Detection of DNA Contamination in Prenatal Samples from Whole Exome Sequencing Data
Sanne P Smeekens1, Raoul Timmermans1, Dineke Westra1
1Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.
Background:
Maternal cell contamination (MCC) in prenatal samples poses a risk for misdiagnosis, and therefore, testing for contamination is necessary during genetic analysis of prenatal specimens. MCC testing is currently performed as a method separate from the diagnostic method. With the increasing application of whole exome sequencing (WES) in prenatal diagnosis, we sought to develop a method to estimate the level of contamination from WES data, aiming to eliminate the need for a separate MCC test.
Methods:
To investigate the impact of MCC on the distribution of the variant allele fraction in WES data, contamination was both simulated in silico and artificially induced. Subsequently, a bioinformatic WES contamination method was developed and validated by comparing its performance to that of the gold standard (short tandem repeat [STR]) MCC test, validated for detecting ≥5% contamination. Finally, post-implementation performance was monitored for a 15-month period.
Results:
During validation, 270 prenatal samples underwent analysis with both WES and the gold standard test. In 259 samples, the results were concordant (248 not contaminated, 11 contaminated with both tests). In 11 samples, contamination was only detected in WES data (2 of which contained ≥5% contamination with WES, which is above the detection limit of the gold standard test). The data of the post-implementation evaluation on 361 samples, of which 68 were contaminated, were in line with the validation data.
Conclusions:
Contamination can reliably be detected in WES data, rendering a separate contamination test unnecessary for the majority of samples.
Insights
Maternal cell contamination in prenatal samples can be reliably detected using whole exome sequencing (WES) data alone. This bioinformatics method eliminates the need for separate contamination testing, improving prenatal diagnosis accuracy.
Area of Science:
- Genetics
- Bioinformatics
- Prenatal Diagnostics
Background:
- Maternal cell contamination (MCC) in prenatal samples risks misdiagnosis during genetic analysis.
- Current MCC testing is a separate procedure from the primary diagnostic method.
- Whole exome sequencing (WES) is increasingly used in prenatal diagnosis.
Purpose of the Study:
- To develop a method for estimating maternal cell contamination levels directly from WES data.
- To eliminate the necessity of a separate MCC testing procedure.
- To integrate contamination assessment into the WES workflow for prenatal samples.
Main Methods:
- Simulated and induced contamination in WES data to study its impact.
- Developed a bioinformatic WES contamination detection method.
- Validated the WES method against the gold standard short tandem repeat (STR) test for MCC detection (≥5% contamination).
- Monitored post-implementation performance over 15 months.
Main Results:
- WES and gold standard tests showed concordant results in 259 out of 270 samples.
- WES detected contamination in 11 samples missed by the gold standard test.
- Post-implementation data on 361 samples supported the validation findings, confirming WES's reliability.
Conclusions:
- WES data can reliably detect maternal cell contamination.
- A separate MCC test is unnecessary for most prenatal samples when using WES.
- The developed bioinformatic method enhances the efficiency and accuracy of prenatal genetic analysis.
