- Email: [email protected]
Y-STR chromosome structure variations: Incidence and implications
Forensic Science International: Genetics Supplement Series xxx (xxxx) xxx–xxx
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/fsigss
Y-STR chromosome structure variations: Incidence and implications Walter Ruben Bozzo, Malena Canteros, Luciana Rabitti, Nicolás Furman, Florencia Gagliardi, Mariana Herrera Piñero* Banco Nacional de Datos Genéticos, Avda. Cordoba 831, C1054AAH, Ciudad Autónoma de Buenos Aires, Argentina
ARTICLE INFO
ABSTRACT
Keyword: Y-STR structure variations
In this study 1178 Y-STR haplotypes of unrelated male donors’ samples were analyzed in order to detect Y-STR structure variations and their implications in forensic samples analysis. DNA was amplified with Yfiler or Yfiler Plus (Applied Biosystems). 19 structure variations (1.6%) were detected: 12 duplications, 5 deletions, 1 deletion/ duplication and 1 complex structure variation. The markers involved were mostly DYF387S1 and DYS19. In 5 samples the structure variations included several Y-STRs. In one particular case, alleles were detected in only 7 markers of the Yfiler Plus kit. These findings are not critical for kinship studies whereas are very important in forensic caseworks interpretation.
1. Introduction
3. Results and discussion
Y-STRs analysis is a frequent practice in forensic genetics laboratories, not only for paternal lineage studies but also for criminalistics cases. Most markers in multiplex kits are single copy. Markers such as DYS385, DYS389II and DYF387S1 are multicopy and generate two alleles in the profile. Structure variations such as silent alleles, deletions, duplications and triplications in some individuals could lead to mistakes in results interpretation. In this study, we analyzed 1178 Y-STR haplotypes of unrelated male donors’ samples, in order to detect Y-STR structure variations and determine their incidence and implications in the analysis of forensic samples.
19 structure variations (1.6%) were detected: 12 duplications, 5 deletions, 1 deletion/duplication, and 1 complex structure variation (Table 1). The markers involved were mostly DYF387S1 and DYS19. In 5 individuals the structure variations included several Y-STR loci. Two adjacent loci were duplicated simultaneously in 2 cases and in one case had a deletion/duplication. One sample had a duplication that involved 4 adjacent loci located along the AZFa region. We could not confirm the lack of an allele in a locus with other kits in order to discard null alleles. Our results are concordant with those reported by Aliferi et al. [1] for population of the United Kingdom and Ireland. We observed some differences with the frequencies published by Purps et al. [2] in which they analyzed a larger sample size. In one male, alleles were detected only in 7 markers with Yfiler Plus kit (Supplementary Fig. 1). Deletion involved the entire Y chromosome long arm and part of short arm. X-STR profile (Argus X-12 QS) is compatible with the presence of two X chromosomes (data not shown). The male phenotype is due to the SRY gene presence confirmed by PCR. This finding could be explained considering the person as an XX male with part of Yp material translocated to an X chromosome due to two separated events: the presence in his father of a Y chromosome paracentric inversion during meiosis ranging from Amelogenin to DYS19 and a translocation of the segment that contains the 7 markers and the SRY gene present in the sample, to the paternal X chromosome (Fig. 1). Deletions involving one or two markers do not produce serious problems when interpreting a Y profile in forensic cases. However,
2. Materials and methods DNA from 1178 male blood samples collected on FTA cards was extracted using a QIAcube system (Qiagen). Y-STRs profiles were obtained with Applied Biosystems commercial kits: Yfiler (514 samples) or Yfiler Plus (664 samples). Capillary electrophoresis was done in an ABI 3500 Genetic Analyzer (Applied Biosystems) and data was analyzed with GeneMapper X-ID software. Structure variations were confirmed by DNA re-extraction and a new amplification. SRY PCR amplification was run in agarose gels. People analyzed signed a consent form accepting the use of their genetic profiles for population studies.
⁎
Corresponding author. E-mail address: [email protected] (M. Herrera Piñero).
https://doi.org/10.1016/j.fsigss.2019.10.102 Received 6 September 2019; Received in revised form 9 October 2019; Accepted 9 October 2019 1875-1768/ © 2019 Elsevier B.V. All rights reserved.
Please cite this article as: Walter Ruben Bozzo, et al., Forensic Science International: Genetics Supplement Series, https://doi.org/10.1016/j.fsigss.2019.10.102
Forensic Science International: Genetics Supplement Series xxx (xxxx) xxx–xxx
W.R. Bozzo, et al.
Table 1 Structure variations detected in the 1178 individuals analyzed. Structure Variations
Amelog.
Alleles
N samples
DUPLICATION DYS19 DYS389II / DYS439 DYS389I / DYS389II / DYS439 / DYS437
X-Y X-Y X-Y
15-16 30-31/11-12 13-14/29-30/10-11/ 15-16 19-20 34-38-39 37-38-39 37-39-40
4 2 1
DYS448 DYF387S1 DYF387S1 DYF387S1 Total DELETION DYS448 DYF387S1 DYS19 Total COMPLEX STRUCTURE VARIANT DYS576, DYS389I, DYS635, DYS389II, DYS460, YGATAH4, DYS448, DYS391, DYS390, DYS438, DYS392, DYS518, DYS570, DYS437, DYS385, DYS439, DYF387S1, DYS533 Total DELETION/DUPLICATION DYS448 / DYF387S1 Total Total Structure Variations
X-Y X-Y X-Y X-Y
1 1 1 2 12
1.00%
X-Y X-Y X-Y
2 2 1 5
0.42%
X
1
X-Y
Fig. 1. Proposed mechanism to interpret the results in the case of XX male. 2
Freq.
del / 34-35-36
1
0.08%
1 1 19
0.08% 1.58%
Forensic Science International: Genetics Supplement Series xxx (xxxx) xxx–xxx
W.R. Bozzo, et al.
duplications or triplications could indicate a mixed DNA profile. The finding and interpretation of partial or very incomplete Y-STR profiles is also relevant. For our XX male case, the profile obtained with autosomal markers could have been interpreted as belonging to a female, since no allele peaks were detected for DYS570, DYS576 and Amelogenin (the three Y-STR present in the PowerPlex Fusion 6C kit, Promega). Since these three markers are consecutive in Y chromosome, the manufacturers should reconsider others Y-STR markers to include in their kits to avoid misinterpretations in these cases. The frequency of structure variations was estimated in 1.58% of the Y-STR haplotypes studied, detecting a higher incidence of duplications. These findings are not critical for kinship studies. But they are relevant in the interpretation of possible DNA mixtures profiles recovered from evidence of
forensic interest. Appendix A. Supplementary data Supplementary material related to this article can be found, in the online version, at doi:https://doi.org/10.1016/j.fsigss.2019.10.102. References [1] A. Aliferi, et al., UK and Irish Y-STR population data – a catalogue of variant alleles, Forensic Sci. Int. Genet. 34 (2018) e1–e6. [2] J. Purps, et al., A global analysis of Y-chromosomal haplotype diversity for 23 STR loci, Forensic Sci. Int. Genet. 12- (2014) 12–23.
3
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/fsigss
Y-STR chromosome structure variations: Incidence and implications Walter Ruben Bozzo, Malena Canteros, Luciana Rabitti, Nicolás Furman, Florencia Gagliardi, Mariana Herrera Piñero* Banco Nacional de Datos Genéticos, Avda. Cordoba 831, C1054AAH, Ciudad Autónoma de Buenos Aires, Argentina
ARTICLE INFO
ABSTRACT
Keyword: Y-STR structure variations
In this study 1178 Y-STR haplotypes of unrelated male donors’ samples were analyzed in order to detect Y-STR structure variations and their implications in forensic samples analysis. DNA was amplified with Yfiler or Yfiler Plus (Applied Biosystems). 19 structure variations (1.6%) were detected: 12 duplications, 5 deletions, 1 deletion/ duplication and 1 complex structure variation. The markers involved were mostly DYF387S1 and DYS19. In 5 samples the structure variations included several Y-STRs. In one particular case, alleles were detected in only 7 markers of the Yfiler Plus kit. These findings are not critical for kinship studies whereas are very important in forensic caseworks interpretation.
1. Introduction
3. Results and discussion
Y-STRs analysis is a frequent practice in forensic genetics laboratories, not only for paternal lineage studies but also for criminalistics cases. Most markers in multiplex kits are single copy. Markers such as DYS385, DYS389II and DYF387S1 are multicopy and generate two alleles in the profile. Structure variations such as silent alleles, deletions, duplications and triplications in some individuals could lead to mistakes in results interpretation. In this study, we analyzed 1178 Y-STR haplotypes of unrelated male donors’ samples, in order to detect Y-STR structure variations and determine their incidence and implications in the analysis of forensic samples.
19 structure variations (1.6%) were detected: 12 duplications, 5 deletions, 1 deletion/duplication, and 1 complex structure variation (Table 1). The markers involved were mostly DYF387S1 and DYS19. In 5 individuals the structure variations included several Y-STR loci. Two adjacent loci were duplicated simultaneously in 2 cases and in one case had a deletion/duplication. One sample had a duplication that involved 4 adjacent loci located along the AZFa region. We could not confirm the lack of an allele in a locus with other kits in order to discard null alleles. Our results are concordant with those reported by Aliferi et al. [1] for population of the United Kingdom and Ireland. We observed some differences with the frequencies published by Purps et al. [2] in which they analyzed a larger sample size. In one male, alleles were detected only in 7 markers with Yfiler Plus kit (Supplementary Fig. 1). Deletion involved the entire Y chromosome long arm and part of short arm. X-STR profile (Argus X-12 QS) is compatible with the presence of two X chromosomes (data not shown). The male phenotype is due to the SRY gene presence confirmed by PCR. This finding could be explained considering the person as an XX male with part of Yp material translocated to an X chromosome due to two separated events: the presence in his father of a Y chromosome paracentric inversion during meiosis ranging from Amelogenin to DYS19 and a translocation of the segment that contains the 7 markers and the SRY gene present in the sample, to the paternal X chromosome (Fig. 1). Deletions involving one or two markers do not produce serious problems when interpreting a Y profile in forensic cases. However,
2. Materials and methods DNA from 1178 male blood samples collected on FTA cards was extracted using a QIAcube system (Qiagen). Y-STRs profiles were obtained with Applied Biosystems commercial kits: Yfiler (514 samples) or Yfiler Plus (664 samples). Capillary electrophoresis was done in an ABI 3500 Genetic Analyzer (Applied Biosystems) and data was analyzed with GeneMapper X-ID software. Structure variations were confirmed by DNA re-extraction and a new amplification. SRY PCR amplification was run in agarose gels. People analyzed signed a consent form accepting the use of their genetic profiles for population studies.
⁎
Corresponding author. E-mail address: [email protected] (M. Herrera Piñero).
https://doi.org/10.1016/j.fsigss.2019.10.102 Received 6 September 2019; Received in revised form 9 October 2019; Accepted 9 October 2019 1875-1768/ © 2019 Elsevier B.V. All rights reserved.
Please cite this article as: Walter Ruben Bozzo, et al., Forensic Science International: Genetics Supplement Series, https://doi.org/10.1016/j.fsigss.2019.10.102
Forensic Science International: Genetics Supplement Series xxx (xxxx) xxx–xxx
W.R. Bozzo, et al.
Table 1 Structure variations detected in the 1178 individuals analyzed. Structure Variations
Amelog.
Alleles
N samples
DUPLICATION DYS19 DYS389II / DYS439 DYS389I / DYS389II / DYS439 / DYS437
X-Y X-Y X-Y
15-16 30-31/11-12 13-14/29-30/10-11/ 15-16 19-20 34-38-39 37-38-39 37-39-40
4 2 1
DYS448 DYF387S1 DYF387S1 DYF387S1 Total DELETION DYS448 DYF387S1 DYS19 Total COMPLEX STRUCTURE VARIANT DYS576, DYS389I, DYS635, DYS389II, DYS460, YGATAH4, DYS448, DYS391, DYS390, DYS438, DYS392, DYS518, DYS570, DYS437, DYS385, DYS439, DYF387S1, DYS533 Total DELETION/DUPLICATION DYS448 / DYF387S1 Total Total Structure Variations
X-Y X-Y X-Y X-Y
1 1 1 2 12
1.00%
X-Y X-Y X-Y
2 2 1 5
0.42%
X
1
X-Y
Fig. 1. Proposed mechanism to interpret the results in the case of XX male. 2
Freq.
del / 34-35-36
1
0.08%
1 1 19
0.08% 1.58%
Forensic Science International: Genetics Supplement Series xxx (xxxx) xxx–xxx
W.R. Bozzo, et al.
duplications or triplications could indicate a mixed DNA profile. The finding and interpretation of partial or very incomplete Y-STR profiles is also relevant. For our XX male case, the profile obtained with autosomal markers could have been interpreted as belonging to a female, since no allele peaks were detected for DYS570, DYS576 and Amelogenin (the three Y-STR present in the PowerPlex Fusion 6C kit, Promega). Since these three markers are consecutive in Y chromosome, the manufacturers should reconsider others Y-STR markers to include in their kits to avoid misinterpretations in these cases. The frequency of structure variations was estimated in 1.58% of the Y-STR haplotypes studied, detecting a higher incidence of duplications. These findings are not critical for kinship studies. But they are relevant in the interpretation of possible DNA mixtures profiles recovered from evidence of
forensic interest. Appendix A. Supplementary data Supplementary material related to this article can be found, in the online version, at doi:https://doi.org/10.1016/j.fsigss.2019.10.102. References [1] A. Aliferi, et al., UK and Irish Y-STR population data – a catalogue of variant alleles, Forensic Sci. Int. Genet. 34 (2018) e1–e6. [2] J. Purps, et al., A global analysis of Y-chromosomal haplotype diversity for 23 STR loci, Forensic Sci. Int. Genet. 12- (2014) 12–23.
3