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Response to letter to the editor PD-17-0390, a comment on "Comparing methods for fetal fraction determination and quality control of NIPT samples".

ABSTRACT:

SUBMITTER: van Beek DM

PROVIDER: S-EPMC5767769 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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Response to letter to the editor PD-17-0390, a comment on "Comparing methods for fetal fraction determination and quality control of NIPT samples".

van Beek Daphne M DM Straver Roy R Weiss Marjan M MM Boon Elles M J EMJ Huijsdens-van Amsterdam Karin K Oudejans Cees B M CBM Reinders Marcel J T MJT Sistermans Erik A EA

Prenatal diagnosis 20171201 12

PMID: 29271028

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Comparing methods for fetal fraction determination and quality control of NIPT samples.

Project description:ObjectiveTo 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.MethodsWe 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.ResultsWe 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.ConclusionWe 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.

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