P4: Y-STR haplotype evidence interpretation using discrete Laplace models of the Philippine and Austronesian reference databases


Jae Joseph Russell B. Rodriguez1,2,3, Mikkel Meyer Andersen4,5, Maria Corazon A. De Ungria1,6

1. DNA Analysis Laboratory, Natural Sciences Research Institute, College of Science, University of the Philippines Diliman, Quezon City, Philippines
2. Genetic and Molecular Biology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines
3. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
4. Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark
5. Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
6. Program on Biodiversity, Ethnicity, and Forensics, Philippine Genome Center, University of the Philippines, Quezon City, Philippines

Description & Aims

Y-chromosome short tandem repeats (Y-STRs) are important tools in forensic DNA investigations, particularly in isolating a male profile from a male-female mixture such as in a sexual assault case [1- 2]. Estimating the frequency of a Y-STR haplotype, however, is not as straightforward as counting its frequency in the reference database, as the database is a rather small sample of all haplotypes presented in the population. This is further complicated by the fact that uniparental haplotypes are inherited from ancestral haplotypes and are related to one another. Various methods have been developed to estimate Y-STR haplotype frequencies (reviewed in [3]). One such method is the discrete Laplace model which calculates the frequency in the population taken as a collection of haplotype subgroups derived from an ancestral haplotype [4,5]. The application of the discrete Laplace method had also been extended to mixtures [6], which is especially relevant in sexual assault cases, where there are multiple assailants or when the victim is male. We previously proposed for the adoption of the discrete Laplace model in interpreting Y-STR DNA matches in the Philippines consistent with the recommendations by the ISFG [7]. However, to provide background in formulating specific guidelines applicable to the national setting, the model has to be tested on actual Philippine haplotypes. One such guideline may pertain to the choice of the reference database to fit the model. The ISFG recommends the use of metapopulations (human populations that share genetic ancestry commonly associated with language groups) as opposed to national databases, which are often defined by political jurisdictions [8]. We conjecture however that the use of the Philippine database may be sufficient. For decades, modern-day political boundaries have largely restricted movements in the vast area of Southeast Asia and the Pacific where populations of Austronesian speakers are spread. Moreover, routine casework is much faster and straightforward if Philippine forensic DNA laboratories use a national database, rather than having to access haplotype databases maintained in many different jurisdictions. We therefore would like to test this proposition by comparing the utility of the two datasets (Philippine vs. Austronesian) while considering different marker combinations that reflect variability in multiplex systems used and the quality of evidence recovered from crime scenes.

We are specifically interested in answering the following questions:

  1. How do Y-STR haplotype frequency estimates vary when the discrete Laplace model is fitted to the Philippine database in contrast to the Austronesian metapopulation?
  2. What is the effect of including the known profile/s in the database before fitting the model?
  3. What is the effect of the number of loci on the likelihood ratios (LRs) calculated for single haplotype matches? for two-person mixtures?
  4. What is the effect of the number of loci on predicting the contributing haplotypes in mixture deconvolution?

To answer these questions, we propose to fit discrete Laplace models on the both the Austronesian dataset and the Philippine dataset in the Y-chromosome Haplotype Reference Database (YHRD) (https://yhrd.org, Release 67-2022/Feb/07) [9]. Likelihood ratios will be calculated on single haplotypes and two-person mixtures randomly drawn from the Philippine database. Lastly, as an exercise in reporting LR results, simulated casework analysis will be performed on haplotype profiles generated in [10]. For further reading see [11-16]. Our observations will form the basis of recommendations on the interpretation of Y-chromosomal STR evidence for forensic DNA laboratories in the Philippines.

[1] Maiquilla SMB, Salvador JM, Calacal GC et al. 2011. Y-STR DNA analysis of 154 female child sexual assault cases in the Philippines. Int J Legal Med. 125(6):817-824
[2] Delfin FC, Madrid BJ, Tan MP, De Ungria MCA. 2005. Y-STR analysis for detection and objective confirmation of child sexual abuse Int J Legal Med. 119(3):158-163
[3] Andersen MM, Balding DJ. 2021. Assessing the forensic value of DNA evidence from Y chromosomes and mitogenomes. Genes. 12, 1209
[4] Andersen MM, Eriksen PS, Morling N. 2013. The discrete Laplace exponential family and estimation of Y-STR haplotype frequencies. J Theor Biol. 329, 39–51
[5] Andersen MM. 2018. Discrete Laplace mixture model with applications in forensic genetics. J Open Source Softw. 3(26), 748
[6] Andersen MM, Eriksen PS, Mogensen HS, Morling N. 2015. Identifying the most likely contributors to a Y-STR mixture using the discrete Laplace method. Forensic Sci Int Genet. 15, 76–83
[7] Rodriguez JJRB, Laude RP, De Ungria MCA. 2021. An integrated system for forensic DNA testing of sexual assault cases in the Philippines. Forensic Sci Int Synerg. 3, 100133 Page 4 of 4
[8] Roewer L, Andersen MM, Ballantyne J et al. 2020. DNA commission of the International Society of Forensic Genetics (ISFG): Recommendations on the interpretation of Y-STR results in forensic analysis. Forensic Sci. Int. Genet. 48, 102308
[9] Willuweit S. and Roewer L. 2015. The new Y Chromosome Haplotype Reference Database. Forensic Sci Int Genet. 15, 43-48
[10] Rodriguez JJRB, Calacal GC, Laude RP, De Ungria MCA. 2017. Non-differential DNA extraction of post-coital samples submitted as evidence for investigating sexual assault cases in the Philippines. Philipp Sci Lett. 10, 14-21
[11] Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Autom Control. 19(6), 716-723
[12] Hurvich CM, Tsai CL. 1989. Regression and time series model selection in small samples. Biometrika. 76(2), 297-307
[13] Schwarz G. 1978. Estimating the dimension of a model. Ann Stat. 6(2), 461-464
[14] Andersen MM, Eriksen PS, Morling N. 2022. Weight of evidence of Y-STR matches computed with the discrete Laplace method: Impact of adding a suspect’s profile to a reference database. bioRxiv DOI: 10.1101/2022.08.25.505269
[15] Andersen MM, Eriksen PS. 2014. disclapmix: Discrete Laplace Mixture Inference Using the EM Algorithm. R Package Version 1.5. http://CRAN.R-project.org/package=disclapmix
[16] Andersen MM, Eriksen PS, Mogensen HS, Morling N. 2015. Identifying the most likely contributors to a Y-STR mixture using the discrete Laplace method. Forensic Sci Int Genet. 15, 76-83


Jae Joseph Russell B. Rodriguez

Date of objection

Expired at November, 14th, 2022

* See FAQ/Glossary (http://yhrd.org/pages/faq) for further explanations of abbreviated terms used here