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The analysis of UAE populations using AmpFℓSTR® Y Filer™: Identification of novel and null alleles

      Abstract

      The analysis of Y chromosome polymorphisms has become common place for the identification of male component in forensic cases. During the development of a Y STR population database for three major populations in the United Arab Emirates (Arab, Indian and Pakistani) using the AmpFℓSTR® Y Filer™ kit, a number of novel and null alleles were discovered.

      Keywords

      1. Introduction

      The analysis of STRs on the 60 Mb Y chromosomes has been used to complement the application of standard autosomal STRs markers. Being haploid and passed through the paternal lineage, the Y markers can be used for human identification in cases such as sexual assaults, paternity testing and missing person investigations [
      • Butler J.M.
      Recent developments in Y-short tandem repeat and Y-single nucleotide polymorphism analysis.
      ,
      • Gill P.
      • Brenner C.
      • Brinkmann B.
      • Budowle B.
      • Carracedo A.
      • Jobling M.A.
      • de Knijff P.
      • Kayser M.
      • Krawczak M.
      • Mayr W.R.
      • Morling N.
      • Olaisen B.
      • Sajantila A.
      • Tyler-Smith C.
      DNA commission of the International Society of forensic genetics: recommendations on forensic analysis using Y-chromosome STRs.
      ].
      The AmpFℓSTR® Y Filer™ kit was developed and validated to amplify 17 loci in a multiplex reaction [
      • Romero R.E.
      • Lizarazo R.
      Validation of the AmpFℓSTR® Y Filer™ kit.
      ]. It includes the nine loci that make up the minimal haplotype (DYS19, DYS389 I/II, DYS390, DYS391, DYS392, DYS393 and DYS385 a/b), additional loci suggested by the Scientific Working Group on DNA Analysis Methods (DYS438 and DYS439) and a further six loci added to increase the discriminating power of the system (DYS456, DYS458, DYS635, YGATA H4, DYS437 and DYS448).
      In order to support the Abu Dhabi Police Forensic Science Department in forensic casework, the Y Filer™ kit was used to create a Y STR database for the three major populations in UAE (Arab, Indian and Pakistani). During the study novel and null alleles were observed.

      2. Methodology

      Blood samples were collected from 414 unrelated healthy male individuals from the three UAE populations: Arab (199), Indian (106) and Pakistani (109). DNA was extracted using a standard phenol–chloroform procedure. Extracts were quantified by gel electrophoresis and diluted accordingly to a concentration of 0.1–1 ng/μl. Amplification of DNA with AmpFℓSTR® Y Filer™ kit was carried out according to manufacture's instruction [

      Applied Biosystem, AmpFℓSTR® Y Filer™ PCR amplification kit. User's Manual, 2004.

      ] in a reduced volume of 8.3 μl. PCR products were run on an ABI Prism® 310. Alleles were genotyped using GenoTyper® software V3.7. Samples showing off-ladder alleles and drop outs were amplified in singleplex reactions and sequenced.

      3. Results and discussion

      From the 414 individuals genotyped, 10 alleles in six different loci were observed to be off-ladder. All the new alleles differ by at least 4 bp from the nearest allele in the allelic ladder. The sequences of the novel alleles are given in Table 1. DYS635 showed the highest number of novel alleles—all the new alleles displayed a deletion of two repeat units from the reference sequence. Also, variation in allele 18 was observed with the two variants originating from different populations.
      Table 1The novel alleles for six different loci observed in the UAE population
      LocusReference sequenceAlleleNew allele sequenceNumber of samples exhibiting new allele
      ArabPakistaniIndian
      DYS635(TCTA)4(TGTA)219(TCTA)4(TGTA)2(TCTA)2(TGTA)2(TCTA)911
      (TCTA)218(TCTA)4(TGTA)2(TCTA)2(TGTA)2(TCTA)82
      (TGTA)2(TCTA)218(TCTA)4(TGTA)2(TCTA)2(TGTA)3(TCTA)71
      (TGTA)0,2(TCTA)17(TCTA)4(TGTA)2(TCTA)2(TGTA)2(TCTA)71
      DYS458(GAAA)n21(GAAA)215
      13(GAAA)131
      DYS19(TAGA)3TAGG(TAGA)n16(TAGA)3TAGG(TAGA)131
      DYS448(AGAGAT)nN42(AGAGAT)n16(AGAGAT)8N(AGAGAT)81
      DYS389 I(TCTG)3(TCTA)n13/16(TCTG)3(TCTA)13 + (TCTG)3(TCTA)101
      DYS456(AGAT)n12(AGAT)125
      In addition to the new alleles, allelic dropouts were detected at four different loci (DYS438, DYS448, DYS389 II and DYS458) in six individuals (Table 2). The sample showing a null allele at DYS438 (Fig. 1) was successfully amplified with PowerPlex® Y System kit. Although the main cause of allelic drop-out is primer binding site mutation, further investigation is required to determine the occurrence of null alleles.
      Table 2The number of Indian and Pakistani individuals exhibiting null alleles at four loci
      PopulationLocusNumber of individuals
      PakistaniDYS4381
      DYS4482
      DYS389 II1
      IndianDYS4582
      Figure thumbnail gr1
      Fig. 1Electropherogram showing drop-out at DYS438 when amplified with Y Filer™.

      Conflict of interest

      None.

      Acknowledgments

      Thanks go to the Abu Dhabi Police for supplying the samples for this study and to Dr. David Ballard from the Institute of Cell and Molecular Science (ICMS) at the Queen Mary's University, London for his help in the sequencing of the samples.

      References

        • Butler J.M.
        Recent developments in Y-short tandem repeat and Y-single nucleotide polymorphism analysis.
        Forensic. Sci. Rev. 2003; 15: 91-111
        • Gill P.
        • Brenner C.
        • Brinkmann B.
        • Budowle B.
        • Carracedo A.
        • Jobling M.A.
        • de Knijff P.
        • Kayser M.
        • Krawczak M.
        • Mayr W.R.
        • Morling N.
        • Olaisen B.
        • Sajantila A.
        • Tyler-Smith C.
        DNA commission of the International Society of forensic genetics: recommendations on forensic analysis using Y-chromosome STRs.
        Forensic. Sci. Int. 2001; 124: 5-10
        • Romero R.E.
        • Lizarazo R.
        Validation of the AmpFℓSTR® Y Filer™ kit.
        Int. Congr. Ser. 2006; 1288: 280-282
      1. Applied Biosystem, AmpFℓSTR® Y Filer™ PCR amplification kit. User's Manual, 2004.