Allele frequencies and population data for 17 Y-STR loci (The AmpFlSTR ® Y-filer™) in Casablanca resident population

Forensic Population Genetics—Short communication

Allele frequencies and population data for 17 Y-STR loci (The AmpFlSTR

Y-filer

) in Casablanca resident population

Adil Laouina^a,b, Brahim El Houate^a, Hakima Yahia^a, Houssine Azeddoug^b, Redouane Boulouiz^a, Faiza Chbel^a,*

aService Biologie-Empreintes Ge´ne´tiques, Laboratoire de Police Scientifique, 4 Rue Bnou Bouraid, Quartir Palmiers-Maarif, Casablanca, Morocco

bDe´partement de Biologie, Faculte´ des Sciences Ain Chock, Universite´ Hassan II, Km 8, Route D’EL Jadida, BP 5366 Maarif, Casablanca, Morocco

1. Sampling

Blood samples were collected from 166 unrelated healthy male individuals with their informed consent, resident in Casablanca metropolitan area, the industrial capital of Morocco where the urban growth is maintained by immigration from all parts of Morocco.

2. Extraction

Genomic DNA was extracted using a standard phenol–chloro- form–isoamyl alcohol method[1].

3. PCR amplifications

The AmpFlSTR¹Y-filer^TM(Applied Biosystems, Foster City, CA, USA) multiplex comprised of nine European minimal loci (DYS389I, DYS390, DYS389II, DYS19, DYS385a/b, DYS393, DYS391 and DYS392), two SWGDAM-extended loci (DYS439, DYS438) and six additional loci (DYS456, DYS458, DYS635/GATA C4, YGATA H4, DYS437 and DYS448). PCR was carried out in a

12.5ml volume containing 0.5 ng DNA template, following the recommendations for the Y-filer^TMkit (Applied Biosystems, Foster City, CA, USA).

4. Typing

The PCR products were separated using capillary electropho- resis on an ABI 3130 PRISM¹ DNA Genetic Analyzer (Applied Biosystems, Foster City, CA, USA) using denaturing polymer POP- 4. GeneScan 500 LIZ was used as the internal lane standard. The 17 Y-STR results were analyzed using GeneMapper ID v.3.2 (Applied Biosystems, Foster City, CA, USA). Allele designations were determined by comparison of the sample fragments with those of allelic ladders provided with the kit. Alleles have been named following the update of the recommendation of DNA Commission (ISFG) [2,3]. Samples were genotyped twice to further ensure result reproducibility and accuracy.

5. Quality control

A quality control check was performed using the proficiency testing of the Y STRs haplotyping quality assurance exercise 2008.

The sample haplotypes were correctly typed with the Y-filer^TM multiplex. Haplotype data was submitted to the Y-Chromosome haplotype reference database (YHRD: www.yhrd.org) and is available with the accession number YA003520.

Forensic Science International: Genetics 5 (2011) e1–e3

A R T I C L E I N F O

Article history:

Received 1 April 2010

Received in revised form 6 October 2010 Accepted 30 October 2010

Keywords:

Y-STRs Haplotype Morocco Y-filer^TM Microvariant

A B S T R A C T

Allele frequencies and population data for 17 Y-STR loci included in the AmpFlSTR¹ Y-filer^TMPCR amplification kit (Applied Biosystems, Foster City, USA), that permit the simultaneous amplification of all the markers included in the actually used European ‘‘extended haplotype’’, DYS19, DYS189I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II, DYS438, DYS439 and also DYS437, DYS448, DYS456, DYS458, DYS635 and Y GATA H4, were obtained from a sample of 166 healthy unrelated males resident in Casablanca (from Morocco). A total of 166 haplotypes were identified, of which 142 were unique. The overall haplotype diversity for the 17 Y-STR loci reached 0.9974, and a discrimination capacity was 0.855.

We report some non-standard situations, including duplications and microvariant alleles.

Crown Copyrightß2010 Published by Elsevier Ireland Ltd. All rights reserved.

* Corresponding author.

E-mail addresses:bio_mail@hotmail.com(A. Laouina),belhouate@gmail.com (B. El Houate),hakimayahia@hotmail.com(H. Yahia),azeddoug@yahoo.fr

(H. Azeddoug),rboulouiz@gmail.com(s.$. Boulouiz),cfaiza75@gmail.com(F. Chbel).

Contents lists available atScienceDirect

Forensic Science International: Genetics

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1872-4973/$ – see front matter . Crown Copyrightß2010 Published by Elsevier Ireland Ltd. All rights reserved.

doi:10.1016/j.fsigen.2010.10.016

6. Analysis of data

Allele frequencies for each locus were calculated by simple gene counting method. Gene and haplotype diversities were calculated according to Nei[4] and comparisons between populations by means of AMOVA, using the Arlequin Software 3.01 [5]. In population comparison, the bilocal system DYS385a/b was not considered and the number of repeats in DYS389I was subtracted from DYS389II.

7. Access to the data

The raw data worksheet and the ARLEQUIN input files are available upon request to the corresponding author.

8. Results

Allele frequencies and gene diversity are shown inTable 1and the identified haplotypes are listed inTable 2.

9. Other remarks

In the study, a total of 142 different haplotypes were identified and are listed inTable 2. Among the 142 haplotypes, 126 of them were individual specific and 12, 1, 2 and 1 haplotypes were shared by 2, 3, 4 and 5 individuals, respectively. The overall haplotypes diversity value was calculated as 0.9974 with a discrimination capacity of 0.855. Gene diversity values of all 17 Y-STR loci ranged from a minimum of 0.171 for DYS392 to a maximum of 0.883 for DYS385a/b. Duplicated alleles were found at following single copy Y-STR markers: DYS19 (1) and DYS448 (2). Microvariants were observed and were reproducible in our analysis following the ISFG guidelines and recommendations[2,3]. The loci with the most number of variant alleles were DYS458 (16 variants including 18.2

and 19.2 alleles) in accordance with previous worldwide investigation defining DYS458 (18.2) as modal allele in North- African clade[6]and DYS385a/b (2 variants including 15.3 allele).

Null allele was observed in one individual at DYS458, a second retyping by decreasing the annealing temperature during PCR reveals a correct profile.

Our haplotype data were compared against the data available in YHRD (http://www.yhrd.org), for populations worldwide typed for the same set of Y-STR loci. The most common haplotype detected in Casablanca population was found in one individual among 70 from Assiut (Egypt) [7], in three individual among 102 in Oran (Algeria)[8], and three Moroccans and seven Tunisians among 60 Moroccans and Tunisians living in Italy[9].

We have compared our data by means of AMOVA calculations using Slatkin linearizedRST[10]for the same set of Y-STR loci with previous published populations from various racial clusters:

European populations data (namely Spain [11–15], Poland[16], Germany[17]), North African populations (Egypt[7], Algeria[8], Tunisia [9]), SubSaharian population (Uganda [18]) and Afro- Americans from USA[19,20], also Asian populations (Japan[21], China[22]). Results showed that our population is more closed to North-African populations such as Algeria (RST= 0.0155), Tunisia (RST= 0.0334) and Egypt (RST= 0.0859), being more distant from the European cluster, such as Spain (RST= 0.2746), Poland (R_ST= 0.2941), Germany (R_ST= 0.2435), Brazil (R_ST= 0.2197). Con- cerning the African and Asian clusters, significant differences was observed with Benin (RST= 0.4226) than Uganda (RST= 0.1747) and with Japan (RST= 0.3754), than China (RST= 0.2004). Results are summarised in the MDS plot (Fig. 1).

Furthermore, comparison of our data to those of population study based on the three common ethnic groups from Morocco namely Arabs, Berbers and Sahraouis[23]revealed no differentia- tion (RST= 0.0010). This is in accordance with the recent demographic change of the studied population. It must be

[()TD$FIG]

stress = 0.0424

Zhejiang, China [Han]

Tokyo, Japan [Japanese]

Algeria

−0.3 −0.2 −0.1 0.0 0.1 0.2 0.3

−0.3−0.2−0.10.00.10.20.3

MDS

Dimension 1

Dimension 2 Belém, Brazil [Admixed Brazilian]

Cologne, Germany [German]

Marche, Italy [Tunisian]

United States [African American]

Wroclaw, Poland [Polish]

Egypt Morocco

Spain Uganda

Casablanca

Fig. 1.Multidimensional scaling (MDS) based on pairwise Fst genetic distance of Casablanca resident population and other populations submitted on YHRD database.

A. Laouina et al. / Forensic Science International: Genetics 5 (2011) e1–e3 e2

remembered that the massive immigration from all regions of Morocco has recently transformed Casablanca into a multiethnici- ty of a Berber Arab speaking and Sahraouis.

Thus, research results will be used in forensic application in Casablanca metropolitan area using the 17-loci in the Y-filer^TM.

This paper follows the guidelines for publication of population data requested by the journal[24].

Acknowledgements

The authors thank Pr. M.M. De Pancorbo (Grupo de Investiga- cio´n Consolidado BIOMICs/Research Group-Spain) and Dr. J. Talbi for reviewing the manuscript. This work was supported by the

‘‘Direction Ge´ne´rale de la Suˆ rete´ Nationale’’.

Appendix A. Supplementary data

Supplementary data associated with this article can be found, in the online version, atdoi:10.1016/j.fsigen.2010.10.016.

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