Inferring the population of origin of DNA evidence within the UK by allele-specific hybridization of Y-SNPs
Introduction
The ability to infer an individual's geographic ancestry from a DNA sample aids prioritisation of enquiries when the source cannot be identified by other means. Although the SGMplus™ loci used in the UK National DNA Database show some allele frequency differences between ethnic appearance groups the inference is often inconclusive [1]. More informative genetic markers include larger panels of autosomal STRs [2], SNPs [3], Alu insertions [4] and mitochondrial DNA sequences [5], whilst the recent application of many polymorphic Y-STRs [6] and Y-SNPs [7] have highlighted some of the strongest associations between alleles and population of origin.
Several characteristics of the Y chromosome make it a particularly useful indicator of ancestral origin. The lack of recombination along the majority of its length has resulted in the sequential accumulation of mutations in slowly evolving SNP haplogroups that reflect the progressive diversification of Y chromosome lineages during the expansion of human populations. These haplogroups have been linked in a phylogenetic tree by the Y Chromosome Consortium (YCC) [8], [9] to reveal the order in which the mutations occurred. Ancient mutations define 18 major lineages (clades A–R), which demonstrate affiliation with the continents in which they arose [10], [11]. Subsequent mutations define subclades that often show more localized distributions reflecting recent human migrations [12], [13], [14]. The geographic association is stronger than for mtDNA haplogroups possibly as a result of genetic drift acting on the higher variance in male reproductive success as well as the historical tendency toward patrilocality in human societies; that is the settlement of males closer to their birthplace than females [15].
The theoretical advantages of using Y-SNPs for predicting biogeographic ancestry can only be converted into useful forensic intelligence if results can be obtained from typical crime stains and related to visually distinguishable populations. In this study, we use samples derived from both volunteer donors and the National DNA Database to determine whether haplogroup frequencies differ significantly between the six “ethnic appearance” categories used on police DNA submission records. To demonstrate the feasibility of forensic Y-SNP haplogrouping we describe the limits of the Signet™ Y-SNP kit (Marligen Biosciences Inc.) in association with the Luminex 100 flow cytometer in the analysis of mock casework samples.
Section snippets
Sample collection
The majority of samples were collected as buccal swabs from individuals visually classified under one of six ethnic appearance (EA) groups, these included 101 EA1 (pale-skinned Caucasian), 41 EA2 (dark-skinned Caucasian), 152 EA3 (African/Afro-Caribbean), 167 EA4 (Indian-subcontinent), 114 EA5 (East Asian) and 52 EA6 (North African/Middle Eastern). Mock casework samples were created to determine the robustness of haplogrouping results. Matched sets of bloodstains, semen and hair roots were
Species specificity
A small number of loci showed cMFIs exceeding l0rfus in cats (Amelogenin-X, SRY465-C and both M18 alleles), dogs (Amelogenin-X) and pigs (M146-C, M124-T and both alleles at P25, M94) whilst sheep, rat, cattle, and chicken produced no artefacts. Because of their closer relationship to humans both male gorilla and chimpanzee produced above background signals at most loci although the inferred SNP combinations were not compatible with the YCC phylogeny [8], [9]. Fewer and weaker signals were seen
Discussion
Experimental evaluation of the Signet™ kit in conjunction with the Luminex 100 detection instrument indicated that reliable and reproducible haplotyping results are generated from 1 ng or more of target template DNA in just two multiplex reactions, which is consistent with the manufacturer's recommended input of 1–8 ng. Below this level there is a risk of generating partial or inconclusive results although no erroneous calls were actually made. Useful results can be generated from a variety of
Acknowledgement
This work was partly funded by the Science Policy Unit of the Home Office.
References (31)
- et al.
Inferring ethnic origin by means of an STR profile
Forensic Sci. Int.
(2001) - et al.
Human population genetic structure and inference of group membership
Am. J. Hum. Genet.
(2003) - et al.
The making of the African mtDNA landscape
Am. J. Hum. Genet.
(2002) - et al.
Comparison of Y chromosome haplotypes in three racial groups and the possibility of predicting ethnic origin
Int. Congress Ser.
(2003) Y chromosomal SNP haplotype diversity in forensic analysis
Forensic Sci. Int.
(2001)- et al.
Origin, diffusion, and differentiation of Y chromosome haplogroups E, and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area
Am. J. Hum. Genet.
(2004) - et al.
Phylogeographic analysis of haplogroup E3b (E-M215) Y chromosomes reveals multiple migratory events within and out of Africa
Am. J. Hum. Genet.
(2004) - et al.
Phylogeography of Y chromosome Haplogroup I reveals distinct domains of prehistoric gene flow in Europe
Am. J. Hum. Genet.
(2004) - et al.
Duplications of the Y chromosome specific loci P25 and 92R7 and forensic implications
Forensic Sci. Int.
(2004) - et al.
A Y Chromosome census of the British Isles
Curr. Biol.
(2003)
Y chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than language
Am. J. Hum. Genet.
Combined use of biallelic and microsatellite Y chromosome polymorphisms to infer affinities among African populations
Am. J. Hum. Genet.
The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations
Am. J. Hum. Genet.
Estimating african american admixture proportions by use of population specific alleles
Am. J. Hum. Genet.
Genetic structure of human populations
Science
Cited by (33)
Simultaneous determination of seven informative Y chromosome SNPs to differentiate East Asian, European, and African populations
2011, Legal MedicineCitation Excerpt :The recently published human Y chromosome tree contains 20 major haplogroups (A–T) and 311 distinct haplogroups that incorporate approximately 600 binary markers [23]. Several protocols for the simultaneous detection of Y-SNPs defining the major clades of the Y chromosome phylogenetic tree have been described for evolutionary and forensic purposes [24–30]. It is very important for forensic investigators to select Y-SNPs based on the intended purpose because large-scale SNP analysis is expensive.
A suspect horse excluded by analysis of species- and male-specific DNA and mtDNA
2011, Forensic Science InternationalA forensic method for the simultaneous analysis of biallelic markers identifying Y chromosome haplogroups inferred as having originated in Asia and the Japanese archipelago
2010, Forensic Science International: GeneticsCitation Excerpt :The geographic origins of some haplogroups have been inferred [5–10] based on the geographic distribution and haplogroup age estimated from Y-STR variations within the haplogroup [11]. Information regarding the ancestral and geographical origin of a biological sample will be potentially useful to crime investigators to narrow down the possible donors of the sample [12–18]. As the number of foreign visitors as crime suspects and victims increases due to globalization, when an individual whose DNA profile matches that of the biological evidence sample cannot be found within a certain period of time, investigators must consider the possibility that the sample was derived from a foreign visitor.
Resolution of African versus non-African origin using a likelihood based method and 11 Y-chromosomal STRs
2008, Forensic Science International: Genetics Supplement SeriesThe golden gene (SLC24A5) differentiates US sub-populations within the ethnically admixed Y-SNP haplogroups
2008, Legal MedicineCitation Excerpt :Such a ‘genetic eyewitness’ would be especially useful in instances where a DNA profile cannot be matched to a donor or when there is no developed suspect, forcing investigators to rely on other evidence such as often unreliable eyewitness accounts. Determining an individual’s ethnogeographic ancestry using carefully selected panels of population specific Y-SNPs is currently being investigated for forensic use [1–7]. Y-SNPs are of interest due to their paternal inheritance, lack of recombination, abundance, and low mutation rate and are commonly used in evolutionary studies for characterizing male population structure [2,4,7–11].