Print Email Facebook Twitter Comparing methods for fetal fraction determination and quality control of NIPT samples Title Comparing methods for fetal fraction determination and quality control of NIPT samples Author van Beek, Daphne M (Amsterdam UMC) Straver, R. (Amsterdam UMC) Weiss, Marian M. (Amsterdam UMC) Boon, Elles M.J. (Amsterdam UMC; Leiden University Medical Center) Huijsdens-van Amsterdam, Karin (Amsterdam UMC) Oudejans, Cees B.M. (Amsterdam UMC) Reinders, M.J.T. (TU Delft Pattern Recognition and Bioinformatics) Sistermans, Erik A. (Amsterdam UMC) Date 2017 Abstract Objective: To compare available analysis methods for determining fetal fraction on single read next generation sequencing data. This is important as the performance of non-invasive prenatal testing (NIPT) procedures depends on the fraction of fetal DNA. Methods: We tested six different methods for the detection of fetal fraction in NIPT samples. The same clinically obtained data were used for all methods, allowing us to assess the effect of fetal fraction on the test result, and to investigate the use of fetal fraction for quality control. Results: We show that non-NIPT methods based on body mass index (BMI) and gestational age are unreliable predictors of fetal fraction, male pregnancy specific methods based on read counts on the Y chromosome perform consistently and the fetal sex-independent new methods SeqFF and SANEFALCON are less reliable but can be used to obtain a basic indication of fetal fraction in case of a female fetus. Conclusion: We recommend the use of a combination of methods to prevent the issue of reports on samples with insufficient fetal DNA; SANEFALCON to check for presence of fetal DNA, SeqFF for estimating the fetal fraction for a female pregnancy and any Y-based method for estimating the fetal fraction for a male pregnancy. To reference this document use: http://resolver.tudelft.nl/uuid:b682233e-9d43-498c-af94-e7208af56c0e DOI https://doi.org/10.1002/pd.5079 ISSN 0197-3851 Source Prenatal Diagnosis, 37 (8), 769-773 Part of collection Institutional Repository Document type journal article Rights © 2017 Daphne M van Beek, R. Straver, Marian M. Weiss, Elles M.J. Boon, Karin Huijsdens-van Amsterdam, Cees B.M. Oudejans, M.J.T. Reinders, Erik A. Sistermans Files PDF 36288169.pdf 965.77 KB Close viewer /islandora/object/uuid:b682233e-9d43-498c-af94-e7208af56c0e/datastream/OBJ/view