Abstract Study question Can prenatal genetic testing accurately predict mtDNA mutation load anddisease transmission to children for families affected by Leigh Syndrome? Summary answer Whole genome mtDNA sequencing for 13513G>A mutation in chorionic villi and amniotic fluid was similar to those measured in babies suggesting accuracy of disease prediction. What is known already Severity of mtDNA disease in children depends on heteroplasmy levels(proportion of mutant to wild-type mtDNA). There is a minimum threshold for the mutant mtDNA heteroplasmy (typically 60%) above which oxidative metabolism is impaired to cause disease. Predicting the disease based on the mutation load measured during embryonic or fetal development is critically needed. However, preimplantation genetics screening for many mtDNA mutations has limitations due to the potential increase in heteroplasmy levels after implantation. We hypothesized that prenatal screening of chorionic villi and/or amniotic fluid during the first trimester of pregnancy could provide more reliable diagnosis of disease occurrence in children. Study design, size, duration We evaluated mtDNA heteroplasmy in biopsies collected from chorionic villi and amniotic fluid at 10- and 16-weeks of gestation, respectively, for two consecutive, naturally conceived pregnancies for a carrier of 13513G>A mutation. Sequencing results were compared to mutations in the blood, skin, and urine of children after birth. Both children were also extensively monitored for a few years for disease occurrence. Participants/materials, setting, methods A family with maternally transmitted Leigh Syndrome including both parents and two existing children were enrolled during the initial phase. Whole mtDNA sequencing was used to confirm the maternal transmission of the mutation by analysis of blood, skin, and urine from asymptomatic parents and the older son and the severely affected younger son. Furthermore, prenatal diagnostics were performed for two consecutive pregnancies and children after birth. Main results and the role of chance The mother carried 13513G>A mutation in the skin (91% heteroplasmy), urine(39%), and blood (6.8%), while no mutation was detected in the father’s samples. The asymptomatic eldest child revealed a low mutation in the skin (14%), urine(23%), and blood (10%). While the younger son diagnosed with Leigh syndrome carried 56% mutation in blood, 86% in skin, and 97% in urine. Heteroplasmy ranging from 0.6% to 40% was also measured in 4 individual immature oocytes retrieved upon hormonal stimulation of the carrier. The family later naturally conceived 2 consecutive pregnancies and requested help with prenatal diagnostics. In the first pregnancy, mutation loads were 27.5% in chorionic villi and 29.5% in amniotic fluid. The family decided to keep the pregnancy which resulted in the birth of a healthy child with low mutations in blood (0.07%) and skin (14.5%). In the second pregnancy, prenatal diagnostics in CVS showed low mutation at 0.11%, resulting in the birth of an unaffected child with mutation loads of 1.4% in blood and 0% in skin. Limitations, reasons for caution Genetic counseling for mtDNA disease transmission is difficult due tocomplex inheritance of heteroplasmic variants for various pathogenicmutations. Inheritance and distribution of mtDNA mutations also influencedby individual family genetics. Therefore, prenatal diagnostic screeningshould be cautiously considered based on the specific circumstances for eachfamily. Wider implications of the findings Prenatal genetic diagnostics for families with mtDNA disease based on whole mtDNA sequencing by the qualified laboratory may accurately predict heteroplasmy levels and disease occurrence in children. However, careful analysis of family history and the likelihood of having low mutation load oocytes was critical for the success of our case. Trial registration number N/A