Noninvasive prenatal diagnosis: from dream to reality

Identification of a novel COL10A1: c.1952 G>T variant in a family with Schmid metaphyseal chondrodysplasia and development of a noninvasive prenatal testing method

Background

The collagen alpha‐1(X) chain gene (COL10A1) is a known causative gene for Schmid metaphyseal chondrodysplasia (SMCD). This study clinically examined a Chinese family (n = 42) for SMCD and inheritance pattern. Fifteen individuals were diagnosed with SMCD based on characteristic skeletal phenotypes with autosomal dominant inheritance mode.

Methods

Four clinically diagnosed patients and three healthy relatives were selected for subsequent genetic tests. Trio‐whole exome sequencing (Trio‐WES) followed by Sanger sequencing and familial co‐segregation analysis were performed to identify SMCD‐associated variants.

Results

COL10A1 (NM_000493.4):c.1952 G>T(p.Trp651Leu) variant was detected only in the four patients and not in the three healthy relatives. The variant was evaluated as “likely pathogenic” according to the American College of Medical Genetics and Genomics variation classification guidelines with evidence of PM2, PM5, PP1, and PP3. To test the presence of the target variant in proband's fetal offspring, we developed a noninvasive prenatal testing method by extracting cell‐free fetal DNA in maternal plasma followed by high‐depth sequencing. The variant was also detected in the fetus and later confirmed by amniocentesis.

Conclusion

We identified a new disease‐causing variant in COL10A1. Cell‐free fetal DNA in maternal peripheral blood can be used as the rapid and noninvasive prenatal diagnostic method to detect the pathogenic/or likely pathogenic variant.

Non-invasive prenatal testing: A diagnostic innovation shaped by commercial interests and the regulation conundrum

Non-invasive prenatal testing (NIPT) is grounded in the analysis of free circulating fetal DNA (cfDNA) in pregnant women's blood. The rolling out of this screening method was in large part driven by commercial firms, which hoped to reach a huge potential market by offering a test that was expected to be risk-free, reliable, inexpensive, and able to detect a wide range of genetic traits of the future child. To date, most predictions about the scope and uses of NIPT have not materialized: in 2020 NIPT detects only a limited number of genetic anomalies, while results have to be confirmed by amniocentesis. NIPT has become a commercial success. Nevertheless the implementation of NIPT has tended to diverge across different national settings. In countries that already have state-sponsored screening for Down risk, NIPT has been offered by the state health insurance to women defined as "high risk", using a variant of the test that detects only three autosomal aneuploidies: trisomy 21, 13 and 18. These countries effectively regulate the supply of NIPT on grounds of cost-effectiveness and reliability. In countries without state-sponsored screening for Down risk, in contrast, multiple versions of NIPT covering a wider range of birth defects are commonly available on the free market, and purchased by women at low as well as high risk of having an affected child. Market-based healthcare systems tend to present women who can afford to pay for NIPT with a largely unregulated choice of technologies - though reimbursement rules imposed by private insurance providers may serve in effect to regulate use by those consumers who cannot afford to pay for tests from their own pockets. This regulatory divergence is shaped by the presence or absence of prior state-sponsored screening programs for Down risk.

Extracellular RNA in a single droplet of human serum reflects physiologic and disease states

Extracellular RNAs (exRNAs) are present in human serum. It remains unclear to what extent these circulating exRNAs may reflect human physiologic and disease states. Here, we developed SILVER-seq (Small Input Liquid Volume Extracellular RNA Sequencing) to efficiently sequence both integral and fragmented exRNAs from a small droplet (5 μL to 7 μL) of liquid biopsy. We calibrated SILVER-seq in reference to other RNA sequencing methods based on milliliters of input serum and quantified droplet-to-droplet and donor-to-donor variations. We carried out SILVER-seq on more than 150 serum droplets from male and female donors ranging from 18 y to 48 y of age. SILVER-seq detected exRNAs from more than a quarter of the human genes, including small RNAs and fragments of mRNAs and long noncoding RNAs (lncRNAs). The detected exRNAs included those derived from genes with tissue (e.g., brain)-specific expression. The exRNA expression levels separated the male and female samples and were correlated with chronological age. Noncancer and breast cancer donors exhibited pronounced differences, whereas donors with or without cancer recurrence exhibited moderate differences in exRNA expression patterns. Even without using differentially expressed exRNAs as features, nearly all cancer and noncancer samples and a large portion of the recurrence and nonrecurrence samples could be correctly classified by exRNA expression values. These data suggest the potential of using exRNAs in a single droplet of serum for liquid biopsy-based diagnostics.

The evidence base for circulating tumour DNA blood-based biomarkers for the early detection of cancer: a systematic mapping review

BACKGROUND

The presence of circulating cell-free DNA from tumours in blood (ctDNA) is of major importance to those interested in early cancer detection, as well as to those wishing to monitor tumour progression or diagnose the presence of activating mutations to guide treatment. In 2014, the UK Early Cancer Detection Consortium undertook a systematic mapping review of the literature to identify blood-based biomarkers with potential for the development of a non-invasive blood test for cancer screening, and which identified this as a major area of interest. This review builds on the mapping review to expand the ctDNA dataset to examine the best options for the detection of multiple cancer types.

METHODS

The original mapping review was based on comprehensive searches of the electronic databases Medline, Embase, CINAHL, the Cochrane library, and Biosis to obtain relevant literature on blood-based biomarkers for cancer detection in humans (PROSPERO no. CRD42014010827). The abstracts for each paper were reviewed to determine whether validation data were reported, and then examined in full. Publications concentrating on monitoring of disease burden or mutations were excluded.

RESULTS

The search identified 94 ctDNA studies meeting the criteria for review. All but 5 studies examined one cancer type, with breast, colorectal and lung cancers representing 60% of studies. The size and design of the studies varied widely. Controls were included in 77% of publications. The largest study included 640 patients, but the median study size was 65 cases and 35 controls, and the bulk of studies (71%) included less than 100 patients. Studies either estimated cfDNA levels non-specifically or tested for cancer-specific mutations or methylation changes (the majority using PCR-based methods).

CONCLUSION

We have systematically reviewed ctDNA blood biomarkers for the early detection of cancer. Pre-analytical, analytical, and post-analytical considerations were identified which need to be addressed before such biomarkers enter clinical practice. The value of small studies with no comparison between methods, or even the inclusion of controls is highly questionable, and larger validation studies will be required before such methods can be considered for early cancer detection.

Trial by Dutch laboratories for evaluation of non-invasive prenatal testing. Part I-clinical impact

Objective

To evaluate the clinical impact of nationwide implementation of genome‐wide non‐invasive prenatal testing (NIPT) in pregnancies at increased risk for fetal trisomies 21, 18 and 13 (TRIDENT study).

Method

Women with elevated risk based on first trimester combined testing (FCT ≥ 1:200) or medical history, not advanced maternal age alone, were offered NIPT as contingent screening test, performed by Dutch University Medical laboratories. We analyzed uptake, test performance, redraw/failure rate, turn‐around time and pregnancy outcome.

Results

Between 1 April and 1 September 2014, 1413/23 232 (6%) women received a high‐risk FCT result. Of these, 1211 (85.7%) chose NIPT. One hundred seventy‐nine women had NIPT based on medical history. In total, 1386/1390 (99.7%) women received a result, 6 (0.4%) after redraw. Mean turn‐around time was 14 days. Follow‐up was available in 1376 (99.0%) pregnancies. NIPT correctly predicted 37/38 (97.4%) trisomies 21, 18 or 13 (29/30, 4/4 and 4/4 respectively); 5/1376 (0.4%) cases proved to be false positives: trisomies 21 (n = 2), 18 (n = 1) and 13 (n = 2). Estimated reduction in invasive testing was 62%.

Conclusion

Introduction of NIPT in the Dutch National healthcare‐funded Prenatal Screening Program resulted in high uptake and a vast reduction of invasive testing. Our study supports offering NIPT to pregnant women at increased risk for fetal trisomy. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.

What's already known about this topic?

Non‐invasive prenatal testing (NIPT) for trisomies 21, 18 and 13 is mainly offered in a commercial setting.

Offering NIPT to pregnant women at increased risk for fetal trisomy leads to a reduction in invasive testing.

What does this study adds?

NIPT implemented as a contingent test under the umbrella of a national health authority‐supported fetal trisomy screening program facilitates optimal counseling with close to 100% follow‐up, results in 86% uptake and confirms a major reduction of invasive tests.

Elevated Levels of Total Cell-Free DNA in Maternal Serum Samples Arise from the Generation of Neutrophil Extracellular Traps

INTRODUCTION

The analysis of cell-free DNA from maternal blood samples has facilitated the noninvasive detection of fetal aneuploidies or hereditary Mendelian disorders. In this context, previous studies have indicated that the pool of cell-free DNA is greater in maternal serum than in plasma samples, necessitating optimized collection and storage protocols. As the source of this increased amount of cell-free DNA is not clear, we have now examined whether neutrophil extracellular traps (NETs) contribute to this material.

MATERIAL AND METHODS

Serum samples were collected in all three trimesters of normal healthy pregnant women, and at term from cases with manifest preeclampsia. The presence of NET-derived material was demonstrated by the detection of cell-free DNA fragments complexed to neutrophil granular proteins (i.e. myeloperoxidase).

RESULTS

Our data indicate that NET-derived cell-free DNA/myeloperoxidase complexes were greater in serum from normal pregnant women than in normal matching nonpregnant controls. This neutrophil chromosomal material increased incrementally throughout gestation and was most pronounced in cases with preeclampsia.

DISCUSSION

By detecting increased levels of cell-free DNA/myeloperoxidase complexes in maternal serum samples, our data indicate that a significant proportion of this material is derived from the generation of NETs.

Biomarker development for presymptomatic molecular diagnosis of preeclampsia: feasible, useful or even unnecessary?

The past decade saw the advent of a number of promising biomarkers to detect pregnancies at risk for preeclampsia (PE), the foremost being those associated with an imbalance of angiogenic factors. In late pregnancy, these are useful for the detection of imminent cases of PE, while earlier they were more predictive for early- than late-onset PE. This suggests that there may be fundamental differences between the underlying pathology of these two PE forms. Therefore, it is possible that such a biological premise may limit the development of biomarkers that will permit the efficacious detection of both early- and late-onset PE via an analysis of first-trimester maternal blood samples. Consequently, a significant increase in our understanding of the underlying pathology of PE, using a variety of approaches ranging from systems biology to animal models, will be necessary in order to overcome this obstacle.