1. A forensic genetics intelligence service for australia
Dennis McNevin
HIDS 2018

2. This is happening now!

3. This is happening now!

4. Privacy, policy and legal

5. Model PIA

6. Phenotypes R Us We type ’em, U catch ’em Genetic Ancestry Lab
What do we call our lab?
Phenotypes R Us
We type ’em, U catch ’em
Genetic Ancestry Lab

7. Funding University of Canberra
Discovery Translation Fund (ANU Connect Ventures)
AMP Tomorrow Fund

8. Genetic markers (Applied Biosystems™)
Precision ID Ancestry Panel
165 autosomal ancestry informative SNPs
HIrisPlex system
23 autosomal phenotype informative SNPs and 1 indel
Iris (eye) colour (blue, brown and intermediate)
Hair colour (blond, brown, red and black)
Hair shade (light and dark)
Available as Ion Ampliseq™ DNA Phenotyping Panel

9. Instrumentation (Applied Biosystems™)
Ion Chef™ Instrument for target enrichment, library preparation, templating and chip loading
Ion PGM™ System for sequencing

10. Chemistry (Applied Biosystems™)
Ion AmpliSeq™ Kit for Chef DL8
Target enrichment, library preparation
4 × 8 IonCode™ barcodes (1-32)
Ion PGM™ Hi-Q™ View Chef Kit
Templating, chip loading
Sequences 4 × 2 pooled libraries
Ion™ Chips
314 v2 BC
316 v2 BC
318 v2 BC

11. Batches 1 to 6 samples 7 to 12 samples
1 × DL8 cartridge (NC, PC, 6 samples)
If < 6 samples, substitute extra PCs
1 or 2 × 314 chips
2 × Hi-Q™ View sequences (can’t use 1)
7 to 12 samples
2 × DL8 cartridges (NC, PC, 6 samples in each)
2 × 314 chips
2 × Hi-Q™ View sequences (no waste)

12. Batches 13 to 24 samples 25 to 48 samples
3 or 4 × DL8 cartridges (NC, PC, 6 samples)
1 or 2 × 316 chips
2 × Hi-Q™ View sequences (can’t use 1)
25 to 48 samples
5 to 8 × DL8 cartridges (NC, PC, 6 samples in each)
2 × 316 chips
2 × Hi-Q™ View sequences (no waste)

13. Prediction algorithms
HID SNP Genotyper Plugin (Applied Biosystems™)
STRUCTURE (
Principal coordinates analysis (PCoA), using the pcoa function (Analyses of Phylogenetics and Evolution or ape package) in R (

14. HID SNP Genotyper
Available as a plugin for the Torrent Suite software on the Ion Server (Applied Biosystems™)
Only uses 151 of the 165 SNP genotypes
Two assignments:
Continental level admixture proportions
Sub-population likelihoods (not applicable for admixed individuals)

15. HID SNP Genotyper

16. HID SNP Genotyper

17. HID SNP Genotyper

18. Reference populations

19. Reference populations
2099 individuals drawn from:
The International Genome Sample Resource (IGSR: Genomes Phase III)
Simons Genome Diversity Project (SGDP:
6 continental populations (Africa, Europe, South Asia, East Asia, America, Oceania)

20. Expanded reference populations
2262 individuals
Inclusion of individuals from the HGDP-CEPH database (
7 continental populations (addition of Middle East)
Some of the 165 SNPs not available in HGDP-CEPH
1 of the 165 SNPs not available in all databases

21. Expanded reference populations
Africa
Middle East
Europe
South Europe
British
North Europe
Other European
South Asia
Gujarati
Other South Asian
East Asia
Japan
Vietnamese
Other East Asian
Oceania (PNG)
America

22. STRUCTURE

23. Principal coordinates analysis

24. Principal coordinates analysis

25. Interpretation HID SNP Genotyper STRUCTURE PCoA Continental BGA
Continental BGA
Sub-populations 1
100% European
European
96% Nth European
Nth European 2
84% Nth European
Sth European
14% Sth European 3
70% European
89% Sth European
30% SW Asian
Middle Eastern 4
45% East Asian
Asian
East Asian
45% European
34% Nth European
11% Mid Eastern 5
83% Sth European
16% Nth European 6
95% European
54% Sth European
42% Nth European

26. Interpretation Interpretation1
The donor of this DNA has a majority ancestral genetic contribution from Northern Europe. Examples include Irish, Danes and Hungarians. They are more likely to have European ancestry than any other continental BGA. They are likely to have a majority of ancestors (eg. parents, grandparents) from Northern Europe. 2
The donor of this DNA has a majority ancestral genetic contribution from Europe. Examples include Irish, Danes and Finns. They are more likely to have European ancestry than any other continental BGA. They are likely to have a majority of ancestors (eg. parents, grandparents) from Europe. 3
The donor of this DNA has a major ancestral genetic contribution from Southern Europe and a minor contribution from South West Asia (Middle East). There are two possibilities:
The donor has ancestors from a region genetically intermediate between Southern Europe and the Middle East. Examples include Ashkenazi Jews, Hungarians, Sardinians, Greeks, Adygei.
The donor has ancestors from Southern Europe and the Middle East (eg. three Southern European grandparents and one Middle Eastern grandparent). 4
The donor of this DNA has major ancestral genetic contributions from Europe and East Asia. Their genotype has high heterozygosity (49%). It is most likely that the donor has ancestors from Europe and East Asia (eg. one European parent and one East Asian parent).

27. Acknowledgements
Shelley Seddon, Michelle Nelson, Sumaiya Quasim, Greg Adcock (University of Canberra)
Victor Pantano, Danaë O’Keefe (UC Engagement)
Dan Power, Lucy Dagostino (Thermo Fisher Scientific)
Chris Phillips and colleagues (University of Santiago de Compostela)
Runa Daniel (Victoria Police Forensic Services Department)

28. Disclaimers
Speaker was provided travel and hotel support by Thermo Fisher Scientific for this presentation, but no remuneration.
When used for purposes other than human identification or paternity testing, the instruments and software modules cited are for research use only. Not for use in diagnostic procedures.
Thermo Fisher Scientific and its affiliates are not endorsing, recommending, or promoting any use or application of Thermo Fisher Scientific products presented by third parties during this seminar.
Information and materials presented or provided by third parties are provided as-is and without warranty of any kind, including regarding intellectual property rights and reported results.
Parties presenting images, text and material represent they have the rights.