Challenges in using massively parallel sequencing technology for forensic DNA analysis in Southeast Asia

Abstract

Massively parallel sequencing (MPS) has caused a paradigm shift in forensic DNA analysis by enabling simultaneous examination of multiple genetic markers with higher resolution. Despite its growing importance, adoption in the 11 Southeast Asian countries remains limited. This paper reviews MPS implementation in forensic DNA laboratories across the region and discusses key adoption challenges. An online survey with the Asian Forensic Sciences Network - DNA Workgroup (AFSN-DNAWG) received 19 responses from seven countries: Brunei Darussalam, Indonesia, Malaysia, the Philippines, Singapore, Thailand, and Vietnam. Eight respondents are using MPS, while 10 of 11 non-users plan to adopt it within five years. Key challenges for users included limited population data, lack of standardized international nomenclature, and incompatibility with existing national DNA databases, which rely on length polymorphisms of short tandem repeat (STR) markers. Non-users cited limited infrastructure, financial constraints due to lack of government support, and insufficient training in managing sequencing data. To expand MPS use, we recommend a strategy combining effective capillary electrophoresis (CE)-based DNA profiling for routine cases with MPS technology for complex cases; establishment of an MPS-capable forensic DNA laboratory per country; and increased regional collaboration to maximize genomic data use common to mainstream and Indigenous populations, which have histories of trade, migration, and cultural interactions. These steps can provide a practical approach to integrating MPS into forensic databasing and casework across Southeast Asia.

Keywords: AFSN; Challenges; DNA; Forensics; MPS; NGS; Southeast Asia; massively parallel sequencing.

Fig. 1

Recommended workflow for integrating MPS in direct identification testing.

Fig. 2

Recommended workflow for integrating MPS in familial relationship testing.