Medical genetics in Indonesia: development, challenges, and future priorities in a diverse middle-income archipelago

Medical genetics in Indonesia is emerging within a highly diverse and geographically complex archipelago. This review outlines current developments, persistent challenges, and future priorities for integrating genetics and genomics into the national health system. Indonesia’s extraordinary ethnic diversity drives heterogeneous patterns of hemoglobinopathies, inherited metabolic disorders, and variable susceptibility to both infectious and non-communicable conditions, underscoring the urgent need for population-specific genomic strategies. Recent national initiatives, including the Indonesia National Genome Project and the Biomedical & Genome Science Initiative (BGSi), signal a growing commitment to precision medicine and genomic infrastructure in this rapidly developing country. Expanding genomic diagnostics, pharmacogenomics, and early precision oncology programs have strengthened clinical capabilities in selected urban referral centers. Nevertheless, access remains highly uneven due to workforce shortages, infrastructure gaps, and the high cost of advanced genomic testing. In oncology, the limited incorporation of genetic and genomic assays into the JKN–INA-CBG (Jaminan Kesehatan Nasional Indonesian Case-Based Groups) reimbursement framework further restricts equitable access, often shifting costs directly to patients. Furthermore, geographic challenges in this spread-out country remain substantial. Key future priorities include large-scale population genome sequencing, systematic integration of genetics into primary healthcare, expansion and professionalization of genetic counseling services, development of robust functional disease models (including patient-derived organoids), and the establishment of translational research platforms. Aligning genomic innovation with national health financing, public health programs, and regulatory frameworks will be essential to ensure that precision medicine is implemented equitably, at scale, and with clinical impact across the Indonesian archipelago. Indonesia’s ethnic diversity drives unique genetic heterogeneity in Southeast Asia. Universal Health Coverage (through JKN) reaches 98% of people in Indonesia but genomics access remains limited. National Genome Project and organoid platforms promise precision medicine application to all. Genetic counseling and prenatal diagnosis need strong primary healthcare integration.