Forensic Science International: Genetics 16 (2015) 205–207
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Letter to the Editor Multistep microsatellite mutation in a case of non-exclusion parentage
A R T I C L E I N F O
A B S T R A C T
Article history: Received 17 September 2014 Received in revised form 21 November 2014 Accepted 29 January 2015
A non-exclusion paternity with multistep mutation in the locus D5S818 was reported. Examination of 39 autosomal short tandem repeats (STR) loci revealed a mismatch of the maternally or paternally transmitted allele in the locus D5S818 in the questioned child. The composition of the alleles of this locus in the mother, the questioned child and the alleged father are 11/13, 7/13 and 13, respectively. The sequence analysis of the regions flanking the locus D5S818 of the mother, the questioned child and the alleged father excluded the possibility of null allele as a cause of the allelic mismatch in the child. The combined paternity index of 39 autosomal STRs is up to 2.461 109. Genotyping of sixteen Y-STR loci in the questioned child matched completely with the alleged father. The results prove that the alleged father is the biological father of the questioned child with four-step or six-step microsatellite mutation in the locus D5S818. ã 2015 Elsevier Ireland Ltd. All rights reserved.
Keywords: Paternity testing STR Multistep mutation D5S818
Dear Editor, DNA profiling of STR loci is a very powerful tool in forensic paternity testing. Generally, a paternity testing follows simple Mendelian inheritance. However, mutations of STR loci, which result in allelic mismatch in the questioned child, may complicate the forensic inference in the case of paternity testing. Multistep mutations only account for a very limited number of STR mutation events and were rarely reported in STR loci compared to single-step mutation [1–7]. We report a maternally transmitted four-step mutation or paternally transmitted six-step mutation at D5S818 locus due to reduction/mutation of repeat quantity. A study of paternity was performed for a male child in our laboratories. Buccal swabs and blood samples were collected from the mother (M), the questioned child (QC) and the alleged father (AF). Informed written permission was obtained from M and AF to use the samples for DNA profiling and subsequent research. Genomic DNA from all samples was extracted by Chelex100 method and was profiled for 39 autosomal STR loci using AmpFlSTR1 Identifiler1 STR Kit (Applied Biosystems, Foster City, CA), AGCU EX22 STR Kit and 21 + 1 STR Kit (AGCU ScienTech Inc., Wuxi City, China) as per manufacturer’s instructions. The AmpFlSTR1 Y-filer STR Kit (Applied Biosystems) was used to obtain 16 Y chromosome STR loci according to the manufacturer’s instruction. All the amplification reactions were performed with GeneAmp PCR system 9700 (PerkinElmer, Norwalk, CT). All the PCR products for STR analysis were run on ABI 3130 Genetic Analyzer and analyzed by GeneMapper ID v3.2 software (Applied Biosystems) for automated profiling. New oligonucleotide sequences http://dx.doi.org/10.1016/j.fsigen.2015.01.011 1872-4973/ ã 2015 Elsevier Ireland Ltd. All rights reserved.
were designed for D5S818 locus region amplification according to GenBank sequence information (AC008512.8) and synthesized. The forward and reverse primer sequences are 50 AACACGCCTTTCCTCTGAAGTG-30 and 50 -TCCACTATCCAGATGGGAGAGG-30 , respectively. The location of primers in the locus D5S818 is shown in Supplementary data 1. DNA samples of M, QC and AF were amplified on GeneAmp PCR system 9700 in a 25 ml reaction volume containing 10 ng DNA, 200 mM dNTPs, 6 pmol each primer, 2.0-U AmpliTaq Gold (Applied Biosystems) and 1 PCR buffer with 1.5 mM MgCl2. Thermal cycling conditions are 95 C for 5 min and then 30 cycles of 94 C for 30 s, 59 C for 30 s, 72 C for 45 s and 72 C for 10 min final extension. The PCR products were separated and purified by QIAquick1 Gel Extraction Kit (Qiagen, Germany). The separated allele fragments were cloned as per the standard procedure. Positive clones were selected and sequenced on ABI 3730 Genetic Analyzer (Applied Biosystems) according to the manufacturer’s instructions. The likelihood ratio (LR) was calculated in standard trio using the frequency of alleles from the Chinese Han population on the basis of Bayesian mathematics [8]. The LR for D5S818 locus was calculated based on the statistical method described by Brenner [9]. Autosomal STR analysis of family members indicates a mismatch of one allele at D5S818 locus in QC by using AmpFlSTR1 Identifiler1 and AGCU EX22 STR Kit. The alleles at D5S818 locus in M, QC and AF are 11/13, 7/13 and 13 (Fig. 1a and b). The allele 13 at D5S818 locus in AF shows a peak height almost twice that of the heterozygous alleles at Amel and FGA loci (Fig. 1c), which indicates the D5S818 locus in AF is homozygote. Furthermore, the sequence of (AGAT)11/(AGAT)13, (AGAT)7/(AGAT)13 and (AGAT)13 repeats was observed for 11/13, 7/13 and 13 alleles of M, QC, and AF (Supplementary data 1). The newly designed primers are located
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Letter to the Editor / Forensic Science International: Genetics 16 (2015) 205–207
Fig. 1. Electrophorogram of genotypes at D5S818 locus using AmpFlSTR1 Identifiler (a) and AGCU EX22 STR Kit; (b) shows the alleles at D5S818 locus in M, QC and AF are 11/ 13, 7/13 and 13, respectively; (c) Electrophorogram of genotypes with peak heights (ht) of AF at loci D5S818, Amel and FGA presents the ratio of peak heights of the alleles 13, X/Y, 22/25 is 0.50/0.59:1: 0.52/0.57.
far from the repeat motifs which result in much longer amplicons with a length of 561–585 bp than the amplification products of AmpFlSTR Identifiler1 (about 125–180 bp) and AGCU EX22 STR Kit (180–230 bp). These results exclude the possibility of sequence variation or presence of SNPs in the primer-binding region as a cause of allele dropout in AF using the two commercial kits. Since the D5S818 STR locus is a simple repeat, nucleotide sequence analysis of the above family does not present the source of mutation. With the above QC alleles, two hypothetical situations can be considered: (1) Allele 13 is inherited from AF and allele 7 exists by loss of four repeats from 11 alleles of M. (2) Allele 13 is obtained from M and allele 7 is acceded to QC by loss of six repeats from 13 alleles of AF. Mutation rates calculated for D5S818 STR allele during maternal and paternal meiotic stage are 0.025% and
0.12% respectively with a total of 0.11% rate [10]. The probability of maternally transmitted mutation is 20.83 times that of paternally transmitted mutation on the statistical method described by Brenner [9]. However, large multistep mutations are so rare that there is not really the empirical data to accurately assess the chance of a four-step versus six-step change [11]. For the same reason Brenner’s mutation formula makes a general assumption that mutations involving increasing numbers of repeats are less common. It seems unreasonable to use this formula to conclude that a six-step mutation is 20.83 times less likely to occur than a four-step mutation, especially since this type of mutation is seen so rarely that there must be some doubt as to whether the mechanism responsible for creating this large change in repeat number is the same as for single or double-step changes. At present, it is difficult
Letter to the Editor / Forensic Science International: Genetics 16 (2015) 205–207
to class this mutation as maternally transmitted four-step mutation rather than paternally transmitted six-step change. Microsatellite mutation occurs more frequently in longer alleles and repeats with simple structure and also seems to be influenced by gender and age (father’s age especially) [1,11]. The D5S818 locus is a simple microsatellite, and the repeat number of AF and M is 11 and 13. Furthermore, the age of AF and M was 46 and 44 years old respectively when M was pregnant, which is more likely to further increase the rate of mutation. These factors could contribute to multistep losses of repeats. According to ISFG guidelines [12] at least three inconsistencies between maternal/paternal and child are to be proved to report the parentage as exclusion. Additional autosomal STR and/or X, Y STR, mitochondrial, HLA haplotype typing are recommended to describe the parentage end result. In further investigation of 39 autosomal STR loci, no additional incompatible STR loci were found finally (the data of genotypes for each locus of the 3 STR kits used are shown in Supplementary data 2). The paternity index obtained in the motherless situation with the relation between the QC and AF is 1.7394 1011. The Maternity Index obtained in the fatherless situation with the relation between the QC and M is 4.8402 1013. The overall LR calculated for all STR loci including the mismatched alleles in standard trios situation is 2.461 109. Furthermore, the genotype of 16 Y-STR loci in QC matched completely with that of AF (the data are shown in Supplementary data 3). Therefore the AF and M was confirmed as the biological father and mother of the QC. Acknowledgements We thank Dr. Yi Shao, AGCU ScienTech Incorporation for extending all the facilities to carry out the sequencing work. This research was supported by the National Natural Science Foundation of China (No. 81202386), and the Fundamental Research Funds for the Central Universities, HUST: No. 2013TS111. Appendix A. Supplementary data
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Yu Xuan Liu Wen Qiong Zhang Yun Shu Jia Lei Zhang Feng Lei Zhou Kun Mei Dai Xin Huang Shao Hua Yi* Department of Forensic Medicine of Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China AGCU ScienTech Incorporation, Wuxi 214174, China
Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j. fsigen.2015.01.011.
Department of Forensic Medicine of Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
References
* Corresponding author. Tel.: +86 27 8369 2645; fax: +86 27 8363 1216. E-mail address:
[email protected] (S. Yi).
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Received 17 September 2014 Received in revised form 21 November 2014 Accepted 29 January 2015