Screening of Fetal Chromosomal Aneuploidy by Noninvasive Prenatal Testing: From Innovation to Setting Public Health Agendas to Potential Impact on Other Fields

The Road Well Traveled: Making Choices, Ensuring Progress While Heeding the "Clarion Call"

The career path of everyone is quite unique based on the goals and the choices we make, and success can take time to unfold. My career choices have been greatly influenced by remarkable mentors and opportunities. Reciprocally I have had the pleasure, as a faculty member, department chair, and medical school dean to mentor promising young physicians and scientists to launch successful careers. We need to continue to attract physicians and scientists to academic medicine to ensure that our field continues to innovate and improve the lives of our patients. To influence positive change, we must stay relentlessly focused and have faith that success will come.

Between Laboratory Reproducibility of DNA Extraction from Human Blood and Fresh Frozen Tissue

Standardization of molecular diagnostics is fundamental for effective application of genetic analyses in personalized medicine. The amount of DNA extracted from a specimen can have a significant impact on diagnostic accuracy, especially in cases where the diagnostic variant has a low concentration such as cancer. Blood and tissue samples were supplied to genetic laboratories to assess the reproducibility of extraction methodologies; DNA was extracted using participants' routine procedures and returned to the external quality assessment provider. The amount of DNA was measured by two independent analytical techniques, fluorescence intensity of intercalating dye and digital PCR; DNA quality was evaluated by DNA integrity number scores. The amount of DNA extracted varied widely between and within participants and for different blood volumes, indicating that consistent diagnostic quality is challenging even within a single test center. The median digital PCR-measured amount of DNA was on average six times higher than the intercalating dye measurements obtained in this study, indicating the possibility that the latter quantitative method may significantly underestimate the amount of DNA, thus making it not fit for purpose. Standardization of genetic diagnostic tests will require a significant improvement in the reproducibility of DNA extraction; this could be achieved if suppliers and users of DNA extraction kits validate their extraction methodology using reliable quantitative measurements or reference materials.

Non-invasive prenatal screening for foetal trisomy: An assessment of reliability and reporting

OBJECTIVE

Non-invasive prenatal screening (NIPS) has been introduced as a routine screening technique for aneuploidies in the clinic. To evaluate its reliability and reporting standardization, the National Center for Clinical Laboratories launched an external quality assessment (EQA) program based on highly simulated samples.

METHODS

Maternal and child paired cell lines were digested by enzymes to obtain DNA fragments for the analysis panel, which were composed of 5% T21, 5% T18, 10% T13, 10% euploid, and 20% T18 samples. The samples were validated and distributed to laboratories along with scenarios and questionnaires for analysis.

RESULTS

Out of 350 participating laboratories, 98.6% correctly identified all samples. The concurrence rates of laboratories for the 5% T21, 5% T18, 10% T13, 10% euploid, and 20% T18 samples were 98.9%, 99.7%, 99.7%, 100%, and 100%, respectively. Enrichment increased the foetal fraction (FF) values by 2 ∼ 3-fold, but the z scores generated by the enrichment group fluctuated greatly. Other FF estimation techniques, such as the size-based and FF-QuantSC methods, generated slightly different FF values from the chr Y-based method. Furthermore, some laboratories omitted the suggestions of results in reports.

CONCLUSIONS

The participating laboratories provided highly reliable results for samples with relatively higher FF values. However, the absence of performance validation, laboratory errors, and low FF values were potential reasons for false-negative results. In addition, enrichment operations should be validated and normalized to guarantee NIPS reproducibility, plus further efforts are required to standardize the NIPS reports.

Can Circulating Tumor DNA Support a Successful Screening Test for Early Cancer Detection? The Grail Paradigm

Circulating tumor DNA (ctDNA) is a new pan-cancer tumor marker with important applications for patient prognosis, monitoring progression, and assessing the success of the therapeutic response. Another important goal is an early cancer diagnosis. There is currently a debate if ctDNA can be used for early cancer detection due to the small tumor burden and low mutant allele fraction (MAF). We compare our previous calculations on the size of detectable cancers by ctDNA analysis with the latest experimental data from Grail’s clinical trial. Current ctDNA-based diagnostic methods could predictably detect tumors of sizes greater than 10–15 mm in diameter. When tumors are of this size or smaller, their MAF is about 0.01% (one tumor DNA molecule admixed with 10,000 normal DNA molecules). The use of 10 mL of blood (4 mL of plasma) will likely contain less than a complete cancer genome, thus rendering the diagnosis of cancer impossible. Grail’s new data confirm the low sensitivity for early cancer detection (<30% for Stage I–II tumors, <20% for Stage I tumors), but specificity was high at 99.5%. According to these latest data, the sensitivity of the Grail test is less than 20% in Stage I disease, casting doubt if this test could become a viable pan-cancer clinical screening tool.

Application value of NIPT for uncommon fetal chromosomal abnormalities

Objective

To investigate the clinical value of noninvasive prenatal testing (NIPT) for fetal chromosomal deletion, duplication, and sex chromosome abnormalities.

Methods

The study included 6239 pregnant women with singletons in the first and second trimester of pregnancy who received NIPT from December 2017 to June 2019. For pregnant women at high risk of deletion, duplication, and sex chromosome abnormalities indicated by NIPT, amniocentesis was recommended for karyotype analysis and chromosome copy number variation detection to verify the NIPT results and analyze chromosome abnormalities. Women at low risk and with no other abnormal results continued with their pregnancies.

Results

Among the 6239 pregnant women who received NIPT, there were 15 cases of chromosomal deletion (12 cases confirmed by amniocentesis), 16 cases of chromosomal duplication (9 cases confirmed by amniocentesis), and 17 cases of sex chromosome abnormalities (11 cases confirmed by amniocentesis). Of these cases, 32 were finally confirmed by amniotic fluid cell karyotype analysis. The coincidence rate was 66.7% (32/48). There were no abnormalities found for the remaining low risk pregnant women during follow-up.

Conclusion

NIPT has good application value in predicting fetal chromosomal deletion, duplication, and sex chromosome abnormalities. It can improve the detection rate of fetal chromosomal abnormalities, but further prenatal diagnosis is needed.