Investigative genetic genealogy – new approach to detect relatedness of individuals

Česká verze

Authors: Korabečná Marie ¹; Šimková Halina ¹; Stenzl Vlastimil ²
Authors place of work: Ústav biologie a lékařské genetiky 1. lékařské fakulty UK a Všeobecné fakultní nemocnice Praha ¹; Kriminalistický ústav Policie České republiky, Praha ²
Published in the journal: Soud Lék., 66, 2021, No. 4, p. 58-65
Category: Přehledový článek

Summary

The development of molecular genetic techniques, coupled with the development of bioinformatic approaches and the expansion of genealogy as a hobby, also brings new possibilities for forensic genetics. The review article compares today’s classical methods of genotyping and determination of kinship based on the analysis of polymorphisms such as short tandem repeats, with the possibilities of investigative genetic genealogy, which uses genotyping based on analysis of hundreds of thousands of single nucleotide polymorphisms, bioinformatics and sharing individual profiles within public databases. We describe the principles of these laboratory techniques and the interpretation of their results. We compare these new approaches with the current practice in forensic laboratories. We stress the importance of the introduction of whole genome sequencing into forensic genetics. Whole genome sequencing allows due its ability to work with degraded DNA samples the preparation of proper material for investigative genetic genealogy which has already proven its usefulness in successfully solving serial murder cases as well as in identifying unknown victims of violent crimes. In addition to methodological approaches and achievements, the limits and ethical aspects of this new field of forensic genetics are also mentioned.

Keywords:

DNA analysis – kinship determination – STR genotyping – investigative genetic genealogy

Zdroje

1. Pang AW, MacDonald JR, Pinto D et al. Towards a comprehensive structural variation map of an individual human genome. Genome Biol 2010; 11: R52.

2. Tang H, Nzabarushimana E. STRScan: targeted profiling of short tandem repeats in whole-genome sequencing data. BMC Bioinformatics 2017; 18(Suppl 11): 398.

3. Butler JM. Short tandem repeat typing technologies used in human identity testing. Biotechniques 2007; 43(4):2–5.

4. Ruitberg CM, Reeder DJ, Butler JM. STRBase: a short tandem repeat dna database for the human identity testing community. Nucleic Acids Res 2001; 29(1): 320–322.

5. Santurro A, Vullo AM, Borro M et al. Personalized Medicine Applied to Forensic Sciences: New Advances and Perspectives for a Tailored Forensic Approach. Curr Pharm Biotechnol 2017; 18(3): 263-273.

6. Butler JM, Coble MD, Vallone PM. STRs vs. SNPs: thoughts on the future of forensic DNA testing. Forensic Sci Med Pathol 2007; 3(3): 200-205.

7. Zidkova A, Horinek A, Kebrdlova V, Korabecna M. Application of the new insertion- deletion polymorphism kit for forensic identification and parentage testing on the Czech population. Int J Legal Med 2013 ; 127(1): 7-10.

8. Chen J, Guo Jt. Comparative assessments of indel annotations in healthy and cancer genomes with next-generation sequencing data. BMC Med Genomics 2020; 13: 170-181.

9. Breslin K, Wills B, Ralf A et al. HIrisPlex-S system for eye, hair, and skin color prediction from DNA: Massively parallel sequencing solutions for two common forensically used platforms. Forensic Sci Int Genet 2019;43: 102152.

10. Palencia-Madrid L, Xavier C, de la Puente M et al. Evaluation of the VISAGE basic tool for appearance and ancestry pediction using PowerSeq chemistry on the MiSeq FGx system. Genes (Basel) 2020; 11(6): 708-718.

11. Bulbul O, Filoglu G. Development of a SNP panel for predicting biogeographical ancestry and phenotype using massively parallel sequencing. Electrophoresis 2018; 39(21): 2743-2751.

12. Kling D, Phillips C, Kennett D, Tillmar A. Investigative genetic genealogy: Current methods, knowledge and practice. Forensic Sci Int Genet 2021;52: 102474.

13. Abecasis GR, Altshuler D, Auton A et al. A map of human genome variation from population- scale sequencing. Nature 2010; 467: 1061–1073.

14. Droździok K, Kabiesz J, Tomsia M, Skowronek R, Rębała K. Mutation analysis of short tandem repeats in a population sample from Upper Silesia (southern Poland). Leg Med (Tokyo) 2018; 33: 1-4.

15. Gusmão L, Butler JM, Carracedo A, et al. DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis. Int J Legal Med 2006; 120(4): 191-200.

16. Tillmar AO, Kling D, Butler JM et al. DNA Commission of the International Society for Forensic Genetics (ISFG): Guidelines on the use of X-STRs in kinship analysis. Forensic Sci Int Genet 2017; 29: 269-275.

17. Pereira R, Pereira V, Gomes I et al. A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR. Int J Legal Med 2012; 126(1): 97-105.

18. Parson W, Gusmão L, Hares DR et al., DNA DNA Commission of the International Society for Forensic Genetics: revised and extended guidelines for mitochondrial DNA typing. Forensic Sci Int Genet 2014; 13: 134-142.

19. Parson W, Ballard D, Budowle B et al. Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements. Forensic Sci Int Genet 2016; 22: 54-63.

20. Rousset, F. Inbreeding and relatedness coefficients: what do they measure? Heredity 2002; 88: 371–380.

21. Egeland T, Mostad PF, Mevâg B, Stenersen M. Beyond traditional paternity and identification cases. Selecting the most probable pedigree. Forensic Sci Int 2000; 110(1): 47-59.

22. Gjertson DW, Brenner CH, Baur MP et al., ISFG: Recommendations on biostatistics in paternity testing. Forensic Sci Int Genet 2007; 1(3-4): 223-231.

23. Drábek J. Validation of software for calculating the likelihood ratio for parentage and kinship. Forensic Sci Int Genet 2009; 3(2): 112-118.

24. Kling D, Tillmar AO, Egeland T. Familias 3 - Extensions and new functionality. Forensic Sci Int Genet 2014; 13: 121-127.

25. Ge J, Budowle B. Forensic investigation approaches of searching relatives in DNA databases. J Forensic Sci 2021; 66(2): 430-443.

26. Karantzali E, Rosmaraki P, Kotsakis A, Le Roux-Le Pajolec MG, Fitsialos G. The effect of FBI CODIS Core STR Loci expansion on familial DNA database searching. Forensic Sci Int Genet 2019; 43: 102129.

27. Greytak EM, Moore C, Armentrout SL. Genetic genealogy for cold case and active investigations. Forensic Sci Int 2019; 299: 103- 113.

28. Tillmar A, Sjölund P, Lundqvist B, Klippmark T, Älgenäs C, Green H. Whole-genome sequencing of human remains to enable genealogy DNA database searches - A case report. Forensic Sci Int Genet 2020;46: 102233.

29. Wendt FR, Rahikainen AL, King JL, Sajantila A, Budowle B. A genome-wide association study of tramadol metabolism from post-mortem samples. Pharmacogenomics J 2020; 20: 94–103.

30. Tillmar AO, Phillips C. Evaluation of the impact of genetic linkage in forensic identity and relationship testing for expanded DNA marker sets. Forensic Sci Int Genet 2017; 26: 58–65.

31. Kling D. On the use of dense sets of SNP markers and their potential in relationship inference, Forensic Sci Int Genet 2019; 39: 19–31.

32. Browning BL, Browning SR. Improving the accuracy and efficiency of identity-by-descent detection in population data, Genetics 2013; 194 (2): 459–471.

33. Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM. Robust relationship inference in genome-wide association studies, Bioinformatics 2010; 26(22): 2867– 2873.

34. Wright S. Coefficients of inbreeding and relationship. Am Nat 1922; 56(645): 330–338.

35. Henn M, Hon L, Macpherson JM, et al. Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples, PLoS One 2012; 7(4): e34267.

36. Burbano HA, Hodges E, Green RE, et al. Targeted investigation of the Neandertal genome by array-based sequence capture. Science 2010; 328(5979): 723-725.