Noninvasive prenatal screening for patients with high body mass index: Evaluating the impact of a customized whole genome sequencing workflow on sensitivity and residual risk

Chromosomal aberration analysis: Novel noninvasive techniques for early-stage cancer screening

OBJECTIVE

Chromosome breakage is a catastrophic event that leads to the progressive development and progression of cancer. In order to analyze the changes of peripheral blood microenvironment of tumor patients, to explore the indicators of non-specific non-invasive tumor early screening. This paper presents a new idea of whether the gene sequence near the DNA damage break point is the gene sequence that controls the unrestricted growth of normal cells.

METHODS

The chromosomal aberrations of peripheral blood lymphocytes were analysed in 60 healthy adult and 49 cancer patients before radiotherapy.

RESULTS

The detection rate of chromosomal aberrations was high in tumor patients, and "dicentric + translocations" of chromosomes were detected in 36 patients (73.47 %). The chi-square test showed statistically significant differences (P < 0.01), and chromosome adhesion and dissolution were observed.

CONCLUSIONS

"Dicentric + Translocation" chromosome can be used as a nonspecific early screening indicator for cancer. This is worthy of further study. This index can be used to determine the genetic basis of various cancers at the gene level to modify the base sequence and prevent the occurrence of cancer. It is worthy of further study, and it can provide a new method for gene therapy of tumors.

Focus on the frontier issue: progress in noninvasive prenatal screening for fetal trisomy from clinical perspectives

The discovery of cell-free fetal DNA (cffDNA) in maternal blood and the rapid development of massively parallel sequencing have revolutionized prenatal testing from invasive to noninvasive. Noninvasive prenatal screening (NIPS) based on cffDNA enables the detection of fetal trisomy through sequencing, comparison, and bioassays. Its accuracy is better than that of traditional screening methods, and it is the most advanced clinical application of high-throughput sequencing technologies. However, the existing sequencing methods are limited by high costs and complex sequencing procedures. These limitations restrict the availability of NIPS for pregnant women. Many amplification methods have been developed to overcome the limitations of sequencing methods. The rapid development of non-sequencing methods has not been accompanied by reviews to summarize them. In this review, we initially describe the detection principles for sequencing-based NIPS. We summarize the rapidly evolving amplification technologies, focusing on the need to reduce costs and simplify the procedures. To ensure that the testing systems are feasible and that the testing processes are reliable, we expand our vision to the clinic. We evaluate the clinical validity of NIPS in terms of sensitivity, specificity, and positive predictive value. Finally, we summarize the application guidelines and discuss the corresponding quality control methods for NIPS. In addition to cffDNA, extracellular vesicle DNA, RNA, protein/peptide, and fetal cells can also be detected as biomarkers of NIPS. With the development of prenatal testing, NIPS has become increasingly important. Notably, NIPS is a screening test instead of a diagnostic test. The testing methods and procedures used in the NIPS process require standardization.

The impact of maternal and geographical factors on the uptake of non-invasive prenatal testing: A retrospective cohort study

OBJECTIVES

The objectives of this study were to investigate recent trends in non-invasive prenatal testing (NIPT) utilisation, including factors associated with geographical variation, and to determine whether maternal or regional characteristics are associated with uptake the of NIPT.

METHODS

This retrospective cohort study included pregnant individuals in Ontario with an expected date of delivery from August 1st, 2016 to March 31st, 2020. Modified Poisson regression was used to estimate rate ratios for NIPT use adjusted for maternal and healthcare covariates.

RESULTS

We found substantial variation in NIPT uptake between regions within the province. The highest uptake was found in urban areas, highest quintile of neighbourhood income and education, for those who were ≥40 years of age and had a history of previous aneuploidy, for those with a prenatal care visit in the first trimester, multiple pregnancy, multigravidity and body mass index within the normal range (18.5-24.9 kg/m² ).

CONCLUSION

Our study demonstrated significant regional and maternal differences in NIPT uptake across Ontario. Given the large sample size and diverse population, our study may have implications for other jurisdictions with large, socio-demographically and geographically diverse populations.

The Impact of HBB ‐related Hemoglobinopathies Carrier Status on Fetal Fraction in Noninvasive Prenatal Screening

Objective

We evaluated whether there is an association between β‐globin (HBB) pathogenic variants and fetal fraction (FF), and whether the association has a clinically relevant impact on non‐invasive prenatal screening (NIPS).

Method

A whole‐genome sequencing NIPS laboratory database was retrospectively queried for women who underwent NIPS and carrier screening of both HBB and the α‐globin genes (HBA1/HBA2). Women affected with either condition were excluded from the study, yielding a cohort size of 15,853. A “corrected FF” was obtained via multivariable linear regression adjusted for the systematic impacts of maternal age, gestational age and BMI. Corrected FF distributions of HBB and HBA1/HBA2 carriers were each compared to non‐carriers using the Kolmogorov‐Smirnov test.

Results

In this cohort, 291 women were carriers for HBB alone, and 1016 were carriers for HBA1/HBA2 alone. The HBB carriers had a lower corrected FF when compared to non‐carriers (p < 0.0001). There was no difference in corrected FF among carriers and non‐carriers of HBA1/HBA2.

Conclusion

Carriers of pathogenic variants in the HBB gene, but not the HBA1/HBA2 genes, are more likely to have lower FF when compared to women with structurally normal hemoglobin. This decrease in FF could result in an elevated test‐failure rate if FF thresholds were used.

What is already known about this topic?

Multiple factors affect fetal fraction during noninvasive prenatal screening (NIPS), such as maternal BMI and gestational age. Patients affected with Hb beta chain‐related hemoglobinopathies have been shown to have lower fetal fraction during NIPS.

What does this study add?

This study demonstrates that HBB carriers—not just affected patients—also have lower fetal fraction on NIPS, adding to the literature of factors that could affect fetal fraction and NIPS performance.

Obesity and no call results: optimal timing of cell-free DNA testing and redraw

BACKGROUND

Fetal fraction of cell-free DNA decreases with increasing maternal weight. Consequently, cell-free DNA screening for fetal aneuploidy has higher screen failures or "no call" rates in women with obesity owing to a low fetal fraction. The optimal timing of testing based on maternal weight is unknown.

OBJECTIVE

This study aimed to identify the optimal timing of initial cell-free DNA testing based on maternal weight and to identify the optimal timing of repeat cell-free DNA testing in cases with an initial screen failure.

STUDY DESIGN

This was a retrospective cohort study of women undergoing cell-free DNA for fetal aneuploidy screening between 9 and 18 weeks through a single laboratory over 1 year from 2018 to 2019. Fetal fraction change per week was calculated, and generalized linear models were used to calculate relative risk and 95% confidence interval of a no call result at given maternal weights and gestational ages.

RESULTS

The vast majority of samples (99.22%) received a test result. The risk of a no call result owing to a low fetal fraction was higher with increasing maternal weight. At 9 to 12 weeks, the rate of a no call result owing to a low fetal fraction in women who weighed <150 lb was 0.14% compared with 17.39% in women weighing >400 lb. Fetal fraction increased with increasing gestational age, although the incremental increase in fetal fraction over time is inversely proportional to maternal weight. At 13 to 18 weeks' gestation, 6.45% of women weighing >400 lb received a no call result owing to a low fetal fraction. In women in the highest weight category, >400 lb, fetal fraction increased 0.5% with each week of gestation.

CONCLUSION

Although the risk of a no call result increases with maternal weight, cell-free DNA screening should be offered to all women at 9 to 12 weeks' gestation, allowing the option to have chorionic villus sampling after a positive test result. Pretest counseling for women with obesity should include the increased chance for a test failure. Most women weighing less than 400 lb will receive a test result and more than 80% of women with a weight of >400 lb will receive a test result at 9 to 12 weeks' gestation. Data regarding the expected increase in cell-free DNA fetal fraction per week may help guide the timing of a redraw to optimize test success.

High-throughput fetal fraction amplification increases analytical performance of noninvasive prenatal screening

Purpose

The percentage of a maternal cell-free DNA (cfDNA) sample that is fetal-derived (the fetal fraction; FF) is a key driver of the sensitivity and specificity of noninvasive prenatal screening (NIPS). On certain NIPS platforms, >20% of women with high body mass index (and >5% overall) receive a test failure due to low FF (<4%).

Methods

A scalable fetal fraction amplification (FFA) technology was analytically validated on 1264 samples undergoing whole-genome sequencing (WGS)–based NIPS. All samples were tested with and without FFA.

Results

Zero samples had FF < 4% when screened with FFA, whereas 1 in 25 of these same patients had FF < 4% without FFA. The average increase in FF was 3.9-fold for samples with low FF (2.3-fold overall) and 99.8% had higher FF with FFA. For all abnormalities screened on NIPS, z-scores increased 2.2-fold on average in positive samples and remained unchanged in negative samples, powering an increase in NIPS sensitivity and specificity.

Conclusion

FFA transforms low-FF samples into high-FF samples. By combining FFA with WGS–based NIPS, a single round of NIPS can provide nearly all women with confident results about the broad range of potential fetal chromosomal abnormalities across the genome.

Noninvasive prenatal screening for patients with high body mass index: Evaluating the impact of a customized whole genome sequencing workflow on sensitivity and residual risk

Objective

Women with high body mass index (BMI) tend to have reduced fetal fraction (FF) during cell‐free DNA‐based noninvasive prenatal screening (NIPS), causing test failure rates up to 24.3% and prompting guidelines that recommend aneuploidy screening other than NIPS for patients with significant obesity. Because alternatives to NIPS are only preferable if they perform better, we compared the respective sensitivities at different BMI levels of traditional aneuploidy screening and a customized whole‐genome sequencing NIPS.

Method

The relationship between FF, aneuploidy, and BMI was quantified from 58 105 patients screened with a customized NIPS that does not fail samples because of low FF alone. Expected analytical sensitivity as a function of aneuploidy and BMI (eg, trisomy 18 sensitivity when BMI = 35) was determined by scaling the BMI‐ and aneuploidy‐specific FF distribution by the FF‐ and aneuploidy‐specific sensitivity calculated from empirically informed simulations.

Results

Across all classes of obesity and assuming zero FF‐related test failures, analytical sensitivity for the investigated NIPS exceeded that of traditional aneuploidy screening for trisomies 13, 18, and 21.

Conclusion

Relative to traditional aneuploidy screening, a customized NIPS with high accuracy at low FF and a low test‐failure rate is a superior screening option for women with high BMI.

What's already known about this topic?

Women with high body mass index (BMI) often receive a test failure on noninvasive prenatal screening (NIPS) because of low fetal fraction (FF).

The American College of Medical Genetics and Genomics recommends offering traditional aneuploidy screening to patients with “significant obesity.”

NIPS offerings differ in their efficacy at low FF.

What does this study add?

Irrespective of BMI and without FF‐based test failures, it is possible for a customized NIPS to provide all women with accurate prenatal screening.