Ethical considerations in establishing reference population DNA databases of Indigenous peoples in Southeast Asia

Reference population DNA databases are essential for accurate forensic statistical calculations, yet Indigenous populations remain significantly underrepresented in most forensic genetic repositories, limiting the scientific accuracy of allele frequency distributions and population genetic parameters in affected countries. This gap is particularly acute in Southeast Asia, where Indigenous peoples comprise substantial populations but are largely absent from forensic databases. This paper reports ethical and governance principles that should be considered in establishing and maintaining Indigenous reference population DNA databases to generate empirically derived allele frequency distributions, characterize population structure, and calculate population-specific theta (θ) values for forensic applications. We propose that such databases should be governed by policies discussed with and approved by authorized Indigenous representatives, with independent academic or government institutions serving as custodians. Effective governance requires culturally informed ethical policies, defined organizational structures, standardized operational procedures, and well-trained staff. Drawing on international precedents from Singapore (Health Science Authority), Malaysia (Jabatan Kimia Malaysia), New Zealand (the New Zealand Institute for Public Health and Forensic Science), and the Philippines (Filipino Genomes Research Program, DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman), we demonstrate that reference population DNA databases can be successfully managed by universities or government agencies that maintain institutional independence from law enforcement while supporting calculations of random match probabilities and likelihood ratios. We identify critical ethical gaps regarding informed consent, community engagement and/or partnership, data ownership, and restrictions on secondary use. We recommend adopting dynamic consent models consistent with Indigenous data sovereignty and the CARE (Collective Benefit, Authority to Control, Responsibility, Ethics) principles. The Philippines is presented as a case study, demonstrating how free, prior, and informed consent (FPIC) frameworks and stakeholder engagement enable the collection of Indigenous population genetic data while respecting Indigenous rights, albeit with their own challenges. Our findings demonstrate that ethical inclusion of Indigenous peoples in forensic database development is essential for generating accurate, population-specific genetic parameters and advancing forensic science that encompasses both broad general populations and smaller Indigenous communities.