Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory.
OBJECTIVES: To implement non-invasive prenatal testing (NIPT) for fetal aneuploidies with semiconductor sequencing in an academic cytogenomic laboratory and to evaluate the first 15 months experience on clinical samples.
METHODS: We validated a NIPT protocol for cell-free fetal DNA sequencing from maternal plasma for the detection of trisomy 13, 18 and 21 on a semiconductor sequencing instrument. Fetal DNA fraction calculation for all samples and several quality parameters were implemented in the workflow. 1081 clinical NIPT samples were analyzed following the described protocol.
RESULTS: NIPT was successfully implemented and validated on 201 normal and 74 aneuploid samples. For trisomy 21, 18 and 13 a specificity of 100%, and a sensitivity of respectively 98%, 94% and 100% was reached and accreditation for the NIPT workflow was obtained. From 1081 clinical samples, 17 samples showed an abnormal result: fourteen trisomy 21 samples, one trisomy 18 and one trisomy 16 were detected. Also a maternal CNV on chromosome 13 was observed, which could potentially lead to a false positive trisomy 13 result, but was reported as normal. One sex discordant result was reported, probably possibly attributable to a vanishing twin. No false-negative results have been reported to date. Moreover, our combined fetal fraction calculation enabled a more reliable risk estimate for trisomy 13, 18 and 21.
CONCLUSIONS: NIPT for trisomy 21, 18 and 13 detection has a very high specificity and sensitivity. Due to several biological phenomena diagnostic invasive confirmation of abnormal results remains required.
AUTHORS: Dheedene A1, Sante T1, Smet M1, Vanbellinghen JF2, Grisart B3, Vergult S1, Janssens S1, Menten B1.
Post date: 19 mei 2016
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