- Email: [email protected]
Allele frequency database for GlobalFiler™ STR loci in Australian and New Zealand populations
G Model FSIGEN 1667 No. of Pages 3
Forensic Science International: Genetics xxx (2016) xxx–xxx
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Correspondence Allele frequency database for GlobalFilerTM STR loci in Australian and New Zealand populations
A R T I C L E I N F O
Article history: Received 4 November 2016 Available online xxx Keywords: GlobalFiler1 Allele frequency Asian Caucasian Aboriginal Australian Polynesian New Zealand
A B S T R A C T
We assign autosomal allele proportions for Caucasian, Asian, self-declared Aboriginal and pure Aboriginal populations from Australia and Caucasian and Eastern and Western Polynesian populations from New Zealand. Population sample sizes vary from 122 to 528. All populations underwent tests for the presence of allelic dependencies (i.e. departures from the expectations of Hardy Weinberg and Linkage equilibrium) and some large dependencies were observed in the Australian Aboriginal populations. We provide allele frequency files for all populations examined. © 2017 Elsevier B.V. All rights reserved.
Dear Editor, Here we provide for the forensic community allele frequencies for the populations listed in Table 1. DNA profiles from individuals designated as:
‘Pure’ Aboriginal (based on possession of a ‘skin name’1 ) Self-declared Aboriginal Self-declared Asian Self-declared New Zealand and Australian Caucasian Self-declared Eastern Polynesian Self-declared Western Polynesian
were compiled from data generated in Forensic Science SA (FSSA), Forensic and Analytical Science Service NSW (FASS) or NT Police, Fire and Emergency Services (PFES) Forensic Biology (NT) and The Institute of Environmental and Scientific Research Limited (ESR). Eastern Polynesians are defined as individuals claiming any proportion of decent from New Zealand Maori, Cook Island (including Rarotonga), Tokelau, Hawaii, Tahiti, French Polynesia, Pitcairn Island, and Easter Island. Western Polynesians are defined as individuals claiming any proportion of decent from Samoa, Tonga and Niue. The reported groups represent the same populations that have previously been profiled using commercial DNA profiling systems with fewer loci [1–5]. Note that due to the process of de-identification the samples go through, it may be the
1 A skin name is given to a section or subsection of an Aboriginal kinship group and is a feature of Australian Aboriginal social origination and family relationships.
case that some individuals that were profiled and made up databases previously published could also be present in the databases reported here. The additional population of SelfDeclared Asian is compiled of individuals within Australia who identify themselves as belonging to any Asian group. Samples were collected from volunteers, suspect and convicted offenders in accordance with local government legislation or volunteers. Volunteers gave informed consent and suspects or convicted offender samples were used in accordance with local legislative requirements. All duplicate profiles were removed from the datasets. 1. Methods All participating Australian laboratories are accredited by the National Association of Testing Authorities (http://www.nata.asn. au/). ESR New Zealand is accredited by the American Society of Crime Laboratory Directors Laboratory Accreditation Board (ASCLD/LAB, http://www.ascld-lab.org/). All laboratories participate in annual external proficiency testing programmes. Amplification: Extracted DNA was amplified using the ThermoFisher – Life Technologies’ GlobalFilerTM Express or GlobalFilerTM testing kits following the manufacturer's recommended guidelines. Typing: Amplified DNA was separated on an Applied Biosystems’ 3130xl or 3500xl. Profiles were analysed using Applied Biosystems’ GeneMapperTM ID-X using in-house determined analytical and stochastic thresholds and stutter management thresholds. Analysis: Genetic Data Analysis (GDA) software (courtesy of Paul Lewis, available at http://www.eeb.uconn.edu/people/plewis/
http://dx.doi.org/10.1016/j.fsigen.2017.02.012 1872-4973/© 2017 Elsevier B.V. All rights reserved.
Please cite this article in press as: D. Taylor, et al., Allele frequency database for GlobalFilerTM STR loci in Australian and New Zealand populations, Forensic Sci. Int. Genet. (2017), http://dx.doi.org/10.1016/j.fsigen.2017.02.012
G Model FSIGEN 1667 No. of Pages 3
2
Correspondence / Forensic Science International: Genetics xxx (2016) xxx–xxx
Table 1 Samples compiled in this study. Australian Caucasian
NZ Caucasian
Asian
Self-declared Aboriginal
Pure Aboriginal
Eastern Polynesian
Western Polynesian
FSSA FASS NT ESR
226 100 202 0
0 0 0 159
213 100 176 0
218 100 0 0
0 0 588 0
0 0 0 170
0 0 0 122
Total
528
159
489
318
588
170
122
software.php) was used to calculate p values for allelic association obtained from the Fisher's exact test. Data was shuffled 10,000 times. 2. Results Graphical representations of the p value data are presented in Figures 1 and 2 (Supplementary data). These allow a level of visual comparison of the results of independence testing. We also assess departures from Hardy Weinberg Equilibrium (HWE) and linkage equilibrium (LE) for the whole dataset using the truncated product method of Zaykin, Zhivotovsky and Weir [6]. This allows us to calculate the p-value for the null hypothesis that all 21 autosomal STR loci are in HWE, or that all 210 pairs of loci are in LE. It is important to note that these tests are not independent and hence the truncated product method can only be used as a guide. The Y-indel locus is present in males only and can take two forms, 1 and 2. The proportion that each of these alleles was present in the reported populations is shown in Table 3. Table 2 shows the p values for the significance tests on all populations using the truncated product method. Whilst Fisher's Exact Test is the method of choice for investigating departures from independence in this situation, it has limited power for samples of small or moderate size. The datasets analysed here are small by international standards. As such it is expected that Fisher's Exact Test would not necessarily be expected to find departures in the datasets if they were present (Table 3). 3. Comparisons to other populations A comprehensive comparison of where these populations sit within a world stage can be seen in [7]. In [7] the Australian Aboriginal populations that would most closely align with the SelfDeclared population in our study are the “Aust_Abor_Spencer” and “Aust_Abor_Riverine” (‘Riverine’ and ‘Spencer’ refer to ancestral Aboriginal regional groups as defined by Horton [8]). Note that [9] found significant admixture in the self-declared Aboriginal population on the Y-Chromosome and it is likely that significant admixture is also present in the Autosomal self-declared Aboriginal dataset reported here. The Pure Aboriginal dataset most closely aligns with the “Aust_Abor_NT” populations of [7] (where NT stands for the Northern Territory of Australia). The Eastern and Western Polynesian populations most closely align with the “E_Polynesian” and “W_Polynesian” populations of [7]. The Australia and New Zealand Caucasian populations would most
Table 3 Allele proportions at Y-indel for males, n = number of observations, p = proportion. Population
1 allele at Y-indel
2 allele at Y-indel
‘Pure’ Aboriginal Self-declared Aboriginal Self-declared Asian Self-declared Australian Caucasian Self-declared New Zealand Caucasian Self-declared eastern Polynesian Self-declared western Polynesian
n = 8, p = 0.018 n = 2, p = 0.007 n = 321, p = 0.772 n = 6, p = 0.015 n = 1, p = 0.007 n = 12, p = 0.095 n = 50, p = 0.424
n = 442, p = 0.982 n = 273, p = 0.993 n = 95, p = 0.228 n = 401, p = 0.985 n = 150, p = 0.993 n = 114, p = 0.905 n = 68, p = 0.576
closely align with the “Cauc_Australian” and “Cauc_NZ” populations of [7]. The Asian population reported in our work is a mixture of Asian groups, based on self-declaration. It is likely that this population would fall within the Asian clades of [7], presented in a mustard colour of the phylogenetic tree provided as supplementary material. 4. Conclusion The most marked deviation from both HWE and LE are in the self-declared Aboriginal group, which is expected given the findings of Walsh and Buckleton [1] who showed that genetic boundaries follow traditional regional or tribal lines rather than jurisdictional ones. Asian, pure Aboriginal, Australian Caucasian and Eastern Polynesian also showed evidence for departures from LE. The pure Aboriginal also showed evidence for departure from HWE. The term ‘pure Aboriginal’ is one that is used by PFES as containing individuals that met several criteria: they live in a remote district, possess a ‘skin’ name or that they were assigned as pure based on information from the investigating officers. The remaining populations comprise individuals whose ethnicity is based on self-declaration. Self-declaration has been questioned in court [10] and there are instances of possible self-declaration bias. For example Wild and Seber [11] note, ‘In recent US censuses there has been a big upsurge in the census counts of American Indians that could not be explained by birth and death statistics’. Taylor et al. [9] noted the presence of admixture in the self-declaration of Aboriginal Australians based on the Y-chromosome, and while the effect would be different on autosomal markers (owing to the different mechanism of inheritance) the results would lead us to expect a high level of autosomal admixture. Addressing this idea Walsh et al. [12] conducted a study to determine whether selfdeclaration was a method that would produce data fit for purpose in forensic applications. They found that the genetic content of
Table 2 p-values obtained by tests for departure from Hardy-Weinberg or Linkage equilibrium. Values below 0.05 are bolded. Australian Caucasian Departure from HWE 0.37 Departure from LE 1.6 10
3
New Zealand Caucasian Asian 0.05 0.14
0.054 3.4 10
Self-declared Aboriginal 22
1.6 10 4.9 10
13 257
Pure Aboriginal 5.2 10 5.4 10
4 53
Eastern Polynesian
Western Polynesian
0.54 0.01
0.17 0.3
Please cite this article in press as: D. Taylor, et al., Allele frequency database for GlobalFilerTM STR loci in Australian and New Zealand populations, Forensic Sci. Int. Genet. (2017), http://dx.doi.org/10.1016/j.fsigen.2017.02.012
G Model FSIGEN 1667 No. of Pages 3
Correspondence / Forensic Science International: Genetics xxx (2016) xxx–xxx
groups that self-declared as full or part New Zealand Maori followed a pattern that would be expected if self-declaration was reporting accurately. It is the author's personal experience that the general consensus of the forensic community is that selfdeclaration, while not a perfect system, produces databases that are fit for forensic use and that other mitigating factors can be applied to Court reported values (i.e. the application of co-ancestry coefficients, the use of databases from multiple populations, or taking into account sampling uncertainty associated with population database construction) so as not to overstate the strength of the findings. Regardless of the results of independence testing, our knowledge of the history of human populations leads us to expect that some level of admixture or substructure exists in all populations. The population databases presented here are of suitable size for the purpose of estimating allele frequencies. For criminal investigations, it is recommended that multi-locus profile probabilities be calculated by the method of Balding and Nichols [13] with conservative values of the inbreeding coefficient (u or FST). The FST values used currently in casework are 0.05, 0.05, 0.05, 0.03, and 0.02 respectively for the Aboriginal, Eastern Polynesian, Western Polynesian, Asian, and Caucasian datasets. These are very conservative values based on the work undertaken by Buckleton et al. [7]. This paper follows the guidelines for publication of population genetic data in the journal [14,15].
3
[3] S.J. Walsh, J.R. Cullen, S.A. Harbison, Allele frequencies for the four major subpopulations of New Zealand at the 10 AMPFlSTR1 SGM PlusTM loci, For. Sci. Int. 122 (2–3) (2001) 189–195. [4] D. Taylor, J. Henry, S. Walsh, South Australian Aboriginal sub-population data for the nine AMPLFlSTR1 Profiler PlusTMshort tandem repeat (STR) loci, For. Sci. Int.: Genet. 2 (2) (2009) e27–e30. [5] J.-A. Bright, C. Allen, S. Fountain, K. Gray, D. Grover, S. Neville, A.L. Poy, D. Taylor, G. Turbett, L. Wilson-Wilde, Australian population data for the twenty Promega PowerPlex 21 short tandem repeat loci, Austr. J. For. Sci. 46 (4) (2014) 442–446. [6] I.W. Evett, B.S. Weir, Interpreting DNA Evidence – Statistical Genetics for Forensic Scientists, Sinauer Associates, Inc, Sunderland, 1998. [7] J. Buckleton, J. Curran, J. Goudet, D. Taylor, A. Thiery, B. Weir, Populationspecific FST values for forensic STR markers: a worldwide survey, For. Sci. Int.: Genet. 23 (2016) 126–133. [8] D. Horton, Aboriginal Australia Map, AIATSIS and Auslig, Canberra, ACT, 1996. [9] D. Taylor, N. Nagle, K.N. Ballantyne, R.A.H. van Oorschot, S. Wilcox, J. Henry, R. Turakulov, R.J. Mitchell, An investigation of admixture in an Australian Aboriginal Y-chromosome STR database, For. Sci. Int.: Genet. 6 (2012) 532– 538. [10] B.S. Weir, DNA statistics in the Simpson matter, Nat. Genet. 11 (1995) 365–368. [11] C.J. Wild, G.A.F. Seber, Chance Encounters, John Wiley and Sons, New York, 2000. [12] S.J. Walsh, C.M. Triggs, J.M. Curran, J.R. Cullen, J.S. Buckleton, Evidence in support of self-declaration as a sampling method for the formation of subpopulation databases, J. For. Sci. 48 (5) (2003) 1091–1093. [13] D.J. Balding, R.A. Nichols, DNA profile match probability calculation: how to allow for population stratification, relatedness, database selection and single bands, For. Sci. Int. 64 (1994) 125–140. [14] Á. Carracedo, J.M. Butler, L. Gusmão, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, New guidelines for the publication of genetic population data, For. Sci. Int.: Genet. 7 (2013) 217–220. [15] Á. Carracedo, J.M. Butler, L. Gusmão, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, Update of the guidelines for the publication of genetic population data, For. Sci. Int.: Genet. 10 (2014) A1–A2.
Conflicts of interest The authors declare no conflict of interest. Acknowledgements This work was supported in part by grant 2011-DN-BX-K541 from the US National Institute of Justice. Points of view in this document are those of the authors and do not necessarily represent the official position or policies of the U.S. Department of Justice. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j. fsigen.2017.02.012. References [1] S.J. Walsh, J. Buckleton, Autosomal microsatellite allele frequencies for 15 regionally defined Aboriginal Australian population datasets, For. Sci. Int. 168 (2007) e29–e42. [2] S.J. Walsh, J.S. Buckleton, Autosomal microsatellite allele frequencies for a nationwide dataset from the Australian Caucasian sub-population, For. Sci. Int. 168 (2–3) (2007) e47–e50.
Duncan Taylora,b,* Forensic Science South Australia, 21 Divett Place, Adelaide, SA, 5000, Australia
a
b
School of Biological Sciences, Flinders University, GPO Box 2100 Adelaide SA 5001, Australia Jo-Anne Bright Catherine McGovern ESR Limited, Private Bag 92021 Auckland New Zealand
Sharon Neville NSW Forensic & Analytical Science Service, NSW Health Pathology, Joseph St, Lidcombe NSW 2141, Australia Denise Grover Forensic Science Branch NT Police, Peter McAulay Centre, Berrimah, PO Box 39764, Winnellie NT 0821, Australia * Corresponding author at: Forensic Science South Australia, 21 Divett Place, Adelaide, SA 5000, Australia. E-mail address: [email protected] (D. Taylor). Received 4 November 2016 Available online xxx
Please cite this article in press as: D. Taylor, et al., Allele frequency database for GlobalFilerTM STR loci in Australian and New Zealand populations, Forensic Sci. Int. Genet. (2017), http://dx.doi.org/10.1016/j.fsigen.2017.02.012
Forensic Science International: Genetics xxx (2016) xxx–xxx
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Correspondence Allele frequency database for GlobalFilerTM STR loci in Australian and New Zealand populations
A R T I C L E I N F O
Article history: Received 4 November 2016 Available online xxx Keywords: GlobalFiler1 Allele frequency Asian Caucasian Aboriginal Australian Polynesian New Zealand
A B S T R A C T
We assign autosomal allele proportions for Caucasian, Asian, self-declared Aboriginal and pure Aboriginal populations from Australia and Caucasian and Eastern and Western Polynesian populations from New Zealand. Population sample sizes vary from 122 to 528. All populations underwent tests for the presence of allelic dependencies (i.e. departures from the expectations of Hardy Weinberg and Linkage equilibrium) and some large dependencies were observed in the Australian Aboriginal populations. We provide allele frequency files for all populations examined. © 2017 Elsevier B.V. All rights reserved.
Dear Editor, Here we provide for the forensic community allele frequencies for the populations listed in Table 1. DNA profiles from individuals designated as:
‘Pure’ Aboriginal (based on possession of a ‘skin name’1 ) Self-declared Aboriginal Self-declared Asian Self-declared New Zealand and Australian Caucasian Self-declared Eastern Polynesian Self-declared Western Polynesian
were compiled from data generated in Forensic Science SA (FSSA), Forensic and Analytical Science Service NSW (FASS) or NT Police, Fire and Emergency Services (PFES) Forensic Biology (NT) and The Institute of Environmental and Scientific Research Limited (ESR). Eastern Polynesians are defined as individuals claiming any proportion of decent from New Zealand Maori, Cook Island (including Rarotonga), Tokelau, Hawaii, Tahiti, French Polynesia, Pitcairn Island, and Easter Island. Western Polynesians are defined as individuals claiming any proportion of decent from Samoa, Tonga and Niue. The reported groups represent the same populations that have previously been profiled using commercial DNA profiling systems with fewer loci [1–5]. Note that due to the process of de-identification the samples go through, it may be the
1 A skin name is given to a section or subsection of an Aboriginal kinship group and is a feature of Australian Aboriginal social origination and family relationships.
case that some individuals that were profiled and made up databases previously published could also be present in the databases reported here. The additional population of SelfDeclared Asian is compiled of individuals within Australia who identify themselves as belonging to any Asian group. Samples were collected from volunteers, suspect and convicted offenders in accordance with local government legislation or volunteers. Volunteers gave informed consent and suspects or convicted offender samples were used in accordance with local legislative requirements. All duplicate profiles were removed from the datasets. 1. Methods All participating Australian laboratories are accredited by the National Association of Testing Authorities (http://www.nata.asn. au/). ESR New Zealand is accredited by the American Society of Crime Laboratory Directors Laboratory Accreditation Board (ASCLD/LAB, http://www.ascld-lab.org/). All laboratories participate in annual external proficiency testing programmes. Amplification: Extracted DNA was amplified using the ThermoFisher – Life Technologies’ GlobalFilerTM Express or GlobalFilerTM testing kits following the manufacturer's recommended guidelines. Typing: Amplified DNA was separated on an Applied Biosystems’ 3130xl or 3500xl. Profiles were analysed using Applied Biosystems’ GeneMapperTM ID-X using in-house determined analytical and stochastic thresholds and stutter management thresholds. Analysis: Genetic Data Analysis (GDA) software (courtesy of Paul Lewis, available at http://www.eeb.uconn.edu/people/plewis/
http://dx.doi.org/10.1016/j.fsigen.2017.02.012 1872-4973/© 2017 Elsevier B.V. All rights reserved.
Please cite this article in press as: D. Taylor, et al., Allele frequency database for GlobalFilerTM STR loci in Australian and New Zealand populations, Forensic Sci. Int. Genet. (2017), http://dx.doi.org/10.1016/j.fsigen.2017.02.012
G Model FSIGEN 1667 No. of Pages 3
2
Correspondence / Forensic Science International: Genetics xxx (2016) xxx–xxx
Table 1 Samples compiled in this study. Australian Caucasian
NZ Caucasian
Asian
Self-declared Aboriginal
Pure Aboriginal
Eastern Polynesian
Western Polynesian
FSSA FASS NT ESR
226 100 202 0
0 0 0 159
213 100 176 0
218 100 0 0
0 0 588 0
0 0 0 170
0 0 0 122
Total
528
159
489
318
588
170
122
software.php) was used to calculate p values for allelic association obtained from the Fisher's exact test. Data was shuffled 10,000 times. 2. Results Graphical representations of the p value data are presented in Figures 1 and 2 (Supplementary data). These allow a level of visual comparison of the results of independence testing. We also assess departures from Hardy Weinberg Equilibrium (HWE) and linkage equilibrium (LE) for the whole dataset using the truncated product method of Zaykin, Zhivotovsky and Weir [6]. This allows us to calculate the p-value for the null hypothesis that all 21 autosomal STR loci are in HWE, or that all 210 pairs of loci are in LE. It is important to note that these tests are not independent and hence the truncated product method can only be used as a guide. The Y-indel locus is present in males only and can take two forms, 1 and 2. The proportion that each of these alleles was present in the reported populations is shown in Table 3. Table 2 shows the p values for the significance tests on all populations using the truncated product method. Whilst Fisher's Exact Test is the method of choice for investigating departures from independence in this situation, it has limited power for samples of small or moderate size. The datasets analysed here are small by international standards. As such it is expected that Fisher's Exact Test would not necessarily be expected to find departures in the datasets if they were present (Table 3). 3. Comparisons to other populations A comprehensive comparison of where these populations sit within a world stage can be seen in [7]. In [7] the Australian Aboriginal populations that would most closely align with the SelfDeclared population in our study are the “Aust_Abor_Spencer” and “Aust_Abor_Riverine” (‘Riverine’ and ‘Spencer’ refer to ancestral Aboriginal regional groups as defined by Horton [8]). Note that [9] found significant admixture in the self-declared Aboriginal population on the Y-Chromosome and it is likely that significant admixture is also present in the Autosomal self-declared Aboriginal dataset reported here. The Pure Aboriginal dataset most closely aligns with the “Aust_Abor_NT” populations of [7] (where NT stands for the Northern Territory of Australia). The Eastern and Western Polynesian populations most closely align with the “E_Polynesian” and “W_Polynesian” populations of [7]. The Australia and New Zealand Caucasian populations would most
Table 3 Allele proportions at Y-indel for males, n = number of observations, p = proportion. Population
1 allele at Y-indel
2 allele at Y-indel
‘Pure’ Aboriginal Self-declared Aboriginal Self-declared Asian Self-declared Australian Caucasian Self-declared New Zealand Caucasian Self-declared eastern Polynesian Self-declared western Polynesian
n = 8, p = 0.018 n = 2, p = 0.007 n = 321, p = 0.772 n = 6, p = 0.015 n = 1, p = 0.007 n = 12, p = 0.095 n = 50, p = 0.424
n = 442, p = 0.982 n = 273, p = 0.993 n = 95, p = 0.228 n = 401, p = 0.985 n = 150, p = 0.993 n = 114, p = 0.905 n = 68, p = 0.576
closely align with the “Cauc_Australian” and “Cauc_NZ” populations of [7]. The Asian population reported in our work is a mixture of Asian groups, based on self-declaration. It is likely that this population would fall within the Asian clades of [7], presented in a mustard colour of the phylogenetic tree provided as supplementary material. 4. Conclusion The most marked deviation from both HWE and LE are in the self-declared Aboriginal group, which is expected given the findings of Walsh and Buckleton [1] who showed that genetic boundaries follow traditional regional or tribal lines rather than jurisdictional ones. Asian, pure Aboriginal, Australian Caucasian and Eastern Polynesian also showed evidence for departures from LE. The pure Aboriginal also showed evidence for departure from HWE. The term ‘pure Aboriginal’ is one that is used by PFES as containing individuals that met several criteria: they live in a remote district, possess a ‘skin’ name or that they were assigned as pure based on information from the investigating officers. The remaining populations comprise individuals whose ethnicity is based on self-declaration. Self-declaration has been questioned in court [10] and there are instances of possible self-declaration bias. For example Wild and Seber [11] note, ‘In recent US censuses there has been a big upsurge in the census counts of American Indians that could not be explained by birth and death statistics’. Taylor et al. [9] noted the presence of admixture in the self-declaration of Aboriginal Australians based on the Y-chromosome, and while the effect would be different on autosomal markers (owing to the different mechanism of inheritance) the results would lead us to expect a high level of autosomal admixture. Addressing this idea Walsh et al. [12] conducted a study to determine whether selfdeclaration was a method that would produce data fit for purpose in forensic applications. They found that the genetic content of
Table 2 p-values obtained by tests for departure from Hardy-Weinberg or Linkage equilibrium. Values below 0.05 are bolded. Australian Caucasian Departure from HWE 0.37 Departure from LE 1.6 10
3
New Zealand Caucasian Asian 0.05 0.14
0.054 3.4 10
Self-declared Aboriginal 22
1.6 10 4.9 10
13 257
Pure Aboriginal 5.2 10 5.4 10
4 53
Eastern Polynesian
Western Polynesian
0.54 0.01
0.17 0.3
Please cite this article in press as: D. Taylor, et al., Allele frequency database for GlobalFilerTM STR loci in Australian and New Zealand populations, Forensic Sci. Int. Genet. (2017), http://dx.doi.org/10.1016/j.fsigen.2017.02.012
G Model FSIGEN 1667 No. of Pages 3
Correspondence / Forensic Science International: Genetics xxx (2016) xxx–xxx
groups that self-declared as full or part New Zealand Maori followed a pattern that would be expected if self-declaration was reporting accurately. It is the author's personal experience that the general consensus of the forensic community is that selfdeclaration, while not a perfect system, produces databases that are fit for forensic use and that other mitigating factors can be applied to Court reported values (i.e. the application of co-ancestry coefficients, the use of databases from multiple populations, or taking into account sampling uncertainty associated with population database construction) so as not to overstate the strength of the findings. Regardless of the results of independence testing, our knowledge of the history of human populations leads us to expect that some level of admixture or substructure exists in all populations. The population databases presented here are of suitable size for the purpose of estimating allele frequencies. For criminal investigations, it is recommended that multi-locus profile probabilities be calculated by the method of Balding and Nichols [13] with conservative values of the inbreeding coefficient (u or FST). The FST values used currently in casework are 0.05, 0.05, 0.05, 0.03, and 0.02 respectively for the Aboriginal, Eastern Polynesian, Western Polynesian, Asian, and Caucasian datasets. These are very conservative values based on the work undertaken by Buckleton et al. [7]. This paper follows the guidelines for publication of population genetic data in the journal [14,15].
3
[3] S.J. Walsh, J.R. Cullen, S.A. Harbison, Allele frequencies for the four major subpopulations of New Zealand at the 10 AMPFlSTR1 SGM PlusTM loci, For. Sci. Int. 122 (2–3) (2001) 189–195. [4] D. Taylor, J. Henry, S. Walsh, South Australian Aboriginal sub-population data for the nine AMPLFlSTR1 Profiler PlusTMshort tandem repeat (STR) loci, For. Sci. Int.: Genet. 2 (2) (2009) e27–e30. [5] J.-A. Bright, C. Allen, S. Fountain, K. Gray, D. Grover, S. Neville, A.L. Poy, D. Taylor, G. Turbett, L. Wilson-Wilde, Australian population data for the twenty Promega PowerPlex 21 short tandem repeat loci, Austr. J. For. Sci. 46 (4) (2014) 442–446. [6] I.W. Evett, B.S. Weir, Interpreting DNA Evidence – Statistical Genetics for Forensic Scientists, Sinauer Associates, Inc, Sunderland, 1998. [7] J. Buckleton, J. Curran, J. Goudet, D. Taylor, A. Thiery, B. Weir, Populationspecific FST values for forensic STR markers: a worldwide survey, For. Sci. Int.: Genet. 23 (2016) 126–133. [8] D. Horton, Aboriginal Australia Map, AIATSIS and Auslig, Canberra, ACT, 1996. [9] D. Taylor, N. Nagle, K.N. Ballantyne, R.A.H. van Oorschot, S. Wilcox, J. Henry, R. Turakulov, R.J. Mitchell, An investigation of admixture in an Australian Aboriginal Y-chromosome STR database, For. Sci. Int.: Genet. 6 (2012) 532– 538. [10] B.S. Weir, DNA statistics in the Simpson matter, Nat. Genet. 11 (1995) 365–368. [11] C.J. Wild, G.A.F. Seber, Chance Encounters, John Wiley and Sons, New York, 2000. [12] S.J. Walsh, C.M. Triggs, J.M. Curran, J.R. Cullen, J.S. Buckleton, Evidence in support of self-declaration as a sampling method for the formation of subpopulation databases, J. For. Sci. 48 (5) (2003) 1091–1093. [13] D.J. Balding, R.A. Nichols, DNA profile match probability calculation: how to allow for population stratification, relatedness, database selection and single bands, For. Sci. Int. 64 (1994) 125–140. [14] Á. Carracedo, J.M. Butler, L. Gusmão, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, New guidelines for the publication of genetic population data, For. Sci. Int.: Genet. 7 (2013) 217–220. [15] Á. Carracedo, J.M. Butler, L. Gusmão, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, Update of the guidelines for the publication of genetic population data, For. Sci. Int.: Genet. 10 (2014) A1–A2.
Conflicts of interest The authors declare no conflict of interest. Acknowledgements This work was supported in part by grant 2011-DN-BX-K541 from the US National Institute of Justice. Points of view in this document are those of the authors and do not necessarily represent the official position or policies of the U.S. Department of Justice. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j. fsigen.2017.02.012. References [1] S.J. Walsh, J. Buckleton, Autosomal microsatellite allele frequencies for 15 regionally defined Aboriginal Australian population datasets, For. Sci. Int. 168 (2007) e29–e42. [2] S.J. Walsh, J.S. Buckleton, Autosomal microsatellite allele frequencies for a nationwide dataset from the Australian Caucasian sub-population, For. Sci. Int. 168 (2–3) (2007) e47–e50.
Duncan Taylora,b,* Forensic Science South Australia, 21 Divett Place, Adelaide, SA, 5000, Australia
a
b
School of Biological Sciences, Flinders University, GPO Box 2100 Adelaide SA 5001, Australia Jo-Anne Bright Catherine McGovern ESR Limited, Private Bag 92021 Auckland New Zealand
Sharon Neville NSW Forensic & Analytical Science Service, NSW Health Pathology, Joseph St, Lidcombe NSW 2141, Australia Denise Grover Forensic Science Branch NT Police, Peter McAulay Centre, Berrimah, PO Box 39764, Winnellie NT 0821, Australia * Corresponding author at: Forensic Science South Australia, 21 Divett Place, Adelaide, SA 5000, Australia. E-mail address: [email protected] (D. Taylor). Received 4 November 2016 Available online xxx
Please cite this article in press as: D. Taylor, et al., Allele frequency database for GlobalFilerTM STR loci in Australian and New Zealand populations, Forensic Sci. Int. Genet. (2017), http://dx.doi.org/10.1016/j.fsigen.2017.02.012