match of Y-STR profiles between alleged relatives (86.0%) or mismatches at no more than 3 loci (14.0%) were observed (Table 1).
      Table 1Number of comparisons and observed mismatches for each of the Y-STR marker system.
      Number of mismatchesNumber of comparisons
      YfilerYfiler PlusCOrDYS-Y
      Total%Total%Total%
      010991.6%4679.3%4781.0%
      197.6%1017.2%813.8%
      200.0%23.4%23.4%
      310.8%00.0%11.7%
      >322not analysed18not analysed10not analysed
      Total1417668
      Table 2 presents the degree of relatedness between participants of each comparison. For Yfiler® in two cases information on the number of meioses was not available and these cases were removed from analysis. Because of this the number of comparisons listed in Table 2 for this marker system (117) is less than the total number of comparisons which were analysed from Table 1 (119).
      Table 2Number of comparisons and total number of meioses for each Y-STR marker system.
      Y-STR marker systemNumber of meiosesTotal number of meioses
      123
      Number of comparisons
      Yfiler257814223
      Yfiler Plus4495117
      COrDYS-Y0580116
      When using Yfiler® (n = 119) a complete match between participants was observed in 91.6% cases, 1 mismatch – in 7.6% cases, and 3 mismatches – in 0.8% cases. When using Yfiler® Plus (n = 58) a complete match between participants was observed in 79.3% cases, 1 mismatch – in 20.7% cases, and 2 mismatches – in 3.4% cases. In cases analysed by COrDYS-Y (n = 58) a complete match between participants was observed in 81.0% cases, 1 mismatch – in 13.8% cases, 2 mismatches – in 3.5% cases, and 3 mismatches – in 1.7% cases. All mismatches detected during the present study were by one STR repeat with a single exception of locus DYS627 (Yfiler® Plus) where a mismatch of two repeats was found in one case. This locus is a rapidly mutating Y-STR [
      • Ballantyne K.N.
      • Goedbloed M.
      • Fang R.
      • et al.
      Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications.
      ]. Overall, mismatches were present at all loci studied with exception of DYS392, DYS437, DYS438, DYS447, DYS448, DYS481 and DYS533. Loci DYS449, DYS460, DYS518, DYS570, and YGATAH4 showed increased mutation frequency with the highest observed in DYS570 (2.56*10−2). The lowest mutation frequency was found in loci DYS389I, DYS390, DYS393 and DYS439 (2.19*10−3).

      4. Conclusions

      The highest number of single inconsistencies observed in our study was for the subgroup tested with Yfiler® Plus. Loci DYS449, DYS460, DYS518, DYS570, and YGATAH4 showed increased mutation frequency with the highest observed in DYS570 (2.56*10−2) while lowest mutation frequency was found in loci DYS389I, DYS390, DYS393 and DYS439 (2.19*10−3).

      Conflict of interest

      None.

      Acknowledgement

      The authors would like to thank I. Kalambet, N. Kalambet, G. Kostinyuk, V. Smelkova, and L. Steverake for laboratory assistance with DNA analysis.

      References

        • Ballantyne K.N.
        • Goedbloed M.
        • Fang R.
        • et al.
        Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications.
        Am. J. Hum. Genet. 2010; 87: 341-353