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Comparing methods for fetal fraction determination and quality control of NIPT samples
Author(s) -
Beek Daphne M.,
Straver Roy,
Weiss Marian M.,
Boon Elles M. J.,
Huijsdensvan Amsterdam Karin,
Oudejans Cees B. M.,
Reinders Marcel J. T.,
Sistermans Erik A.
Publication year - 2017
Publication title -
prenatal diagnosis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.956
H-Index - 97
eISSN - 1097-0223
pISSN - 0197-3851
DOI - 10.1002/pd.5079
Subject(s) - fetus , fraction (chemistry) , medicine , pregnancy , gestational age , fetal weight , obstetrics , biology , genetics , chemistry , organic chemistry
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. © 2017 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.