Brief Communication
Mutation rate at 17 Y-STR loci in ‘‘Father/Son’’ pairs from moroccan population
Adil Laouina
a,b, Sellama Nadifi
b, Redouane Boulouiz
a, Marzouk El Arji
a, Jalal Talbi
a, Brahim El Houate
a, Hakima Yahia
a, Faiza Chbel
a,⇑aService Biologie-Empreintes Génétiques, Laboratoire de Police Scientifique, 4 Rue Bnou Bouraid, Quartir Palmiers-Maarif, Casablanca, Morocco
bGenetic and Molecular Pathology Laboratory, Medical School, Hassan II University, 19 rue Tarik Bnou Ziad, Casablanca, Morocco
a r t i c l e i n f o
Article history:
Received 24 September 2012
Received in revised form 31 January 2013 Accepted 15 March 2013
Available online 25 April 2013 Keywords:
Y-STRs Moroccan AmpFlSTR Yfiler™
Mutational events
a b s t r a c t
Precise knowledge of mutation rate at Y-STRs loci is essential for a correct evaluation of typing results in forensic casework and specially kinship genetic studies. In this study, we have examined 252 confirmed and unrelated father/son sample pairs from Moroccan population using the 17 Y-STR markers DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4 of the AmpFlSTR Yfiler™ kit used in routine case- work. We observed a total of 15 single repeat mutations between fathers and sons as mutational events.
Nine mutations resulted in the gain of a repeat in the son and six resulted in a loss of a repeat. The average mutation rate in the studied sample is 3.510 3(95% CI 2–5.810 3). Furthermore, Y-STRs mutation occurrence seems to be 4 times more frequent than autosomal STRs mutation in this sample.
Ó2013 Elsevier Ireland Ltd. All rights reserved.
1. Introduction
Y-chromosome short tandem repeats (Y-STRs) testing is impor- tant for a number of different applications of human genetics including forensic evidence examination, paternity testing, study- ing human migration patterns throughout history, and genealogical research[1–3]. A majority of the Y-chromosome is transferred di- rectly from father to son without recombination. To shuffle its genes and provide greater genetic variety to future generations, random mutations are the only mechanisms for variation over time between paternally related males. Mutational rates events have been estimated for a large number of markers and from multigen- eration pedigrees [4] or simply independent father/son pairs [5–15]. Both locus-specific mutation rates and allele-specific muta- tion trends have been investigated[6,16,17]. However, there has been little data comparing mutations rates across populations. In this article we present a study of a Moroccan males sample in order to estimate mutational rates for the 17 Y-STRs included in Amp- FlSTRÒYfilerTM(Applied Biosystems [AB], Foster City, CA) multiplex kit used in casework.
2. Materials and methods
Samples were collected from paternity cases data tests involv- ing males whose biological relationship were previously confirmed by autosomal STRs using AmpFlSTR Identifiler kit (AB) with PI val- ues above 10,000. A total of 252 father/son pairs from Morocco after obtaining informed consent to be involved in this study.
DNA samples were then examined with the 17 Y-STRs of AmpFlSTR Yfiler™ (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385 a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y- GATA-H4, DYS437, DYS438, DYS448) kit (AB) in the following con- ditions: PCR amplification of the Yfiler loci was performed using 0.5–1 ng of DNA template and half volume reactions for a total of 12.5
l
l instead of the 25l
l suggested by the manufacturer[18].The PCR products were analyzed using capillary electrophoresis ABIÒPrism 3130 (AB). Analysis of DNA fragments was performed by GeneMapper ID v.3.2 (AB). Data analysis was carried out using the Arlequin Software 3.01 [19], and the confidence interval (CI) was estimated from the binomial standard deviation[20].
3. Results and discussion
The analysis revealed that among 252 sons, we have identified 250 different haplotypes, of which 236 were unique and the overall haplotype diversity is 0.997. Concerning the 252 father/son pairs corresponding to a total of 4284 meiotic events from analyzing 17 Y-STRs included in the AmpFlSTRÒYfilerTM(AB) PCR amplifica- tion kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, 1344-6223/$ - see front matterÓ2013 Elsevier Ireland Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.legalmed.2013.03.003
⇑ Corresponding author. Tel.: +002 1266 073 7639.
E-mail addresses: [email protected] (A. Laouina), nadifi[email protected] (S. Nadifi),[email protected](R. Boulouiz),[email protected](M. El Arji), [email protected](J. Talbi),[email protected](B. El Houate),hakimayahia@
hotmail.com(H. Yahia),[email protected](F. Chbel).
Legal Medicine 15 (2013) 269–271
Contents lists available atSciVerse ScienceDirect
Legal Medicine
j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / l e g a l m e d
DYS456, DYS458, DYS635, and Y-GATA-H4) in 252 (per locus) father/son pairs. Fifteen single-step mutations were identified among all of the allele transfers in the sample. Nine of these muta- tions between fathers and sons resulted in the gain of a repeat while six mutations resulted in the loss of a repeat (Table 1). The occurrence of the mutation was confirmed by a second amplifica- tion and genotyping. We detected double mutational events with a simple repeat loss at both DYS458 and DYS385a loci within the same father/son sample pair. In this study we observed some non-uniform alleles that have been previously reported [21,22]
such as one duplication and triplication at DYS448 in two cases, and two different microvariants (18.2, 19.2) at DYS458 locus.
The observed locus-specific mutation rate ranged between 0 for DYS19, DYS389I, DYS392, DYS438, DYS439, DYS448 and 1.1910 2 (95% CI 2.5–34.4) for DYS389II locus. The average mutation rate across all markers in this study was 3.510 3 (95% CI 2–5.810 3). This rate is higher than those calculated by Sanchez-Diz et al.[14]in a sample of 701 father/son pairs In Iberian and Latin American groups (2.210 3), by Viera-Silva et al. [23] in a sample of 95 father/son pairs from Portugal (1.8510 3) and by Farfan et al.[24]in 226 father/son pairs in Southern Spain groups. Using all of them the same 17 Y-STRs set.
So, even if number of father/son pairs varied between the three studies, no significant differences in mutation rate were observed.
Similar mutation rate was found in Norway’s population (2.310 3) in a sample of 1766 father/son pairs but using only 9 Y-STRs loci by Dupuy et al. [6]. The same mutation rate was found by Lee et al.[10]in Korean population (2.310 3) using a high number of loci (22 Y-STRs) in a sample size equal to 369 father/son pairs. For admixed populations, the mutation rate found is higher than those calculated for Caucasian and Asians popula- tions cited up, in U.S. admixed sample of 399 father/son pairs using 17 Y-STRs, the mutation rate found was 3.1310 3(Decker et al.
[13]) and in a sample of 950 father/son pairs of Afro–Americans using 17 Y-STRs, the mutation rate is 3.010 3(Ge et al.[16]).
These results are similar to what we found in our study and also to result reported by Onofri et al.[25]in Italian admixed popula- tion from different ethnic groups: Caucasians, Asians and Africans (2.95510 3in a sample of 433 father/son pairs using 17 Y-STRs).
Our results are in general agreement with the aforementioned works. We found that mutation rates are positively correlated with population diversity and not with sample size or number of Y-STRs loci used.
In the sample studied none of these Y-STRs mutational events have been linked to autosomal STRs mutation events, which con- firm the independence of the two mechanisms. Indeed, we have checked eventually occurrence of the autosomal mutation and we have observed 4 mutations which are displayed in Table 2.
The occurrence of the 4 mutations was confirmed by a second amplification and genotyping with a different kit (PowerPlex 16, Promega Corporation Madison, Wisconsin).
A total of four mutations were observed, in CSF1P0, D3S1358, D16S539 and D2S1338. A comparison of results from Tables 1 and 2 show that the occurrence of mutation at Y-STRs loci is around four times more than autosomal STRs of studied sample.
In conclusion the knowledge about mutation rates of Y-STRs used in forensic casework and paternity testing is very important for a correct interpretation of results. As a consequence of observed mutation rates, the criterion for exclusion in paternity testing should be defined. Finally, mutations across the different Y-STR loci appear to be independent of each other.It would be important to characterize more father/son pairs in order to estimate more reli- able locus/allele specific mutation rates for the most widely used markers in both population and forensic genetics.
References
[1]Gusmao L, Sanchez-Diz P, Calafell F, et al. Mutation rates at Y chromosome specific microsatellites. Hum Mutat 2005;26:520–8.
[2]Bianchi NO, Catanesi CI, Baillet G, Martinez-Marignac VL, Bravi CM, Vidal-Rioja LB, et al. Characterization of ancestral and derived Y-chromosome haplotypes of new world native populations. Am J Hum Genet 1998;63:1862–71.
[3]Kayser M, Caglia A, Corach D, et al. Evaluation of Y-chromosomal STRs: a multicenter study. Int J Leg Med 1997;110:125–33.
[4]Heyer E, Puymirat J, Dieltjes P, Bakker E, de Knijff P. Estimating Y chromosome specific microsatellite mutation frequencies using deep rooting pedigrees.
Hum Mol Genet 1997;6:799–803.
[5]Kayser M, Roewer L, Hedman M, et al. Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs. Am J Hum Genet 2000;66:1580–8.
[6]Dupuy BM, Stenersen M, Egeland T, Olaisen B. Y-chromosomal microsatellite mutation rates: differences in mutation rate between and within loci. Hum Mutat 2004;23:117–24.
[7]Kurihara R, Yamamoto T, Uchihi R, et al. Mutations in 14 Y-STR loci among Japanese father–son haplotypes. Int J Leg Med 2004;118:125–31.
[8]Ballard DJ, Phillips C, Wright G, et al. A study of mutation rates and the characterisation of intermediate, null and duplicated alleles for 13 Y chromosome STRs. Forensic Sci Int 2005;155:65–70.
[9]Hohoff C, Dewa K, Sibbing U, Hoppe K, Forster P, Brinkmann B. Y-chromosomal microsatellite mutation rates in a population sample from Northwestern Germany. Int J Leg Med 2007;121:359–63.
[10]Lee HY, Park MJ, Chung U, Lee HY, Yang WI, Cho SH, et al. Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father–son pairs. Int J Leg Med 2007;121:128–35.
[11]Budowle B, Adamowicz M, Aranda XG, Barna C, et al. Twelve short tandem repeat loci Y chromosome haplotypes genetic analysis on populations residing in North America. Forensic Sci Int 2005;150:1–15.
[12]Shi MS, Tang JP, Bai RF, Yu XJ, Lv JY, Hu B. Haplotypes of 20 Y-chromosomal STRs in a population sample from southeast China (Chaoshan area). Int J Leg Med 2007;21:9827–37.
[13]Decker A, Kline M, Redman J, Reid T, Butler J. Analysis of mutations in father–
son pairs with 17 Y-STR loci. Forensic Sci Int Genet 2008;2:e31–5.
[14]Sanchez-Diz P. Population and segregation data on 17 Y-STRs: results of a GEP- ISFG collaborative study. Int J Leg Med 2008;122:529–33.
[15]Vieira-Silva C, Dario P, Ribeiro T, Lucas I, Geada H, Espinheira R. Y-STR mutational rates determination in South Portugal Caucasian population.
Forensic Sci Int Genet 2009;2:60–1.
Table 1
Mutation count, rates and 95% confidence interval (CI) for the 17 Y-STR loci studied in Moroccan population sample.
Locus Count Allele transmission
Mutation rate (10 3)
95%
CI(10 3)
DYS19 0 252 0.00 0–14.5
DYS389I 0 252 0.00 0–14.5
DYS389II 3 252 11.9 2.5–34.4
DYS390 1 252 4.0 0.1–21.9
DYS391 1 252 4.0 0.1–21.9
DYS392 0 252 0.00 0–14.5
DYD393 1 252 4.0 0.1–21.9
DYS385 3 504 6.0 1–28.4
DYS438 0 252 0.00 0–14.5
DYS439 0 252 0.00 0–14.5
DYS437 2 252 7.9 1–28.4
DYS456 1 252 4.0 0.1–21.9
DYS458 1 252 4.0 0.1–21.9
DYS635 1 252 4.0 0.1–21.9
Y-GATA- H4
1 252 4.0 0.1–21.9
DYS448 0 252 0.00 0–14.5
Total 15 4284 3.5 2–5.8
Table 2
Summary of autosomal mutations in 252 father/son sample pairs using Identifiler (AB) and Powerplex 16.
Sample Locus Allele (father) Allele (child) Allele (mother)
P059 CSF1PO 8,10 8,11 8,8
P200 D3S1358 15,17 16,16 16,19
P247 D2S1338 19,22 17,20 17,21
P248 D16S539 10,12 11,11 11,12
270 A. Laouina et al. / Legal Medicine 15 (2013) 269–271
[16]Jianye Ge, Bruce B, Xavier G A, John V P, Arthur J E, Ranajit C. Mutation rates at Y chromosome short tandem repeats in Texas populations. Forensic Sci Int Genet 2009;3:179–84.
[17]Farfan MJ, Prieto V. Mutations at 17 Y-STR loci in father–son pairs from Southern Spain. Forensic Sci Int Genet 2009;2:425–6.
[18] AmpFlSTRÒYfilerÒPCR Amplification Kit User Guide, Applied Biosystems, Foster City, CA.
[19] http://statpages.org/confint.html.
[20]Excoffier LG, Laval S, Schneider S. Arlequin version 3.0: an integrated software package for population genetics data analysis. Evol Bioinf Online 2005;1:47–50.
[21] http://www.yhrd.org/.
[22]Laouina A, Houate B, Yahia H, Azeddoug H, Boulouiz R, Chbel F. Allele frequencies and population data for 17 Y-STR loci (the AmpFlSTRÒY-filer™) in Casablanca resident population. Forensic Sci Int 2011;1:e1–3.
[23]Vieira-Silva C, Dario P, Ribeiro T, Lucas I, Geada H, Espinheira R. Y-STR mutational rates determination in South Portugal Caucasian population.
Forensic Sci Int Suppl Series 2009;2:60–1.
[24]Farfan MJ, Prieto V. Mutations at 17 Y-STR loci in father–son pairs from Southern Spain. Forensic Sci Int Suppl Series 2009;2:425–6.
[25]Valeri O, Loredana B, Adriano T. Evaluating Y-chromosome STRs mutation rates: a collaborative study of the Ge.F.I.-ISFG Italian group. Forensic Sci Int Genet Suppl Series 2009;2:419–20.
A. Laouina et al. / Legal Medicine 15 (2013) 269–271 271
