Quantitation of fetal DNA fraction in maternal plasma using circulating single molecule amplification and re-sequencing technology (cSMART)

Insights into non-informative results from non-invasive prenatal screening through gestational age, maternal BMI, and age analyses

The discovery of cell-free fetal DNA fragments in the maternal plasma initiated a novel testing method in prenatal care, called non-invasive prenatal screening (NIPS). One of the limitations of NIPS is the necessity for a sufficient proportion of fetal fragments in the analyzed circulating DNA mixture (fetal fraction), otherwise, the sample is uninterpretable. We present the effect of gestational age, maternal body mass index (BMI), and maternal age on the fetal fraction (FF) of the sample. We retrospectively analyzed data from 5543 pregnant women with a single male fetus who underwent NIPS from which 189 samples received a repeat testing due to an insufficient FF. We showed the relationship between the failure rate of the samples after the repeated analysis, the FF, and the gestational age at the first sampling. Next, we found that different maternal BMI categories affect the FF and thus the chance of an informative redraw. A better understanding of the factors affecting the FF will reduce the number of non-informative calls from repeated analyzes. In this study, we provide helpful information to clinicians on how to approach non-informative analyses.

Non-intuitive trends of fetal fraction development related to gestational age and fetal gender, and their practical implications for non-invasive prenatal testing

Discovery of fetal cell-free DNA fragments in maternal blood revolutionized prenatal diagnostics. Although non-invasive prenatal testing (NIPT) is already a matured screening test with high specificity and sensitivity, the accurate estimation of the proportion of fetal fragments, called fetal fraction, is crucial to avoid false-negative results. In this study, we collected 6999 samples from women undergoing NIPT testing with a single male fetus to demonstrate the influence of fetal fraction by the maternal and fetal characteristics. We show several fetal fraction discrepancies that contradict the generally presented conventional view. At first, the fetal fraction is not consistently rising with the maturity of the fetus due to a drop in 15 weeks of maturation. Secondly, the male samples have a lower fetal fraction than female fetuses, arguably due to the smaller gonosomal chromosomes. Finally, we discuss not only the possible reasons why this inconsistency exists but we also outline why these differences have not yet been identified and published. We demonstrate two non-intuitive trends to better comprehend the fetal fraction development and more precise selection of patients with sufficient fetal fraction for accurate testing.

Performance of ImproGene Cell-Free DNA Tubes for Stabilization and Analysis of cfDNA in Blood Samples

BACKGROUND

With the development of liquid biopsy technology, the demand for noninvasive prenatal testing (NIPT) is increasing rapidly. The aim of the study is to evaluate the effects of different blood collection tubes on plasma cfDNA and NIPT quality control.

METHODS

We investigated hemolysis, cfDNA concentration, and fragment distribution within blood samples stored in EDTA, ImproGene, and Streck tubes. The effects of ImproGene and Streck tubes on NIPT quality control were evaluated.

RESULTS

The ImproGene tubes prevented the time-dependent increase of cfDNA concentration and preserved the cfDNA fragment size distribution. For NIPT quality control, there is no significant difference in cfDNA, library concentration, and fetal fraction between ImproGene and Streck tubes samples. GC content of the samples in ImproGene tubes was closer to the human genome.

CONCLUSION

The ImproGene cfDNA tube has excellent performance and is an effective choice for storing blood samples for NIPT testing or other cfDNA analysis.

Noninvasive Prenatal Testing of Methylmalonic Acidemia cblC Type Using the cSMART Assay for MMACHC Gene Mutations

Noninvasive prenatal testing (NIPT) for monogenic disorders has been developed in recent years; however, there are still significant technical and analytical challenges for clinical use. The clinical feasibility of NIPT for methylmalonic acidemia cblC type (cblC type MMA) was investigated using our circulating single-molecule amplification and re-sequencing technology (cSMART). Trios molecular diagnosis was performed in 29 cblC type MMA-affected children and their parents by traditional Sanger sequencing. In the second pregnancy, invasive prenatal diagnosis (IPD) of the pathogenic MMACHC gene was used to determine fetal genotypes, and NIPT was performed using a novel MMACHC gene–specific cSMART assay. Maternal–fetal genotypes were deduced based on the mutation ratio in maternal plasma DNA. Concordance of fetal genotypes between IPD and NIPT, and the sensitivity and specificity of NIPT were determined. After removing two cases with a low P value or reads, the concordance ratio for NIPT and IPD was 100.00% (27/27), and the sensitivity and specificity were 100.00% (54.07–100.00%) and 100.00% (83.89–100.00%), respectively. This study demonstrates that NIPT using the cSMART assay for cblC type MMA was accurate in detecting fetal genotypes. cSMART has a potential clinical application as a prenatal diagnosis and screening tool for carrier and low-risk genotypes of cblC type MMA and other monogenic diseases.

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

A paradigm shift in noninvasive prenatal screening has been made with the discovery of cell-free fetal DNA in maternal plasma. Noninvasive prenatal screening is primarily used to screen for fetal aneuploidies, and has been used globally. Fetal fraction, an important parameter in the analysis of noninvasive prenatal screening results, is the proportion of fetal cell-free DNA present in the total maternal plasma cell-free DNA. It combines biological factors and bioinformatics algorithms to interpret noninvasive prenatal screening results and is an integral part of quality control. Maternal and fetal factors may influence fetal fraction. To date, there is no broad consensus on the factors that affect fetal fraction. There are many different approaches to evaluate this parameter, each with its advantages and disadvantages. Different fetal fraction calculation methods may be used in different testing platforms or laboratories. This review includes numerous publications that focused on the understanding of the significance, influencing factors, and interpretation of fetal fraction to provide a deeper understanding of this parameter.

Noninvasive prenatal diagnosis for pregnancies at risk for β-thalassaemia: a retrospective study

OBJECTIVE

To evaluate the clinical feasibility of noninvasive prenatal diagnosis (NIPD) for β-thalassaemia using circulating single molecule amplification and re-sequencing technology (cSMART).

DESIGN

Through carrier screening, 102 pregnant Chinese couples carrying pathogenic HBB gene variants were recruited to the study. Pregnancies were managed using traditional invasive prenatal diagnosis (IPD). Retrospectively, we evaluated the archived pregnancy plasma DNA by NIPD to evaluate the performance of our cSMART assay for fetal genotyping.

SETTING

Chinese prenatal diagnostic centres specialising in thalassaemia testing.

POPULATION

Chinese carrier couples at high genetic risk for β-thalassaemia.

METHODS

Fetal cell sampling was performed by amniocentesis and HBB genotypes were determined by reverse dot blot. NIPD was performed by a newly designed HBB cSMART assay and fetal genotypes were called by measuring the allelic ratios in the maternal cell-free DNA.

MAIN OUTCOME MEASURES

Concordance of HBB fetal genotyping between IPD and NIPD and the sensitivity and specificity of NIPD.

RESULTS

Invasive prenatal diagnosis identified 29 affected homozygotes or compound heterozygotes, 54 heterozygotes and 19 normal homozygotes. Compared with IPD results, 99 of 102 fetuses (97%) were correctly genotyped by our NIPD assay. Two of three discordant samples were false positives and the other sample involved an incorrect call of a heterozygote carrier as a homozygote normal. Overall, the sensitivity and specificity of our NIPD assay was 100% (95% CI 88.06-100.00%) and 97.26% (95% CI 90.45-99.67%), respectively.

CONCLUSIONS

This study demonstrates that our cSMART-based NIPD assay for β-thalassaemia has potential clinical utility as an alternative to IPD for pregnant HBB carrier couples.

TWEETABLE ABSTRACT

A new noninvasive test for pregnancies at risk for β-thalassaemia.

Fetal fraction and noninvasive prenatal testing: What clinicians need to know

The fetal fraction (FF) is a function of both biological factors and bioinformatics algorithms used to interpret DNA sequencing results. It is an essential quality control component of noninvasive prenatal testing (NIPT) results. Clinicians need to understand the biological influences on FF to be able to provide optimal post-test counseling and clinical management. There are many different technologies available for the measurement of FF. Clinicians do not need to know the details behind the bioinformatics algorithms of FF measurements, but they do need to appreciate the significant variations between the different sequencing technologies used by different laboratories. There is no universal FF threshold that is applicable across all platforms and there have not been any differences demonstrated in NIPT performance by sequencing platform or method of FF calculation. Importantly, while FF should be routinely measured, there is not yet a consensus as to whether it should be routinely reported to the clinician. The clinician should know what to expect from a standard test report and whether reasons for failed NIPT results are revealed. Emerging solutions to the challenges of samples with low FF should reduce rates of failed NIPT in the future. In the meantime, having a "plan B" prepared for those patients for whom NIPT is unsuccessful is essential in today's clinical practice.

Single-Molecule Sequencing: A New Approach for Preimplantation Testing and Noninvasive Prenatal Diagnosis Confirmation of Fetal Genotype

We investigated the potential of next-generation sequencing (NGS) as an alternative method for preimplantation genetic testing of monogenic disease (PGT-M) with human leukocyte antigen (HLA) matching and for noninvasive prenatal diagnosis follow-up. The case involved parents who were carriers of the Fanconi anemia complementation group G (FANCG) 260delG mutation. After clinical PGT using conventional short tandem repeat and mutation analysis, two euploid disease-free embryos were transferred, resulting in a twin pregnancy. Using the original embryo whole genome amplification products from 10 embryos, NGS confirmed the genotypes of the eight nontransferred embryos for both mutation status and HLA combination. NGS also confirmed that the two transferred embryos, which resulted in a twin pregnancy, were euploid, Fanconi disease free, and HLA matched to their sick sibling. At 15 weeks' gestation, noninvasive prenatal diagnosis of the maternal cell-free DNA determined fetal fractions of 14% and 6.6% for twins 1 and 2, respectively. The maternal plasma FANCG 260delG mutation ratio was measured at 46.2%, consistent with the presence of a carrier fetus and a normal fetus. These findings provide proof of concept that NGS has clinical utility as a safe and effective PGT-M method for embryo genotyping as well as more complex direct HLA matching. In addition, NGS can be used to confirm the original PGT-M and HLA matching embryo results in early pregnancy without the need for invasive prenatal diagnosis.

Development and validation of a haplotype-free technique for non-invasive prenatal diagnosis of spinal muscular atrophy

OBJECTIVE

To develop a technique for non-invasive prenatal diagnosis of spinal muscular atrophy and validate its performance.

STUDY DESIGN

Pregnant women with 1 copy of SMN1 and male fetuses were enrolled. Seventeen women were included in test set A, and 10 of them were selected into test set B randomly and blinded. The two sets were tested independently by two different researchers blinded to fetal genotypes. Fetal DNA fractions were calculated based on the relative proportion of mapped chromosome Y sequencing reads. An algorithm was developed to decide fetal SMN1 copy numbers.

RESULTS

The concordance rate with the results of MLPA testing of amniocyte DNA was 94.12% in test set A and 90% in set B. For all tests with a classifiable result, the percent of agreement with the results of MLPA testing of amniocyte DNA was up to 100% (25/25).

CONCLUSION

We have developed a direct, rapid, and low-cost technique, which has a potential to be utilized for first-trimester non-invasive prenatal diagnosis and screening for spinal muscular atrophy with considerable reliability and feasibility.

Noninvasive fetal genotyping in pregnancies at risk for PKU using a comprehensive quantitative cSMART assay for PAH gene mutations: a clinical feasibility study

OBJECTIVE

To assess the diagnostic performance of a novel circulating single molecule amplification and re-sequencing technology (cSMART) method for noninvasive prenatal testing (NIPT) of Phenylketonuria (PKU).

DESIGN

Blinded NIPT analysis of pregnancies at high risk for PKU.

SETTING

Shanghai Xinhua Hospital and Hunan Jiahui Genetics Hospital, China.

POPULATION

Couples (n = 33) with a child diagnosed with PKU.

METHODS

Trio testing for pathogenic PAH mutations was performed by Sanger sequencing. In second pregnancies, invasive prenatal diagnosis (IPD) was used to determine fetal genotypes. NIPT was performed using a PAH gene-specific cSMART assay. Based on the plasma DNA mutation ratio relative to the fetal DNA fraction, fetal genotypes were assigned using a maximum-likelihood algorithm.

MAIN OUTCOME MEASURES

Concordance of fetal genotyping results between IPD and NIPT, and the sensitivity and specificity of the NIPT assay.

RESULTS

Compared with gold standard IPD results, 32 of 33 fetuses (96.97%) were accurately genotyped by NIPT. The sensitivity and specificity of the NIPT assay was 100.00% (95% CI 59.04-100.00%) and 96.15% (95% CI 80.36-99.90%), respectively.

CONCLUSIONS

The novel cSMART assay demonstrated high accuracy for correctly calling fetal genotypes. We propose that this test has useful clinical utility for the rapid screening of high-risk and low-risk pregnancies with a known history of PKU on one or both sides of the family.

TWEETABLE ABSTRACT

NIPT of couples at high risk for PKU using a full-coverage cSMART PAH gene test.

Uncertainty of fetal fraction determination in Non-Invasive Prenatal Screening by highly polymorphic SNPs

Fetal fraction and the chromosome representation are the two key quantities used in Non-Invasive Prenatal Screening (NIPS) to determine the aneuploidy status of a fetus. Several methods for fetal fraction determination have been proposed in the literature, including a class of the methods, denoted snpFF, based on high-coverage targeted sequencing of highly polymorphic Single Nucleotide Polymorphisms (SNPs). The variant of snpFF, investigated here, has similar properties as the other variants of snpFF. We point out that the variability of the individual informative SNPs-based estimates of fetal fraction increases with the increase of fetal fraction. At 4% fetal fraction the Inter-Quartile Range (IQR) of the individual estimates of fetal fraction is around 3% and it increases to 6% at 15% fetal fraction. snpFF cannot detect fetal fraction below 2.5% because the number of informative SNPs becomes too small, even zero.

Non-invasive prenatal testing of pregnancies at risk for phenylketonuria

BACKGROUND

Phenylketonuria (PKU) is a common metabolic disorder caused predominately by mutations in the phenylalanine hydroxylase (PAH) gene. The aim of the study was to design and validate the performance of a non-invasive prenatal test (NIPT) for PKU using circulating single molecule amplification and resequencing technology (cSMART).

METHODS

A total of 18 couples at genetic risk for having a child with PKU were recruited to the study. Gold standard invasive prenatal diagnosis (IPD) was performed on amniocyte or villus cell DNA by Sanger sequencing, targeting the known parental PAH mutations. Retrospectively, NIPT was also performed on stored maternal plasma samples from the 18 pregnancies by a multiplex cSMART assay designed to target all known DNA variants in the PAH gene.

RESULTS

Benchmarking against IPD results, NIPT correctly genotyped all fetuses, including six compound heterozygotes with PKU, four normal non-carriers of PKU and eight heterozygote carriers of PKU comprising five cases of a maternally inherited mutation and three cases of a paternally inherited mutation.

CONCLUSIONS

The NIPT cSMART PKU assay was highly sensitive and specific for mutation detection and correct assignment of fetal genotypes. Based on comprehensive mutation coverage across the PAH gene, the assay may initially have clinical utility as a pregnancy screening test for high-risk carrier couples.

Fetal fraction evaluation in non-invasive prenatal screening (NIPS)

An important factor in quality control of non-invasive prenatal screening (NIPS) or testing (NIPT) is a sufficient percentage of fetal DNA to avoid false-negative results. Here we evaluate 14,379 shallow whole-genome sequenced diagnostic NIPS samples, as well as negative controls, for both technical and biological factors that can influence fetal fraction and its assessment. Technically, bioinformatics analyses can have a profound impact on fetal fraction determination. We found best performance for fetal fraction determination with the Y chromosome based tool DEFRAG for male fetuses and the count based tool SeqFF for female fetuses. Biologically, gestational age of up to 21 weeks and maternal age had no influence on fetal fraction, while an increase in weight and BMI had a negative influence on fetal fraction. While a trend was observed, no statistically significant difference in fetal fraction was found between trisomy and normal samples. Overall, these results confirm the influence of biological factors and give insight into technical factors that can affect fetal fractions in NIPS.

Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models

The recent advances in next-generation sequencing (NGS) technologies have enabled the development of effective high-throughput noninvasive prenatal screening (NIPS) assays for fetal genetic abnormalities using maternal circulating cell-free DNA (ccfDNA). An important NIPS quality assurance is quantifying the fetal proportion of the sampled ccfDNA. For methods using allelic read count ratios from targeted sequencing of single-nucleotide polymorphisms (SNPs), systematic biases and errors may reduce accuracy and diminish assay performance. We collected ccfDNA NIPS MiSeq sequencing data from an amplicon-based 92 SNP panel along with complementary low-depth whole-genome sequencing (WGS) on 243 normal male fetus pregnancies along with additional 144 nonpregnant female donor samples. Using fetal fraction estimates based on X and Y chromosome WGS coverage as gold standard, we compared an existing SNP-based approach, FetalQuant, to a more flexible Bayesian hierarchical modeling strategy that borrows information across interrogated SNPs to character SNP-level error rates and biases to improve fetal fraction estimates. Posterior distributions for SNP-level model parameters indicate most SNPs exhibited modest to moderate extrabinomial variation and a consistent underrepresentation of fetal alleles, with some extreme outliers in both regards. Fetal fraction estimates using FetalQuant, naive to these SNP properties, were relatively poor (R² = 0.14, root mean squared error [RMSE] = 0.050), particularly when the true fetal fraction was low (<5%). In contrast, by quantifying SNP-level biases and error rates, our proposed approach demonstrated improved performance by reducing the bias and variability in fetal fraction estimates (R² = 0.794, RMSE = 0.025). Using high-depth targeted SNP sequencing data, we identified a high degree of variability in distributional properties across SNP allelic read counts. These results highlight the benefits of leveraging hierarchical modeling for SNP-based fetal quantification assays (FQAs) and the need to properly calibrate FQAs dependent on NGS allelic ratio data.

A quantitative cSMART assay for noninvasive prenatal screening of autosomal recessive nonsyndromic hearing loss caused by GJB2 and SLC26A4 mutations

PurposeThe aim of this study was to assess the performance of a noninvasive prenatal screening (NIPS) assay for accurate fetal genotyping of pregnancies at genetic risk for autosomal recessive nonsyndromic hearing loss (ARNSHL).MethodsA total of 80 pregnant couples carrying known mutations in either the GJB2 or SLC26A4 genes associated with a risk for ARNSHL were recruited to the study. Fetal amniocyte samples were genotyped by invasive prenatal screening (IPS), whereas the cell-free fetal DNA present in maternal plasma samples was genotyped using a novel NIPS method based on circulating single-molecule amplification and resequencing technology (cSMART).ResultsIPS of the 80 at-risk pregnancies identified 20 normal homozygote, 42 heterozygote, 5 affected homozygote, and 13 affected compound heterozygote fetuses. Benchmarking against IPS, 73 of 80 fetuses (91.3%) were correctly genotyped by the cSMART NIPS assay. A low fetal DNA fraction (<6%) was identified as the main contributing factor in five of seven discordant NIPS results. At fetal DNA fractions >6%, the sensitivity and specificity of the cSMART assay for correctly diagnosing ARNSHL were 100 and 96.5%, respectively.ConclusionBased on key performance indicators, the cSMART NIPS assay has clinical potential as an alternative to traditional IPS of ARNSHL.