Clinical Experience with Genome-Wide Noninvasive Prenatal Screening in a Large Cohort of Twin Pregnancies

Advancing Non-Invasive Prenatal Screening: A Targeted 1069-Gene Panel for Comprehensive Detection of Monogenic Disorders and Copy Number Variations

We introduce an innovative, non-invasive prenatal screening approach for detecting fetal monogenic alterations and copy number variations (CNVs) from maternal blood.

METHOD

Circulating free DNA (cfDNA) was extracted from maternal peripheral blood and processed using the VeriSeq NIPT Solution (Illumina, San Diego, CA, USA), with shallow whole-genome sequencing (sWGS) performed on a NextSeq550Dx (Illumina). A customized gene panel and bioinformatics tool, named the "VERA Revolution", were developed to detect variants and CNVs in cfDNA samples. Results were compared with genomic DNA (gDNA) extracted from fetal samples, including amniotic fluid and chorionic villus sampling and buccal swabs.

RESULTS

The study included pregnant women with gestational ages from 10 + 3 to 15 + 2 weeks (mean: 12.1 weeks). The fetal fraction (FF), a crucial measure of cfDNA test reliability, ranged from 5% to 20%, ensuring adequate DNA amount for analysis. Among 36 families tested, 14 showed a wild-type genotype. Identified variants included two deletions (22q11.2, and 4p16.3), two duplications (16p13 and 5p15), and eighteen single-nucleotide variants (one in CFTR, three in GJB2, three in PAH, one in RIT1, one in DHCR7, one in TCOF1, one in ABCA4, one in MYBPC3, one in MCCC2, two in GBA1 and three in PTPN11). Significant concordance was found between our panel results and prenatal/postnatal genetic profiles.

CONCLUSIONS

The "VERA Revolution" test highlights advancements in prenatal genomic screening, offering potential improvements in prenatal care.

Diagnostic accuracy of cell-free fetal DNA in maternal blood in detecting chromosomal anomalies in twin pregnancy: systematic review and meta-analysis

OBJECTIVE

To report the diagnostic accuracy of cell-free fetal DNA (cfDNA) in maternal blood in detecting fetal chromosomal anomalies in twin pregnancy.

METHODS

PubMed, MEDLINE, EMBASE and Cochrane databases were searched from inception to November 2023. The inclusion criteria were twin pregnancy undergoing cfDNA screening for trisomies 21, 18 and 13, monosomy X and/or other sex-chromosome aneuploidies (SCA). The index test was cfDNA screening. The reference standard was pre- or postnatal karyotyping (in the case of a positive cfDNA result) or neonatal phenotypic assessment (in case of a negative cfDNA result). The quality of included studies was assessed using the revised quality assessment of diagnostic accuracy studies (QUADAS-2) tool. Summary estimates of diagnostic accuracy were computed using a bivariate random-effects model.

RESULTS

Thirty-five studies were included in the systematic review and meta-analysis. cfDNA had a high accuracy in detecting trisomy 21 in twin pregnancy, with a sensitivity of 98.8% (95% CI, 96.5-100%) and specificity of 100% (95% CI, 99.9-100%). Sensitivity and specificity were 94.9% (95% CI, 75.9-99.1%) and 100% (95% CI, 99.9-100%), respectively, for trisomy 18 and 84.6% (95% CI, 54.6-98.1%) and 100% (95% CI, 99.9-100%), respectively, for trisomy 13. We could not compute the diagnostic accuracy of cfDNA in detecting monosomy X, owing to an absence of positive cases, while cfDNA had a sensitivity of 100% (95% CI, 71.5-100%) and specificity of 99.8% (95% CI, 99.7-99.9%) for other SCA. The accuracy of cfDNA in detecting the common trisomies was similar in dichorionic and monochorionic twin pregnancies.

CONCLUSIONS

cfDNA has high diagnostic accuracy in detecting trisomies 21 and 18 in twin pregnancy, irrespective of chorionicity. Estimation of diagnostic accuracy for trisomy 13 and other SCA was limited by the small number of affected cases and the difficulty associated with detecting false-negative cases of other SCA, and thus requires confirmation in larger studies. © 2024 International Society of Ultrasound in Obstetrics and Gynecology.

Clinical outcomes of screen-positive genome-wide cfDNA cases for trisomy 20: results from the global expanded NIPT Consortium

Trisomy 20 has been shown to be one of the most frequent rare autosomal trisomies in patients that undergo genome-wide noninvasive prenatal testing. Here, we describe the clinical outcomes of cases that screened positive for trisomy 20 following prenatal genome-wide cell-free (cf.) DNA screening. These cases are part of a larger cohort of previously published cases. Members of the Global Expanded NIPT Consortium were invited to submit details on their cases with a single rare autosomal aneuploidy following genome-wide cfDNA screening for retrospective analysis. Clinical details including patient demographics, test indications, diagnostic testing, and obstetric pregnancy outcomes were collected. Genome-wide cfDNA screening was conducted following site-specific laboratory procedures. Cases which screened positive for trisomy 20 (n = 10) were reviewed. Clinical outcome information was available for 90% (9/10) of our screen-positive trisomy 20 cases; the case without diagnostic testing ended in a fetal demise. Of the nine cases with outcome information, one was found to have a mosaic partial duplication (duplication at 20p13), rather than a full trisomy 20. Only one case in the study cohort had placental testing; therefore, confined placental mosaicism could not be ruled out in most cases. Adverse pregnancy outcomes were seen in half of the cases, which could suggest the presence of underlying confined placental mosaicism or mosaic/full fetal trisomy 20. Based on our limited series, the likelihood of true fetal aneuploidy is low but pregnancies may be at increased risk for adverse obstetric outcomes and may benefit from additional surveillance.

Non-invasive prenatal test identifies circulating cell-free DNA chromosomal abnormalities derived from clonal hematopoiesis in aggressive hematological malignancies

Liquid biopsy is a minimally invasive diagnostic tool for identification of tumor-related mutations in circulating cell-free DNA (cfDNA). The aim of this study was to investigate feasibility, sensitivity, and specificity of non-invasive prenatal test (NIPT) for identification of chromosomal abnormalities in cfDNA from a total of 77 consecutive patients with non-Hodgkin B-cell lymphomas, Hodgkin lymphoma (HL), or plasma cell dyscrasia. In this case series, half of patients had at least one alteration, more frequently in chromosome 6 (23.1%), chromosome 9 (20.5%), and chromosomes 3 and 18 (16.7%), with losses of chromosome 6 and gains of chromosome 7 negatively impacting on overall survival (OS), with a 5-year OS of 26.9% and a median OS of 14.6 months, respectively (P = 0.0009 and P = 0.0004). Moreover, B-cell lymphomas had the highest NIPT positivity, especially those with aggressive lymphomas, while patients with plasma cell dyscrasia with extramedullary disease had a higher NIPT positivity compared to conventional cytogenetics analysis and a worse outcome. Therefore, we proposed a NIPT-based liquid biopsy a complementary minimally invasive tool for chromosomal abnormality detection in hematological malignancies. However, prospective studies on larger cohorts are needed to validate clinical utility of NIPT-based liquid biopsy in routinely clinical practice.