Interfering effect of maternal cell contamination on invasive prenatal molecular genetic testing

Detection of DNA Contamination in Prenatal Samples from Whole Exome Sequencing Data

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.

Maternal cell contamination in postnatal umbilical cord blood samples implies a low risk for genetic misdiagnoses

OBJECTIVE

Maternal cell contamination (MCC) poses a risk for misdiagnosis in prenatal genetic testing, and is examined in accredited diagnostic laboratories However, the awareness of possible MCC in perinatal/postnatal genetic testing, mainly of umbilical cord blood (CB), is lower.

METHOD

We investigated the rate of MCC in DNA from both umbilical CB samples and umbilical cord samples that were sent to our diagnostic laboratory for diagnostic testing between 1995 and 2021 (n = 236).

RESULTS

MCC was detected in 4% of umbilical CB samples, and in one umbilical cord sample. Particularly tests enriching for a specific variant are very sensitive for low amounts of MCC, as we emphasize here with a false positive diagnosis of myotonic dystrophy type 1 in a newborn.

CONCLUSIONS

Overall, with appropriate collection and use, umbilical CB and umbilical cord samples are suitable for genetic testing based on the low rates of MCC and misdiagnosis. These findings do however underline the importance of routine MCC testing in umbilical CB samples and umbilical cord samples for both requesting clinicians and diagnostic genetic laboratories.

Prenatal diagnosis of thalassemia in 695 pedigrees from southeastern China: a 10-year follow-up study

Thalassaemia is highly prevalent in southeastern China. This 10-year follow-up study aimed to characterize the genotype and karyotype of thalassaemia in fetal samples derived from thalassemia carriers in Fujian province, southeastern China. A total of 476 prenatal samples from 472 couples carrying α-thalassaemia traits and 224 samples from 223 couples carrying β-thalassaemia traits were collected for STR analysis, detection of thalassemia genotypes and karyotyping. The common deletional α-thalassemias and rare thalassemia genotypes were detected using Gap-PCR assay, and the common β-globin gene mutations were detected using PCR-RDB assay. We detected 43.49% prevalence of α-thalassaemia minor, 26.05% prevalence of α-thalassaemia intermediate and major and 1.89% prevalence of rare form among the 476 prenatal samples from couples with α-thalassaemia, and 85 fetuses with β-thalassemia heterozygote, 16 with homozygote and 21 with double heterozygote, and a rare β^{IVS-2-654(C→T)} /Chinese G_γ (^A γδβ)⁰  genotype among the 224 prenatal samples from couples with β-thalassemia. Karyotyping showed 7 fetuses with abnormal karyotypes. Totally 153 pregnancies were terminated, and genetic diagnosis of thalassemia using fetal umbilical cord blood following induction of labor showed consistent results with prenatal diagnosis. No thalassemia phenotypes were identified in normal infants half a year after birth, and the infants with α-thalassemia and β-thalassemia minor had no or mild anemia symptoms, but normal development, while 15 babies with hemoglobin H disease presented moderate anemia symptoms. Our data suggest the pregestational screening of thalassemia, notably compound and rare forms of thalassemia, for couples carrying thalassemia traits.