Application of FF-QuantSC for the Precise Estimation of Fetal Fraction in Non-invasive Prenatal Testing in Two SRY-Translocation Cases

Abstract

Background: Non-invasive prenatal testing (NIPT) is a commonly employed clinical method to screen for fetal aneuploidy, while the Y chromosome-based NIPT method is regarded as the gold standard for the estimation of fetal fraction (FF) of male fetuses. However, when the fetus has a derivative Y chromosome thereby containing a partial Y chromosome, the Y chromosome-based NIPT method cannot accurately calculate FF. Therefore, alternative methods to precisely calculate FF are required. Methods: Two prenatal cases could not be detected effectively using the Y chromosomebased NIPT method because of low FF. According to the Y chromosome-based method, the FF of the fetuses were 1.730 ± 0.050% (average gestation week: 18 +1) and 2.307 ± 0.191% (average gestation week: 20 +0) for cases 1 and 2, respectively. Using various genetic diagnostic techniques, including the BoBs™ assay, karyotype analysis, improved nucleolus-organizing region (NOR)-banding analysis, Affymetrix CytoScan 750K Array, and fluorescence in situ hybridization (FISH) analysis, we determined the genetic defects of two fetuses with translocations of the SRY locus. Further, we reassessed the FF using FF-QuantSC and X chromosome-based methods. The distribution diagram of reads for chromosome Y was also analyzed. Results: The FF of the fetuses determined by FF-QuantSC were 10.330% (gestation week: 18 +4) in case 1 and 9.470% (gestation week: 21 +4) in case 2, while the FF of the fetuses determined using the X chromosome-based method were 8.889% (gestation week: 18 +4) in case 1 and 2.296% (gestation week: 21 +4) in case 2. Both the distribution diagrams of reads for chromosome Y of the two cases showed the deletion in the long arm of the Y chromosome. Conclusion: For repeatedly low FF samples detected using the Y chromosome-based NIPT method for a long gestational week, we believe that FF-QuantSC and distribution diagrams of reads could be used as a supplement to NIPT, especially for rare cases of sex reversal caused by SRY translocation.

Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review

“…Re-evaluations using the FF-QuantSC method and analysis of distribution patterns of Y-chromosome reads may lead to more accurate results for samples with a repeatedly low FF, especially for derived chromosomes containing part of the Y-chromosome (121). In this manner, rare cases of sex reversal caused by SRY translocation could avoid being misjudged as detection failures by Y-chromosome-based FF calculation methods.…”

Non‐invasive cell‐free DNA‐based approach for the diagnosis of clinical miscarriage: A retrospective study

“…We used a Y‐chromosome‐based FF estimator and the native algorithm default. Y‐chromosome‐based methods provide accurate FF estimates in male fetus pregnancies, 41,42 allowing non‐informative case reclassification and more accurate/objective assessments of concordance rates and cfDNA testing performance.…”

“…40 We used a Y-chromosome-based FF estimator and the native algorithm default. Y-chromosome-based methods provide accurate FF estimates in male fetus pregnancies, 41,42 F I G U R E 1 Fetal fraction variation according to gestational age. No significant differences were found in FF among the different GAs studied, suggesting that the time of fetal arrest does not influence the informativeness of the results.…”

The effect of hemolysis on quality control metrics for noninvasive prenatal testing

“…After pooling, denaturation and cyclization were carried out to generate single-stranded DNA circles, which would then form DNA Nanoballs (DNBs) by rolling circle replication (RCR). These DNBs were then quantified (8–40 ng/µL) and loaded onto sequencing chips, followed by sequencing on the MGISEQ-2000 sequencing platform (MGI, Shenzhen, China) [ 24 , 25 ].…”

“…For a male fetus, the fetal fraction could be calculated by the proportion of reads mapping to the Y chromosome relative to those mapping to the whole genome. The fetal fraction in pregnancies with female fetuses was estimated using the FF-QuantSC algorithm previously developed by BGI [ 25 , 28 ].…”