Discordant noninvasive prenatal testing and cytogenetic results: a study of 109 consecutive cases

Abstract

The evaluation of circulating cell-free DNA by massively parallel shotgun or targeted sequencing to determine the risk of fetal aneuploidy has been rapid and extensive. Recent published studies have demonstrated the incremental value of the use of cell-free DNA for noninvasive prenatal testing (NIPT). 1 Various methods and technologies have been used for NIPT, with impressive results. In one study, NIPT demonstrated 100% sensitivity for both trisomy 21 and trisomy 18, with a specificity of ≥99.7% for both. 1 Data recently presented by two independent groups in 2013 2 and 2014 3 prompted us to review the concordance of results among cases with positive or negative NIPT results referred to Quest Diagnostics for confirmation with cytogenetic studies. MATERIALS AND METHODSWe evaluated the results from 109 consecutive specimens prenatally and/or postnatally studied by standard karyotyping, fluorescence in situ hybridization analysis (AneuVysion; Abbott Molecular/Vysis, Abbott Park, IL), and/or oligo-single-nucleotide polymorphism microarrays (CytoScanHD; Affymetrix, Santa Clara, CA) after NIPT. The NIPT providers were listed in 42 cases and included Panorama (Natera, San Carlos, CA; 20 cases), Harmony (Ariosa Diagnostics, San Jose, CA; 13 cases), MaterniT21 (Sequenom, San Diego, CA; 8 cases), and Verifi (Illumina, Redwood City, CA; 1 case). The most common initial NIPT-positive result was trisomy 21 (41 cases), followed by trisomy 18 (25 cases), trisomy 13 (16 cases), sex chromosome aneuploidy (16 cases), trisomy 16 (3 cases), monosomy 21 (2 cases), and 1 case each of triploidy and microdeletion of 22q11.2. Four samples negative for NIPT but positive for ultrasound findings were included. RESULTSCytogenetic results were positive for trisomy 21 in 38 of the 41 NIPT-positive cases (true-positive rate: 93%) and for trisomy 18 in 16 of the 25 NIPT-positive cases (true-positive rate: 64%) ( Table 1). The true-positive rate was only 44% (7/16 cases) for trisomy 13 and 38% (6/16 cases) for sex chromosome aneuploidy. A total of six cases with positive NIPT results for either monosomy 21, trisomy 16, triploidy, or 22q11.2 microdeletion had normal cytogenetic findings. Only one case had very-lowlevel mosaicism (~5-10%) for trisomy 16. Confined placental mosaicism was confirmed in two cases (2/105, 2%): one with 3% mosaic for trisomy 18 and another with a mosaic segmental uniparental disomy for 11p15.5-p11.2. A false-negative result for NIPT was identified in nonmosaic trisomies 9 and 21, a marker chromosome, and a mosaic sex chromosome aneuploidy.The findings from our laboratory and those presented by the above-mentioned two groups (n = 80 and n = 46) show that Purpose: Recent published studies have demonstrated the incremental value of the use of cell-free DNA for noninvasive prenatal testing with 100% sensitivity for trisomies 21 and 18 and a specificity of ≥99.7% for both. Data presented by two independent groups suggesting positive results by noninvasive prenatal testing were not confirmed by cytogenetic studies. Methods:C...

Diagnostic cytogenetic testing following positive noninvasive prenatal screening results: a clinical laboratory practice resource of the American College of Medical Genetics and Genomics (ACMG)

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Expanding noninvasive prenatal testing to include microdeletions and segmental aneuploidy: cause for concern?

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Noninvasive Prenatal Screening for Genetic Diseases Using Massively Parallel Sequencing of Maternal Plasma DNA

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