Open Access

Multiplex genotyping system for efficient inference of matrilineal genetic ancestry with continental resolution

Investigative Genetics20112:6

https://doi.org/10.1186/2041-2223-2-6

Received: 20 December 2010

Accepted: 23 March 2011

Published: 23 March 2011

Abstract

Background

In recent years, phylogeographic studies have produced detailed knowledge on the worldwide distribution of mitochondrial DNA (mtDNA) variants, linking specific clades of the mtDNA phylogeny with certain geographic areas. However, a multiplex genotyping system for the detection of the mtDNA haplogroups of major continental distribution that would be desirable for efficient DNA-based bio-geographic ancestry testing in various applications is still missing.

Results

Three multiplex genotyping assays, based on single-base primer extension technology, were developed targeting a total of 36 coding-region mtDNA variants that together differentiate 43 matrilineal haplo-/paragroups. These include the major diagnostic haplogroups for Africa, Western Eurasia, Eastern Eurasia and Native America. The assays show high sensitivity with respect to the amount of template DNA: successful amplification could still be obtained when using as little as 4 pg of genomic DNA and the technology is suitable for medium-throughput analyses.

Conclusions

We introduce an efficient and sensitive multiplex genotyping system for bio-geographic ancestry inference from mtDNA that provides resolution on the continental level. The method can be applied in forensics, to aid tracing unknown suspects, as well as in population studies, genealogy and personal ancestry testing. For more complete inferences of overall bio-geographic ancestry from DNA, the mtDNA system provided here can be combined with multiplex systems for suitable autosomal and, in the case of males, Y-chromosomal ancestry-sensitive DNA markers.

Background

Establishing the geographic region of a person's genetic origin - also called bio-geographic ancestry - is of forensic relevance when the short tandem repeat (STR) profile of trace DNA found at a crime scene does not match that of a suspect or does not yield any matches in a criminal DNA database because it may provide investigative leads to finding unknown persons [1]. Similarly, such information can be useful for locating antemortem samples or putative relatives of unidentified body remains, including disaster victim identification [2]. Furthermore, inferring geographic information from DNA data is important in population history studies [3, 4] and has gained attention in the growing field of personal ancestry testing [5, 6].

Several years of intensive research into the understanding of the geographic distribution of human genetic diversity present in the non-recombining mitochondrial genome and respective parts of the Y-chromosome (NRY), mostly for population history purposes, have produced an immense body of knowledge allowing us to pick specific mtDNA and NRY markers with restricted (sub)continental distributions [4, 7, 8]. MtDNA is especially useful for forensic application due to its high copy number (hundreds to thousands of copies per cell) and small size (16.6 kb), which allows the analysis of small amounts of degraded DNA often encountered in crime-scene situations [9]. Although mtDNA only reveals information about matrilineal ancestry, it can be seen as a first step toward a more comprehensive picture of personal ancestry when combined with suitable NRY and autosomal DNA evidence [10, 11]. Furthermore, investigating the geographic origin of mtDNA in comparison to that of the Y-chromosome in a population can also reveal insights into sex-biased aspects of human population history such as those caused by patri- or matrilocal residence patterns [12].

In human population genetics studies, the typical approach for mtDNA analysis consists of sequencing the first hypervariable segment (HVS1), sometimes in combination with HVS2, within the non-coding control region (see, for example [13, 14]), whereas in forensics it has nowadays become standard practice to sequence the entire control region [15]. Although haplogroup inference from HVS sequence data is possible for many mtDNA haplogroups, not all haplogroups present suitable diagnostic variants in HVS1 and/or HVS2 that allow an unequivocal assignment. In such cases, simple nucleotide polymorphisms (SNPs; i.e. single-nucleotide polymorphisms as well as small insertions and deletions) from the coding region of mtDNA are required in order to establish the haplogroup status. Moreover, because SNP typing assays are usually more sensitive and consume less DNA than sequencing, in many cases it might be desirable to perform SNP genotyping alone (in the absence of HVS data) or prior to HVS sequencing [16, 17].

Several mtDNA SNP multiplex assays have already been developed focussing on particular geographic subregions (see, for example, [18]) or on the dissection of particular haplogroups (see, for example, [19]). However, what is missing so far is an mtDNA SNP multiplex system that includes the mtDNA haplogroups of major continental distribution. We describe a sensitive genotyping system based on single-base primer extension technology, consisting of three independent multiplex assays that together include 36 SNPs determining 43 mtDNA haplo-/paragroups that allow the inference of matrilineal bio-geographic ancestry at the level of continental resolution.

Results and discussion

Multiplexes and targeted haplogroups

MtDNA coding-region SNPs defining the major haplogroups that occur in Africa, Western Eurasia, Eastern Eurasia and Native America were carefully selected (Figure 1) and combined into three multiplex genotyping assays (Figures 2, 3, 4) each consisting of a polymerase chain reaction (PCR) amplification step and a subsequent single-base primer extension step (Tables 1, 2, 3). The haplogroups detectable with Multiplex 1 and 2 are broadly similar to those typed by the Genographic Project [20] with some noticeable exceptions. Multiplex 1 (Figure 2) was designed to target haplogroups L0/L1, L2/L4/L6, L3, M, M1, C, D, N, N1, I, W, A, X and R. Due to the homoplasy of some of the selected markers in the worldwide mtDNA phylogeny [7], Multiplex 1 can additionally detect some (relatively rare) haplogroups that were not originally intended, namely L0k/L0d1a/L0d3, L5, X2a1, R11/B6 and B4a1. The hierarchical organization of the mitochondrial SNPs in Multiplex 1 ensures that all these haplogroups, intended and unintended, are well differentiable (Figure 2). Some haplogroups are only identified with Multiplex 1 on a broad level and, in those cases, additional genotyping with Multiplex 2 or 3 is needed to achieve further haplogroup resolution and final geographic inferences. Multiplex 2 (Figure 3) targets haplogroup R and haplogroups nested within R, namely R0, HV, HV0a (which includes V), H, R9 (which includes F), B, J, T, U, U6 and U8b (which includes K). A notable difference with the Genographic Project SNP panel [20] is that we included in our multiplexes haplogroups M1 and U6 which have a predominantly African distribution, probably due to back-migration events to Africa [21]. As such, Multiplex 1 and 2 together offer a convenient method for the classification of unknown mtDNAs into any of the major worldwide mtDNA haplogroups. However, they do not allow for the differentiation of the Native American subsets of otherwise Eastern Eurasian haplogroups A, B, C and D and Western Eurasian/African haplogroup X. Therefore, we designed a third assay, Multiplex 3 (Figure 4), which specifically aims at detecting the Native American haplogroups A2, B2, C1, C4c, D1, D4h3a and X2a, as well as Eskimo/Siberian haplogroups A2a, A2b, D2a and D3 and Eastern Eurasian haplogroup C1a [22]. Together, the three multiplexes include 36 different coding-region mtDNA SNPs (of which 34 are single-nucleotide transitions/transversions and two are small insertion/deletion polymorphisms). It should be noted that, despite the fact that haplogroups M1, C and D within macrohaplogroup M, haplogroups N1, A, W and X within macrohaplogroup N, and haplogroups R0, R9, B, JT and U within macrohaplogroup R, can be detected with the method, much of the Southern Asian, East/Southeast Asian and Oceanic variation within M, N and R remains unresolved (denoted as M*, N* and R*, respectively, in Figure 1). However, this is inevitable given the large number of independent haplogroups descending from M, N and R but it can be overcome by developing additional multiplex assays that specifically target the relevant subhaplogroups for those regions.
Figure 1

Overall phylogenetic scheme of targeted mtSNPs with geographic haplogroup classification. The combined use of the three multiplex assays allows any person's mtDNA to be classified into one of the colour-labelled haplogroups. Colours correspond to the geographic origin of the haplogroups as indicated. SNP position numbers are relative to the revised Cambridge Reference Sequence (rCRS). Deletion mutations are denoted by the suffix 'd'. Recurrent SNPs are underlined. The numbers 1, 2 or 3 in square brackets shown for each SNP refer to the respective multiplex assay in which the SNP is included. Note: haplogroups F, K and V are encompassed within R9, U8b and HV0a, respectively, as indicated because this does not follow logically from the nomenclature.

Figure 2

Marker phylogeny and haplogroup-defining genotypes of Multiplex 1. Recurrent SNPs are underlined. Boxed alleles indicate for each haplogroup those SNPs that are minimally required to define that haplogroup. If additional genotyping is required for more detailed haplogroup inference, the respective additional multiplex to be genotyped subsequently is noted.

Figure 3

Marker phylogeny and haplogroup-defining genotypes of Multiplex 2. Boxed alleles indicate for each haplogroup those SNPs that are minimally required to define that haplogroup. The allelic states of deletion polymorphism 8281-8289 are denoted as 'a' (ancestral) and 'd' (deletion), respectively. If additional genotyping is required for more detailed haplogroup inference, the respective additional multiplex to be genotyped subsequently is noted.

Figure 4

Marker phylogeny and haplogroup-defining genotypes of Multiplex 3. Boxed alleles indicate for each haplogroup those SNPs that are minimally required to define that haplogroup. The allelic states of deletion polymorphism 290-291 are denoted as 'a' (ancestral) and 'd' (deletion), respectively.

Table 1

Primer details for Multiplex 1.

 

PCR amplification

Single-base extension

Site

Primer sequences (5'-3')

Concentration (μM)

Amplicon size (bp)

Primer sequence (5'-3') (5' aspecific tail in lowercase italics)

Concentration (μM)

Length (nt)

Orientation

Alleles (dye)

769

F

ACATCACCCCATAAACAAATAGG

1.000

158

act(gact) 10 CGTTTTGAGCTGCATTG

2.000

60

R

A (red), G (yellow)

 

R

AGCGTTTTGAGCTGCATTG

1.000

      

1243

F

AATCGATAAACCCCGATCAA

0.040

93

actgact CGATCAACCTCACCACC

0.150

24

F

C (yellow), T (red)

 

R

TGCGCTTACTTTGTAGCCTTC

0.040

      

1736

F

GCTAAACCTAGCCCCAAACC

0.200

106

t(gact) 2 gac TCAATTTCTATCGCCTATACTTTAT

0.150

37

R

A (red), G (yellow)

 

R

CTATTGCGCCAGGTTTCAAT

0.200

      

3552

F

CGCTGACGCCATAAAACTCT

4.000

128

actgact AGGGGGGTTCATAGTAGAAG

4.000

27

R

A (red), C (blue), T (green)

 

R

GTATGGGGAGGGGGGTTC

4.000

      

4883

F

TGACATCCGGCCTGCTT

0.075

114

(gact) 4 g CATGACAAAAACTAGCCCC

0.300

36

F

C (yellow), T (red)

 

R

TGGATAAGATTGAGAGAGTGAGGA

0.075

      

7146

F

AGACCAAACCTACGCCAAAA

0.150

130

ct(gact) 9 ga TACGCCAAAATCCATTTC

0.300

58

F

A (green), G (blue)

 

R

GGTGTATGCATCGGGGTAGT

0.150

      

10034

F

TCTCCATCTATTGATGAGGGTCT

0.300

108

ct(gact) 4 g GTACCGTTAACTTCCAATTAACTAG

0.150

44

F

C (yellow), T (red)

 

R

TTAAGGCGAAGTTTATTACTCTTTTT

0.300

      

10238

F

GCGTCCCTTTCTCCATAAAA

0.250

80

ct(gact) 4 gac CTCCATAAAATTCTTCTTAGTAGCTAT

0.300

48

F

C (yellow), T (red)

 

R

GGGTAAAAGGAGGGCAATTT

0.250

      

10400

F

GCCCTAAGTCTGGCCTATGA

0.150

90

ct(gact) 5 gac CGTTTTGTTTAAACTATATACCAATTC

0.300

52

R

C (blue), T (green)

 

R

TGAGTCGAAATCATTCGTTTT

0.150

      

12705

F

CCCAAACATTAATCAGTTCTTCAA

0.180

102

t(gact) 6 g TTAATCAGTTCTTCAAATATCTACTCAT

0.150

54

F

C (yellow), T (red)

 

R

TCTCAGCCGATGAACAGTTG

0.180

      

12950

F

TCCTCGCCTTAGCATGATTT

0.200

101

act(gact) 11 TGAGGCTTGGATTAGCG

0.500

64

R

A (red), C (blue), G (yellow)

 

R

GAGGCCTAGTAGTGGGGTGA

0.200

      

13966

F

ACCGCACAATCCCCTATCTA

0.250

132

ct(gact) 13 GCAGGTTTTGGCTCG

0.500

69

R

A (red), G (yellow)

 

R

AGGTGATGATGGAGGTGGAG

0.250

      

15301

F

CCACCCTCACACGATTCTTT

0.080

119

ct(gact) 4 ATTCTTTACCTTTCACTTCATCTT

0.150

42

F

A (green), G (blue)

 

R

GGTGATTCCTAGGGGGTTGT

0.080

      
Table 2

Primer details for Multiplex 2.

 

PCR amplification

Single-base extension

Site

Primer sequences (5'-3')

Concentration (μM)

Amplicon size (bp)

Primer sequence (5'-3') (5' aspecific tail in lowercase italics)

Concentration (μM)

Length (nt)

Orientation

Alleles (dye)

2706

F

CGAGGGTTCAGCTGTCTCTT

0.040

88

(gact) 10 GTCTTCTCGTCTTGCTGTGT

0.100

60

R

A (red), G (yellow)

 

R

AGGGTCTTCTCGTCTTGCTG

0.040

      

3348

F

CAGTCAGAGGTTCAATTCCTCTT

0.200

142

act(gact) 11 g GGAATGCCATTGCGAT

0.200

64

R

A (red), G (yellow)

 

R

GGGCCTTTGCGTAGTTGTAT

0.200

      

3480

F

CGCTGACGCCATAAAACTCT

0.120

120

act(gact) 2 ga GCCATAAAACTCTTCACCAA

0.150

33

F

A (green), G (blue)

 

R

AGGGGGGTTCATAGTAGAAG

0.120

      

8281-8289

F

GAAATCTGTGGAGCAAACCAC

0.500

179/170

(gact) 2 g CCCTATAGCACCCCCTCTA

0.700

28

F

a (yellow), d (blue)*

 

R

AGAGGTGTTGGTTCTCTTAATCTTT

0.500

      

11251

F

TGAACGCAGGCACATACTTC

0.100

92

t(gact) 5 gac CCCCTACTCATCGCACT

0.050

41

F

A (green), G (blue)

 

R

TGAGCCTAGGGTGTTGTGAG

0.100

      

11719

F

GGCGCAGTCATTCTCATAATC

0.100

85

(gact) 6 GCAGAATAGTAATGAGGATGTAAG

0.150

48

R

A (red), G (yellow)

 

R

TGTGAGTGCGTTCGTAGTTTG

0.100

      

12308

F

CAGCTATCCATTGGTCTTAGGC

2.000

169

t(gact) 9 gac TGGTCTTAGGCCCCAA

3.000

56

F

A (green), G (blue)

 

R

GATTTTACATAATGGGGGTATGAGT

2.000

      

12705

F

ACTTCTCCATAATATTCATCCCTGT

1.300

184

act(gact) 5 g TTAATCAGTTCTTCAAATATCTACTCAT

0.800

52

F

C (yellow), T (red)

 

R

TCTCAGCCGATGAACAGTTG

1.300

      

13368

F

CGCCTTCTTCAAAGCCATAC

0.250

127

ct(gact) 2 gac TAAGGTTGTGGATGATGGA

0.300

32

R

A (red), G (yellow)

 

R

GGTGAGGGAGGTTGAAGTGA

0.250

      

13928

F

CAGCCCTAGACCTCAACTACCT

0.040

119

ct(gact) 5 ga AACATACTCGGATTCTACCCTA

0.040

46

F

C (yellow), G (blue)

 

R

ATAGGGGATTGTGCGGTGT

0.040

      

14766

F

TCAACTACAAGAACACCAATGACC

0.050

109

c GACCCCAATACGCAAAA

0.150

18

F

C (yellow), T (red)

 

R

ATCATGCGGAGATGTTGGAT

0.050

      

15904

F

CATCCGTACTATACTTCACAACAATC

1.000

184

act(gact) 4 GGCCTGTCCTTGTAGTATAAA

0.600

40

F

C (yellow), T (red)

 

R

GGTGCTAATGGTGGAGTTAAAGA

1.000

      

* a, ancestral; d, deletion.

Table 3

Primer details for Multiplex 3.

 

PCR amplification

Single-base extension

Site

Primer sequences (5'-3')

Concentration (μM)

Amplicon size (bp)

Primer sequence (5'-3') (5' aspecific tail in lowercase italics)

Concentration (μM)

Length (nt)

Orientation

Alleles (dye)

290-291

F

CGCTTTCCACACAGACATCA

0.350

94/92

(gact) 6 gac CCACACAGACATCATAACAAAA

0.350

49

F

a (green), d (red)*

 

R

GGGTTTGGCAGAGATGTGTT

0.350

      

2092

F

TTGCCCACAGAACCCTCTAA

0.300

141

act(gact) 3 ga CTCTAAATCCCCTTGTAAATTTAA

0.400

41

F

C (yellow), T (red)

 

R

AATTGGTGGCTGCTTTTAGG

0.300

      

3330

F

CAGTCAGAGGTTCAATTCCTCTT

0.100

142

act(gact) 7 CGATTAGAATGGGTACAATGAG

0.150

53

R

C (blue), T (green)

 

R

GGGCCTTTGCGTAGTTGTAT

0.100

      

3826

F

TGAAGTCACCCTAGCCATCA

0.200

168

ct(gact) 3 GGTCATGATGGCAGGAGTA

0.200

33

R

C (blue), T (green)

 

R

AAGGGGGTTCGGTTGGT

0.200

      

6285

F

GAGCAGGAACAGGTTGAACA

0.300

237

actgactga CCTGCTAAGGGAGGGTAGA

0.450

28

R

A (red), G (yellow)

 

R

GGAGAGATAGGAGAAGTAGGACTGC

0.300

      

6374

 

same amplicon as 6285

  

ctgact TTGATGGCCCCTAAGAT

0.300

23

R

C (blue), T (green)

11177

F

TTCACAGCCACAGAACTAATCA

0.200

164

ct(gact) 10 gac GCGTTCAGGCGTTCTG

0.600

61

R

C (blue), T (green)

 

R

AGTGCGATGAGTAGGGGAAG

0.200

      

11365

F

CACCCTAGGCTCACTAAACATTC

0.100

160

t(gact) 9 g CTTAATATGACTAGCTTACACAATAGC

0.100

65

F

C (yellow), T (red)

 

R

TTCGACATGGGCTTTAGGG

0.100

      

11959

F

CCCCCACTATTAACCTACTGG

0.200

190

act(gact) 10 gac CTCCTACTTACAGGACTCAACAT

0.150

69

F

A (green), G (blue)

 

R

TCTCGTGTGAATGAGGGTTTT

0.200

      

12007

 

same amplicon as 11959

  

ct(gact) 9 gac GGTGGGTGAGTGAGCC

0.300

57

R

A (red), G (yellow)

14433

F

CTCCATCGCTAACCCCACTA

0.400

170

(gact) 6 GCTATTGAGGAGTATCCTGAG

0.300

45

R

C (blue), T (green)

 

R

TTCTGAATTTTGGGGGAGGT

0.400

      

14502

 

same amplicon as 14433

  

act(gact) 3 ga CATCATTCCCCCTAAATAAA

0.450

37

F

C (yellow), T (red)

* a, ancestral; d, deletion.

Design and optimization

The successful dessign of a useful multiplex single-base extension assay requires careful consideration of the SNPs and their PCR amplification primers as well as extension primers, followed by extensive laboratory testing [23]. One criterion of SNP selection was the overall level of homoplasy of the marker in the entire mtDNA phylogeny [7]. For each haplogroup, one or several defining SNPs are available; in the latter case care was taken to select the more stable (phylogenetically less recurrent) SNP sites. Nevertheless, some of the selected SNPs do occur more than once in the phylogeny (underlined in Figure 1) as discussed above. Notably, Multiplex 1 contains two tri-allelic SNPs: nucleotide position (np) 3552 is either a T (ancestral state), an A (haplogroup C), or a C (haplogroup X2a1); and np 12950 is either an A (ancestral state), a C (haplogroup M1) or a G (haplogroups L5, R11 and B6). Primer design using Primer3Plus [24] considered small amplicon size and avoided numt amplification [25]. The compatibility of primers within the same multiplex was checked with AutoDimer [26], especially avoiding 3' end complementarities. Amplicon sizes were kept small, ranging from 80 to 237 bp with an average of 133 bp (Tables 1, 2, 3), in order to facilitate the amplification of (partially) degraded DNA typically encountered in forensic settings as well as in population history studies when using difficult source materials (for example, ancient DNA). All primers were first tested in singleplex before combining them in a multiplex. Primers that showed substantial artifacts were replaced by alternatively designed primers. In order to ensure electrophoretic separation of extension primer products, extension primers within the same multiplex were given different lengths by adding 5' non-homologous (poly)GACT tails (Tables 1, 2, 3). Peak heights in the electropherograms (Figures 5, 6) were balanced by adjusting primer concentrations in the PCR and extension reactions (Tables 1, 2, 3).
Figure 5

Electropherograms of Multiplex 1-3 for a European and an African individual, using varying amounts of initial DNA template. (A) European individual of haplogroup J; (B) African individual of haplogroup L3*(xM,N). The three multiplex assays were each performed on five different starting amounts of DNA template, ranging from 0.25 ng to 0.001 ng. Grey circles indicate marker dropouts that occur at the very low DNA concentration whereas grey arrows indicate cases where allele calling becomes difficult due to artefacts that come up at the low DNA concentrations.

Figure 6

Electropherograms of Multiplex 1-3 for a Native American and an East Asian individual, using varying amounts of initial DNA template. (A) Native American individual of haplogroup C1*(xC1a); (B) East Asian individual of haplogroup R9. The three multiplex assays were each performed on five different starting amounts of DNA template, ranging from 0.25 ng to 0.001 ng. Grey circles indicate marker dropouts that occur at the very low DNA concentration whereas grey arrows indicate cases where allele calling becomes difficult due to artefacts that come up at the low DNA concentrations.

Haplogroup distribution and inferring bio-geographic ancestry

The labels used to describe the geographic affiliations of the haplogroups (Figure 1) mostly correspond to one of four regions or continents of the world, namely Africa, Western Eurasia, Eastern Eurasia and Native America, consistent with the terminology used in human genetics and anthropology literature. With some haplogroups, however, only combined regions can be inferred, namely Western Eurasia/Africa, Western Eurasia/Southern Asia, Eastern Eurasia/Oceania, Native America/Eastern Eurasia and Eastern Eurasia/Southern Asia/Oceania (Figure 1). While these geographic designations are convenient descriptors of the 'center of gravity' of haplogroup occurrence, it is important to keep in mind that, instead of sharp genetic borders, there exist transition areas between continents. Populations from the Middle East, for example, carry a considerable portion of African mtDNA lineages [27]. Similarly, Northern Africa has a relatively large portion of Western Eurasian mtDNA lineages [28, 29]. In addition, the Central Asian mtDNA pool is composed of Western Eurasian, Eastern Eurasian and, to a lesser extent, also Southern Asian components [30, 31]

Furthermore, one should be aware that traditional distribution patterns of genetic variation, including mtDNA, may have been affected by (evolutionary recent) migration/admixture events, including as a result of colonialism, so that some populations carry portions of ancestry from multiple geographic regions. The most prominent case is, perhaps, the American continent where, due to colonization by Europeans which started around the beginning of the 16th century and the subsequent European introduction of African slaves, the current population carries a mixture of Native American, Western Eurasian and African mtDNA lineages, in varying proportions depending on the subpopulation [10, 11, 14, 32, 33]. Other well-known cases include Madagascar (African and Eastern Eurasian lineages) [13], and coastal/island parts of Near Oceania, as well as all of Remote Oceania (Oceanic and Eastern Eurasian lineages) [34]. In addition, groups of more or less recent immigrants often carry a mixture of 'native' lineages and lineages typical from the area to which they moved. For example, Polish Roma, having an ultimate origin in India, harbour both Southern Asian and Western Eurasian mtDNA variants [35]. Finally, rare cases have been reported where European individuals carried African mtDNA haplogroups without being aware of any African ancestry [36]. Therefore, for any bio-geographic ancestry prediction purposes, mtDNA evidence should be interpreted in the context of the relevant local demographic history. Also, because mtDNA only reflects the matrilineal portion of a person's genetic ancestry, ideally the markers should be combined with evidence obtained from autosomal and/or (when dealing with male DNA) Y-chromosome markers, to obtain a more accurate picture of a person's overall ancestry.

Sensitivity testing

In order to establish the sensitivity of our multiplex assays we performed tests with different starting amounts of genomic DNA, ranging from 25 ng to 1 pg of template DNA, for four individuals originating from different continents and with respective diagnostic haplogroups: a European with haplogroup J; an African with L3*(xM,N); a Native American with C1*(xC1a); and an East Asian with R9 (Figures 5, 6). This enabled us to monitor the behaviour of the different SNP alleles with decreasing amounts of template DNA. Overall, we observed high sensitivity and basically full profiles could be obtained with all three multiplexes for all four individuals with as little as 4 pg of DNA template (with the only exception of 13368 in Multiplex 2 that sometimes caused difficulties in allele calling with 4 pg and lower). Marker dropouts for some SNPs in all the individuals and all three multiplexes (except for Multiplex 1 in the European and the African sample and with Multiplex 3 in the European) started to occur only at the 1 pg level, as well as allele-calling difficulties for some other SNPs in all three multiplexes (Figures 5, 6). The achieved sensitivity is similar to that of two previously published mtDNA multiplex assays [18, 37] but, presumably, higher than that of many other published mtDNA multiplexes which typically require 1-10 ng DNA (for example [19, 3840]; although many such studies do not provide details on sensitivity). Furthermore, the achieved sensitivity of our assays is significantly higher than that of commercially available STR multiplexes [4143], which can be expected due to the higher relative abundance of mtDNA as compared to nuclear DNA. When working with ancient DNA or forensic trace DNA, it might be useful to quantify the amount of human DNA prior to genotyping because, in such situations, human DNA often represents only a fraction of total DNA due to the presence of non-human (for example, bacterial, fungal, or others) DNA.

Illustration of the method application

In order to illustrate the reliability of our method in inferring bio-geographic ancestry from mtDNA, we compared in worldwide individuals, their haplogroup status as determined from full mtDNA sequence data and their population affiliation known from the sampling region, with the haplogroup and corresponding geographic information obtainable from our multiplex SNP assays (Table 4). The data used for this purpose consisted of 75 samples from the Centre d'Etude du Polymorphisme Humain-Human Genome Diversity Project (CEPH-HGDP) panel [44] for which entire mitochondrial genome sequences are available [45]. From the full mtDNA sequences we extracted the alleles of those SNP sites that are included in our assays and used the resulting genotypes to infer haplogroups and respective geographic regions of matrilineal origin. In all cases, the haplogroups inferable by our assays were consistent with the full sequence-based haplogroups (although a more detailed haplogroup assignment could be achieved from the sequence data as expected); accordingly, the regions of bio-geographic ancestry derived from the assay-inferable haplogroups were in agreement with the individuals' sampling origins (Table 4). For example, sample HGDP01076 is an individual from Sardinia (Italy) whose full mtDNA sequence can be classified as haplogroup J2b1a; our assays would predict the haplogroup of this person as J with Western Eurasian geographic origin. Notably, the HGDP samples from Pakistan exhibit both Western Eurasian and Southern Asian haplogroups (for example, HGDP00163 belongs to Western Eurasian haplogroup H2a and HGDP00165 belongs to Southern Asian haplogroup M30), consistent with previous observations (see Discussion above). Similarly, the Bedouin samples belong to both African as well as Western Eurasian haplogroups.
Table 4

Established haplogroup and geographic origin versus haplogroup and geographic origin as inferable by Multiplex 1-3, for 75 CEPH-HGDP individuals.

GenBank accession

HGDP ID

HGDP population/sampling region

Full sequence-based haplogroup*

Multiplex-inferred haplogroup

Multiplex-inferred matrilineal origin

EU597551.1

HGDP00003

Brahui (Pakistan)

R2

R*(xR0,R9,R11,B,JT,U)

E Eurasia/S Asia/Oceania

EU597563.1

HGDP00005

Brahui (Pakistan)

M5a2a

M*(xM1,C,D)

E Eurasia/S Asia/Oceania

EU597574.1

HGDP00007

Brahui (Pakistan)

H2b

H

W Eurasia

EU597492.1

HGDP00163

Sindhi (Pakistan)

H2a

H

W Eurasia

EU597504.1

HGDP00165

Sindhi (Pakistan)

M30

M*(xM1,C,D)

E Eurasia/S Asia/Oceania

EU597516.1

HGDP00167

Sindhi (Pakistan)

M2a1a

M*(xM1,C,D)

E Eurasia/S Asia/Oceania

EU597528.1

HGDP00213

Pathan (Pakistan)

K2a5

U8b [incl. K]

W Eurasia

EU597540.1

HGDP00214

Pathan (Pakistan)

U9b1

U*(xU6,U8b)

W Eurasia/S Asia

EU597552.1

HGDP00216

Pathan (Pakistan)

J1d

J

W Eurasia

EU597564.1

HGDP00277

Kalash (Pakistan)

U4a1

U*(xU6,U8b)

W Eurasia/S Asia

EU597575.1

HGDP00279

Kalash (Pakistan)

U4a1

U*(xU6,U8b)

W Eurasia/S Asia

EU597493.1

HGDP00281

Kalash (Pakistan)

R0a

R0a

W Eurasia/Africa

EU597489.1

HGDP00458

Biaka_Pygmies (CAR)

L1c1a2a1

L0*(xL0k,L0d1a,L0d3)/L1

Africa

EU597501.1

HGDP00459

Biaka_Pygmies (CAR)

L1c1a1a1b1

L0*(xL0k,L0d1a,L0d3)/L1

Africa

EU597513.1

HGDP00460

Biaka_Pygmies (CAR)

L1c1a1a1b

L0*(xL0k,L0d1a,L0d3)/L1

Africa

EU597525.1

HGDP00463

Mbuti_Pygmies (DRC)

L2a2b1

L2/L4/L6

Africa

EU597537.1

HGDP00467

Mbuti_Pygmies (DRC)

L0a2b

L0*(xL0k,L0d1a,L0d3)/L1

Africa

EU597549.1

HGDP00468

Mbuti_Pygmies (DRC)

L2a2b1

L2/L4/L6

Africa

EU597495.1

HGDP00545

Papuan (New Guinea)

Q1

M*(xM1,C,D)

E Eurasia/S Asia/Oceania

EU597507.1

HGDP00546

Papuan (New Guinea)

P1d1

R*(xR0,R9,R11,B,JT,U)

E Eurasia/S Asia/Oceania

EU597519.1

HGDP00547

Papuan (New Guinea)

Q3a1

M*(xM1,C,D)

E Eurasia/S Asia/Oceania

EU597573.1

HGDP00608

Bedouin (Israel)

I5a1

I

W Eurasia

EU597491.1

HGDP00609

Bedouin (Israel)

L2a1

L2/L4/L6

Africa

EU597503.1

HGDP00610

Bedouin (Israel)

U7

U*(xU6,U8b)

W Eurasia/S Asia

EU597515.1

HGDP00675

Palestinian

H13a1

H

W Eurasia

EU597527.1

HGDP00676

Palestinian

U5a1a1

U*(xU6,U8b)

W Eurasia/S Asia

EU597539.1

HGDP00677

Palestinian

HV0c

HV*(xHV0a,H)

W Eurasia

EU597569.1

HGDP00709

Colombian

B2e

B2

Native America

EU597580.1

HGDP00710

Colombian

B2

B2

Native America

EU597554.1

HGDP00714

Cambodian

M51a1

M*(xM1,C,D)

E Eurasia/S Asia/Oceania

EU597566.1

HGDP00715

Cambodian

B5a1a

B4*(xB4a1,B2)/B5

E Eurasia

EU597577.1

HGDP00716

Cambodian

M17c

M*(xM1,C,D)

E Eurasia/S Asia/Oceania

EU597531.1

HGDP00788

Melanesian (Bougainville)

B4a1a1a1

B4a1

E Eurasia/Oceania

EU597543.1

HGDP00789

Melanesian (Bougainville)

Q1c

M*(xM1,C,D)

E Eurasia/S Asia/Oceania

EU597486.1

HGDP00792

Colombian

A2

A2*(xA2a,A2b)

Native America

EU597556.1

HGDP00807

Orcadian (Orkney)

X2b

X*(xX2a)

W Eurasia/Africa

EU597568.1

HGDP00808

Orcadian (Orkney)

H5b

H

W Eurasia

EU597579.1

HGDP00810

Orcadian (Orkney)

H5b

H

W Eurasia

EU597555.1

HGDP00823

Melanesian (Bougainville)

B4a1a1a

B4a1

E Eurasia/Oceania

EU597518.1

HGDP00945

Yakut (Siberia)

Z3a1

M*(xM1,C,D)

E Eurasia/S Asia/Oceania

EU597530.1

HGDP00946

Yakut (Siberia)

D5a2a2

D*(xD1,D3,D2a,D4h3a)

E Eurasia

EU597542.1

HGDP00947

Yakut (Siberia)

C5a1

C*(xC1,C4c)

E Eurasia

EU597498.1

HGDP00998

Karitiana (Brazil)

D1

D1

Native America

EU597510.1

HGDP01000

Karitiana (Brazil)

D1e

D1

Native America

EU597526.1

HGDP01028

Bantu_Herero (S-Africa)

L3d3a

L3*(xM,N)

Africa

EU597514.1

HGDP01033

Bantu_Zulu (S-Africa)

L0d1a1

L0k/L0d1a/L0d3

Africa

EU597502.1

HGDP01034

Bantu_Tswana (S-Africa)

L0d1b1

L0*(xL0k,L0d1a,L0d3)/L1

Africa

EU597533.1

HGDP01037

Pima (Mexico)

C1c1

C1*(xC1a)

Native America

EU597545.1

HGDP01039

Pima (Mexico)

C1b

C1*(xC1a)

Native America

EU597557.1

HGDP01040

Pima (Mexico)

C1b

C1*(xC1a)

Native America

EU597508.1

HGDP01075

Sardinian (Italy)

U5b3a1a

U*(xU6,U8b)

W Eurasia/S Asia

EU597520.1

HGDP01076

Sardinian (Italy)

J2b1a

J

W Eurasia

EU597532.1

HGDP01077

Sardinian (Italy)

H1

H

W Eurasia

EU597544.1

HGDP01147

North_Italian

U5a2b

U*(xU6,U8b)

W Eurasia/S Asia

EU597505.1

HGDP01224

Mongola (China)

B4a1c4

B4a1

E Eurasia/Oceania

EU597517.1

HGDP01225

Mongola (China)

C4a1

C*(xC1,C4c)

E Eurasia

EU597529.1

HGDP01226

Mongola (China)

A4a1a

A*(xA2)

E Eurasia

EU597538.1

HGDP01255

Mozabite (Algeria)

H

H

W Eurasia

EU597550.1

HGDP01256

Mozabite (Algeria)

V

HV0a [incl. V]

W Eurasia

EU597562.1

HGDP01257

Mozabite (Algeria)

U6a1a

U6

W Eurasia/Africa

EU597541.1

HGDP01327

She (China)

M7c1b

M*(xM1,C,D)

E Eurasia/S Asia/Oceania

EU597553.1

HGDP01328

She (China)

B4b1a2

B4*(xB4a1,B2)/B5

E Eurasia

EU597565.1

HGDP01329

She (China)

F4a1

R9 [incl. F]

E Eurasia

EU597576.1

HGDP01337

Naxi (China)

A4c1

A*(xA2)

E Eurasia

EU597494.1

HGDP01338

Naxi (China)

A11b

A*(xA2)

E Eurasia

EU597506.1

HGDP01339

Naxi (China)

B4a1

B4a1

E Eurasia/Oceania

EU597567.1

HGDP01377

French_Basque

HV0

HV*(xHV0a,H)

W Eurasia

EU597578.1

HGDP01378

French_Basque

T1a1

T

W Eurasia

EU597496.1

HGDP01379

French_Basque

K1a4a1

U8b [incl. K]

W Eurasia

EU597497.1

HGDP01402

Adygei (Russia_Caucasus)

U1a1

U*(xU6,U8b)

W Eurasia/S Asia

EU597509.1

HGDP01403

Adygei (Russia_Caucasus)

H1c

H

W Eurasia

EU597521.1

HGDP01404

Adygei (Russia_Caucasus)

H2a1

H

W Eurasia

EU597561.1

HGDP01408

Bantu (Kenya)

L2a1f

L2/L4/L6

Africa

EU597572.1

HGDP01411

Bantu (Kenya)

L1c2a1a

L0*(xL0k,L0d1a,L0d3)/L1

Africa

EU597490.1

HGDP01412

Bantu (Kenya)

L3b1a1

L3*(xM,N)

Africa

* According to Build 11 of the mtDNA tree available at http://www.phylotree.org [7].

Conclusions

We developed an efficient and sensitive method for the multiplex genotyping of informative mtDNA SNPs, allowing for the inference of a person's matrilineal bio-geographic ancestry at a continental level. We would like to emphasize that matrilineal ancestry must be seen as reflecting only one aspect of the overall bio-geographic ancestry of a person [5, 6, 46]. A more accurate establishment of the overall bio-geographic ancestry is achievable when mtDNA is used in conjunction with informative Y-chromosomal (in the case of males) [8] and autosomal ancestry-informative DNA markers [4750], especially when a person's biological ancestors are from different geographic regions resulting in mixed bio-geographic ancestry.

Methods

Reaction conditions

Multiplex PCR amplification was carried out in a reaction volume of 6 μL, containing 1x GeneAmp PCR Gold buffer (Applied Biosystems, CA, USA), 4.5 mM MgCl2 (Applied Biosystems), 100 μM of each dNTP (Roche, Mannheim, Germany), 0.35 units of AmpliTaq Gold DNA polymerase (Applied Biosystems), 0.001 to 1 ng genomic DNA template, and PCR primers (desalted; Metabion, Martinsried, Germany) in concentrations as specified in Tables 1, 2, 3. The reactions were performed in a Dual 384-well GeneAmp PCR System 9700 (Applied Biosystems) using optical 384-well reaction plates (Applied Biosystems), with the following cyclic conditions: 10 min at 95°C; followed by 30 cycles of 94°C for 15 s; 60°C for 45 s; and a final extension at 60°C for 5 min. PCR products were purified by adding 1.5 μL ExoSAP-IT (USB Corporation, OH, USA) to 6 μL PCR product, followed by incubation at 37°C for 15 min and 80°C for 15 min. Multiplex single-base primer extension was carried out in a reaction volume of 5 μL, containing 1 μL SNaPshot Ready Reaction Mix (Applied Biosystems), 1 μL purified PCR product and extension primers (HPLC-purified; Metabion, Martinsried, Germany) in concentrations as specified in Tables 1, 2, 3. The reactions were performed in a Dual 384-well GeneAmp PCR System 9700 (Applied Biosystems) using optical 384-well reaction plates (Applied Biosystems), with the following cycling conditions: 2 min at 96°C; followed by 25 cycles of 96°C for 10 s; 50°C for 5 s; and 60°C for 30 s. The reaction products were purified by adding 1 unit of Shrimp Alkaline Phosphatase (USB Corporation) to 5 μL of extension product, followed by incubation at 37°C for 45 min and 75°C for 15 min. PCR and extension primer details can be found in Table 1 for Multiplex 1, in Table 2 for Multiplex 2 and in Table 3 for Multiplex 3.

Extended primers were separated by capillary electrophoresis on a 3130xl Genetic Analyzer (Applied Biosystems) using POP-7 polymer by loading a mixture of 1 μL purified extension product, 8.8 μL Hi-Di formamide (Applied Biosystems) and 0.2 μL GeneScan-120 LIZ internal size standard (Applied Biosystems). Results were analysed using GeneMapper version 3.7 software (Applied Biosystems).

Dilution series

For the purpose of sensitivity testing, genomic DNA from four individuals of different matrilineal continental origin was extracted from buccal swabs. For each individual, the DNA was diluted to obtain a solution of precisely 1 ng/μL as determined by two independent Quantifiler (Applied Biosystems) measurements. All Quantifiler assays were carried out according to manufacturer's recommendations. A dilution series was made from each of the four 1 ng/μL DNA solutions, producing concentrations of 0.25, 0.063, 0.016, 0.004 and 0.001 ng/μL for each individual. Concentrations of the dilutions were measured again and confirmed by triplicate Quantifiler measurements. The Quantifiler assays were carried out according to the manufacturer's recommendations, except for the addition of two extra dilutions to the recommended standard curve to be able to measure the very low DNA concentrations.

Abbreviations

HVS: 

hypervariable segment

mtDNA: 

mitochondrial DNA

mtSNP: 

mitochondrial SNP

np: 

nucleotide position

NRY: 

non-recombining portion of the Y-chromosome

PCR: 

polymerase chain reaction

SNP: 

simple nucleotide polymorphism

STR: 

short tandem repeat.

Declarations

Acknowledgements

This work was funded in part by the Netherlands Forensic Institute (NFI) and received additional support from a grant from the Netherlands Genomics Initiative (NGI)/Netherlands Organization for Scientific Research (NWO) within the framework of the Forensic Genomics Consortium Netherlands (FGCN).

Authors’ Affiliations

(1)
Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam

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