Assessment and Clinical Utility of a Non-Next-Generation Sequencing-Based Non-Invasive Prenatal Testing Technology

Background: Rolling-circle replication (RCR) is a novel technology that has not been applied to cell-free DNA (cfDNA) testing until recently. Given the cost and simplicity advantages of this technology compared to other platforms currently used in cfDNA analysis, an assessment of RCR in clinical laboratories was performed. Here, we present the first validation study from clinical laboratories utilizing RCR technology. Methods: 831 samples from spontaneously pregnant women carrying a singleton fetus, and 25 synthetic samples, were analyzed for the fetal risk of trisomy 21 (T21), trisomy 18 (T18) and trisomy 13 (T13), by three laboratories on three continents. All the screen-positive pregnancies were provided post-test genetic counseling and confirmatory diagnostic invasive testing (e.g., amniocentesis). The screen-negative pregnancies were routinely evaluated at birth for fetal aneuploidies, using newborn examinations, and any suspected aneuploidies would have been offered diagnostic testing or confirmed with karyotyping. Results: The study found rolling-circle replication to be a highly viable technology for the clinical assessment of fetal aneuploidies, with 100% sensitivity for T21 (95% CI: 82.35–100.00%); 100.00% sensitivity for T18 (71.51–100.00%); and 100.00% sensitivity for T13 analyses (66.37–100.00%). The specificities were >99% for each trisomy (99.7% (99.01–99.97%) for T21; 99.5% (98.62–99.85%) for T18; 99.7% (99.03–99.97%) for T13), along with a first-pass no-call rate of 0.93%. Conclusions: The study showed that using a rolling-circle replication-based cfDNA system for the evaluation of the common aneuploidies would provide greater accuracy and clinical utility compared to conventional biochemical screening, and it would provide comparable results to other reported cfDNA methodologies.     

Maternal serum cell-free fetal DNA levels are increased in cases of trisomy 13 but not trisomy 18

Cell-free fetal DNA in the maternal circulation is a potential noninvasive marker for fetal aneuploidies. In previous studies with Y DNA as a fetal-specific marker, levels of circulating fetal DNA were shown to be elevated in women carrying trisomy 21 fetuses. The goal of this study was to determine whether cell-free fetal DNA levels in the serum of pregnant women carrying fetuses with trisomies 13 or 18 are also elevated. Archived maternal serum samples from five cases of male trisomy 13 and five cases of male trisomy 18 were studied. Each case was matched for fetal gender, gestational age, and duration of freezer storage to four or five control serum samples presumed to be euploid after newborn medical record review. Real-time quantitative polymerase chain reaction amplification of DYS1 was performed to measure the amount of male fetal DNA present. Unadjusted median serum fetal DNA concentrations were 97.5 GE/ml (genomic equivalents per milliliter; 29.2-187.0) for the trisomy 13 cases, 31.5 GE/ml (18.6-77.6) for the trisomy 18 cases, and 40.3 GE/ml (3.7-127.4) for the controls. Fetal DNA levels in trisomy 13 cases were significantly elevated ( P=0.016) by analysis of variance of the ranks of values within each matched set. In contrast, fetal DNA levels in trisomy 18 cases were no different from the controls ( P=0.244). Second trimester maternal serum analytes currently used in screening do not identify fetuses at high risk for trisomy 13. Fetal DNA may facilitate noninvasive screening for trisomy 13 provided that a gender-independent fetal DNA marker can be developed.     

Prenatal screening for trisomy 18 with free beta human chorionic gonadotrophin as a marker.

OBJECTIVE--To determine the relation between maternal serum alpha fetoprotein and free beta human chorionic gonadotrophin concentrations in pregnancies complicated by trisomy 18 and establish whether prenatal biochemical screening for this condition could be developed in a way similar to that proposed for trisomy 21. DESIGN--Serum alpha fetoprotein and free beta human chorionic gonadotrophin concentrations in women with singleton pregnancies affected by cytogenetically confirmed trisomy 18, uncomplicated by neural tube defect or ventral wall defect, were identified from prospective trisomy 21 screening programmes. Additionally, stored maternal serum from similar pregnancies was analysed retrospectively. Analyte concentrations from singleton unaffected pregnancies were identified from a prospective screening programme as controls. Statistical parameters of the affected and unaffected populations were compiled. SETTING--Biochemical screening laboratories in Britain and the United States. SUBJECTS--52 women with singleton pregnancies complicated by trisomy 18; control population of 6661 women with unaffected singleton pregnancies. MAIN OUTCOME MEASURES--Median values of each analyte and their distribution in the affected and unaffected populations; detection rate of trisomy 18 and the false positive rate. RESULTS--Maternal serum alpha fetoprotein and free beta human chorionic gonadotrophin concentrations were significantly lower in pregnancies complicated by trisomy 18 (median values 0.71 and 0.37 respectively). By using a multivariate risk algorithm incorporating maternal age risk of trisomy 18 and the concentration of the two biochemical markers it was predicted that 50% of trisomy 18 cases (unaffected by neural tube defect or ventral wall defect) could be detected with a 1% false positive rate. CONCLUSION--Second trimester biochemical screening for trisomy 18 could be a valuable addition to trisomy 21 screening programmes.     

False Negative NIPT Results: Risk Figures for Chromosomes 13, 18 and 21 Based on Chorionic Villi Results in 5967 Cases and Literature Review

Non-invasive prenatal testing (NIPT) demonstrated a small chance for a false negative result. Since the “fetal” DNA in maternal blood originates from the cytotrophoblast of chorionic villi (CV), some false negative results will have a biological origin. Based on our experience with cytogenetic studies of CV, we tried to estimate this risk. 5967 CV samples of pregnancies at high risk for common aneuplodies were cytogenetically investigated in our centre between January 2000 and December 2011. All cases of fetal trisomy 13, 18 and 21 were retrospectively studied for the presence of a normal karyotype or mosaicism < 30% in short-term cultured (STC-) villi. 404 cases of trisomies 13, 18 and 21 were found amongst 5967 samples (6,8%). Of these 404 cases, 14 (3,7%) had a normal or low mosaic karyotype in STC-villi and therefore would potentially be missed with NIPT. It involved 2% (5/242) of all trisomy 21 cases and 7.3% (9/123) of all trisomy 18 cases. In 1:426 (14/5967) NIPT samples of patients at high risk for common aneuploidies, a trisomy 18 or 21 will potentially be missed due to the biological phenomenon of absence of the chromosome aberration in the cytotrophoblast.     

A maternal serum screen for trisomy 18: an extension of maternal serum screening for Down syndrome.

The feasibility of extending second-trimester maternal blood screening for Down syndrome so as to include screening for trisomy 18 was examined using stored maternal serum samples collected for neural tube-defect screening. There were 12 samples from trisomy 18 pregnancies and 390 controls. The median maternal serum concentration of alpha-fetoprotein, free alpha-subunit human chorionic gonadotrophin, free beta-subunit human chorionic gonadotrophin, intact human chorionic gonadotrophin, total estriol, unconjugated estriol, estradiol, human placental lactogen, and progesterone were lowered in those pregnancies affected by trisomy 18 when compared with unaffected pregnancies matched for racial origin, maternal age, gestational age, and sample-storage duration. At an estimated odds risk of 1:400, 83.3% of affected pregnancies were detected using an algorithm which combines the maternal age-related risk with the maternal serum concentrations of unconjugated estriol, free alpha-subunit human chorionic gonadotrophin, free beta-subunit human chorionic gonadotrophin, estradiol, and human placental lactogen. The associated false-positive rate was 2.6%. At high risk odds of 1:10, the detection rate was 58.3%, with an associated false-positive rate of 0.3%. beta-Subunit human chorionic gonadotrophin and unconjugated estriol were the most powerful discriminators. It is possible to incorporate into existing Down syndrome screening programs an algorithm for detecting trisomy 18 with high sensitivity and specificity.     

Ultrasonographic soft markers of aneuploidy in second trimester: are we lost?

Chromosomal abnormalities occur in 0.1% to 0.2% of live births, and the most common clinically significant aneuploidy among live-born infants is Down syndrome (trisomy 21). Other sonographically detectable aneuploidies include trisomy 13, 18, monosomy X, and triploidy. Second-trimester ultrasound scan detects 2 types of sonographic markers suggestive of aneuploidy. Markers for major fetal structural abnormalities comprise the first type; the second type of markers are known as "soft markers" of aneuploidy. These latter markers are nonspecific, often transient, and can be readily detected during the second-trimester ultrasound. The most commonly studied soft markers of aneuploidy include a thickened nuchal fold, rhizomelic limb shortening, mild fetal pyelectasis, echogenic bowel, and echogenic intracardiac focus and choroid plexus cyst. There is a great deal of interest in the ultrasound detection of aneuploidy, as evidenced by the large number of publications in the literature on this topic. Unfortunately, studies evaluating the significance of the soft markers of aneuploidy vary widely and show contradictory results. In this article, we review the most common ultrasonographic soft markers used to screen aneuploidy and discuss ultrasonographic technique and measurement criteria for the detection of soft markers. We also review the clinical relevance of soft markers to aneuploidy risk assessment and evidence-based strategies for the management of affected pregnancies with each of these markers in light of current literature.     

The Feasibility Study of Non-Invasive Fetal Trisomy 18 and 21 Detection with Semiconductor Sequencing Platform

Objective

Recent non-invasive prenatal testing (NIPT) technologies are based on next-generation sequencing (NGS). NGS allows rapid and effective clinical diagnoses to be determined with two common sequencing systems: Illumina and Ion Torrent platforms. The majority of NIPT technology is associated with Illumina platform. We investigated whether fetal trisomy 18 and 21 were sensitively and specifically detectable by semiconductor sequencer: Ion Proton.

Methods

From March 2012 to October 2013, we enrolled 155 pregnant women with fetuses who were diagnosed as high risk of fetal defects at Xiamen Maternal & Child Health Care Hospital (Xiamen, Fujian, China). Adapter-ligated DNA libraries were analyzed by the Ion Proton™ System (Life Technologies, Grand Island, NY, USA) with an average 0.3× sequencing coverage per nucleotide. Average total raw reads per sample was 6.5 million and mean rate of uniquely mapped reads was 59.0%. The results of this study were derived from BWA mapping. Z-score was used for fetal trisomy 18 and 21 detection.

Results

Interactive dot diagrams showed the minimal z-score values to discriminate negative versus positive cases of fetal trisomy 18 and 21. For fetal trisomy 18, the minimal z-score value of 2.459 showed 100% positive predictive and negative predictive values. The minimal z-score of 2.566 was used to classify negative versus positive cases of fetal trisomy 21.

Conclusion

These results provide the evidence that fetal trisomy 18 and 21 detection can be performed with semiconductor sequencer. Our data also suggest that a prospective study should be performed with a larger cohort of clinically diverse obstetrics patients.     

Contribution of ultrasonographic examination to the prenatal detection of trisomy 21: experience from 19 European registers

The objective of this study was to evaluate the contribution of ultrasound scanning to the prenatal detection of trisomy 21 in a large unselected European population. Data from 19 congenital malformation registers in 11 European countries were included. The prenatal ultrasound screening programs in the countries ranged from no routine screening to three ultrasound investigations per patient. Routine serum screening was offered in four of the 11 countries and routine screening on the basis of maternal age amniocentesis in all. The results show that overall 53% of cases of trisomy 21 were detected prenatally with a range from 3% in Lithuania to 88% in Paris. Ninety-eight percent of women whose babies were diagnosed before 24 weeks gestation chose to terminate the pregnancy. Centres/countries that offer serum screening do not have a significantly higher detection rate of trisomy 21 when compared to those that offer maternal age amniocentesis and anomaly scanning only. Fifty percent of trisomy 21 cases were born to women aged 35 years or more. In conclusions, second trimester ultrasound plays an important role in the prenatal diagnosis of trisomy 21. Of those cases prenatally diagnosed, 64% of cases in women <35 years and 36% of those in women >or=35 years were detected because of an ultrasound finding. Ultrasound soft markers accounted for 84% of the scan diagnoses. There is evidence of increasing maternal age across Europe with 50% of cases of trisomy 21 born to women aged 35 years or more.     

孕中期超声联合无创产前基因筛查在检出染色体异常胎儿中的应用价值

摘要 目的：孕中期超声联合无创产前基因筛查（NIPT）在染色体异常胎儿检出中的应用价值。方法：选取2019年8月～2021年12月在石家庄市妇幼保健院产前检查的2000例孕中期孕妇,均接受超声检查和NIPT筛查。以羊水穿刺或引产后高通量测序结果为金标准,四格表法分析孕中期超声联合NIPT在染色体异常胎儿检出中的应用价值。结果：2000例孕中期孕妇中,超声检查共检出软指标异常37例,结构指标异常30例。NIPT筛查检出高风险孕妇17例,其中21-三体综合征11例、18-三体综合征6例。超声软指标和结构指标联合NIPT诊断胎儿染色体异常的灵敏度、特异度、阳性预测值、阴性预测值、漏诊率、误诊率、准确率分别为95.00%、99.95%、95.00%、99.95%、5.00%、0.05%、99.90%。结论：联合孕中期超声和NIPT可提高检出高风险染色体异常胎儿的灵敏度,降低漏诊率,对于早发现染色体异常胎儿具有重要价值,进而提高生育质量。     

Screening for aneuploidy in twin pregnancies: maternal age- and race-specific risk assessment between 9-14 weeks.

The aim of this study was to calculate the risk for aneuploidy in twin pregnancies between 9-14 weeks utilizing maternal age, race and dizygotic twinning rates. Using previously published risks for aneuploidy in singletons and twins at the time of amniocentesis and at term, we calculated new risk estimates for twins at 9-14 weeks gestation or at the time of chorionic villus sampling. Using these tables, the risk for trisomy 21 in at least one fetus of a twin gestation in a 32-year-old at 9-14 weeks is 1/285 for Whites and for African-Americans. This is equivalent to the risk for trisomy 21 (1/265) in a 35-year-old woman with a singleton at the same gestational age. The risks for trisomies 18 and 13 also follow similar trends. In counseling women with twin pregnancies at the time of first trimester nuchal translucency screening or chorionic villus sampling, it should be noted that the maternal age-related risk for aneuploidy for a 32-year-old is equivalent to that of a 35-year-old woman with a singleton gestation.     

Fetal nuchal translucency thickness

In the early 1990s Nicolaides introduced screening for trisomy 21 by fetal nuchal translucency thickness measurement with ultrasound between 11-13(+6) weeks. Already in 1866 L. Down noted that common features of patients with trisomy 21 are a skin being too large for the body and a flat face with a small nose. While detection rates for trisomy 21, given an invasive testing rate of 5%, were only 30% for screening by maternal age and 65% for screening by maternal serum triple test, the detection rate for screening by nuchal translucency combined with maternal age was 75% and this could be increased to 90% in combination with maternal serum screening (serum B-human chorionic gonadotropin and pregnancy-associated plasma protein-A) at 11-13(+6) weeks. The additional soft markers in the first trimester are the fetal nasal bone, the Doppler velocity waveform in the ductus venosus and tricuspid regurgitation and these markers can be used to further increase the detection rate of trisomy 21. In addition increased nuchal translucency thickness can also identify other chromosomal defects (mainly trisomy 13 and 18 and monosomy X) and major congenital malformations (mainly cardiac defects) and genetic syndromes.     

Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing

Massively parallel sequencing of DNA molecules in the plasma of pregnant women has been shown to allow accurate and noninvasive prenatal detection of fetal trisomy 21. However, whether the sequencing approach is as accurate for the noninvasive prenatal diagnosis of trisomy 13 and 18 is unclear due to the lack of data from a large sample set. We studied 392 pregnancies, among which 25 involved a trisomy 13 fetus and 37 involved a trisomy 18 fetus, by massively parallel sequencing. By using our previously reported standard z-score approach, we demonstrated that this approach could identify 36.0% and 73.0% of trisomy 13 and 18 at specificities of 92.4% and 97.2%, respectively. We aimed to improve the detection of trisomy 13 and 18 by using a non-repeat-masked reference human genome instead of a repeat-masked one to increase the number of aligned sequence reads for each sample. We then applied a bioinformatics approach to correct GC content bias in the sequencing data. With these measures, we detected all (25 out of 25) trisomy 13 fetuses at a specificity of 98.9% (261 out of 264 non-trisomy 13 cases), and 91.9% (34 out of 37) of the trisomy 18 fetuses at 98.0% specificity (247 out of 252 non-trisomy 18 cases). These data indicate that with appropriate bioinformatics analysis, noninvasive prenatal diagnosis of trisomy 13 and trisomy 18 by maternal plasma DNA sequencing is achievable.     

Evidence of compliance with and effectiveness of guidelines for noninvasive prenatal testing in China: a retrospective study of 189,809 cases

In China,the medical guidelines recommend performing noninvasive prenatal testing (NIPT) with caution for pregnant women aged 35 years or older.However,the Mother and Child Health Care Law suggests that all primiparous women whose age is older than 35 years undergo prenatal diagnosis.These two inconsistent suggestions/recommendations have made obstetricians confused about whether to offer NIPT to these older pregnant women.To face this issue and find out the solution we performed a retrospective study of 189,809 NIPT samples collected from 28 provincial-leveled administrative units in China.Of 1,564women with high-risk pregnancies who underwent NIPT,459 (29.3%) did not participate in follow-up.The compound sensitivity and specificity of NIPT for trisomies 21,18 and 13 detection was 99.1%(95%CI,98.0%-99.6%) and 99.9%(95%CI,98.8%-99.9%),respectively.In secundiparous women,NIPT showed high sensitivity and specificity similar to that in primiparous women.The observed risk for trisomies 21 and 18 significantly increased when the maternal age was 39 and older.After the publication of the current NIPT policy,the follow-up rate at our center was 97.9%;however,a large number of women are not in maternal and infant care networks nationwide,and that makes the follow-up rate outside our center relatively low.Our study shows that to balance the prevention of major aneuploidies and the limited resources for prenatal diagnosis,the cut-off age of 35for invasive prenatal diagnosis might be unnecessary.Although the NIPT guidelines are well written,how to practice it effectively,especially in less industrialized areas,is worth discussing.     

Trisomies 13 and 18: prenatal diagnosis and epidemiologic studies in Hawaii, 1986-1997

Using a birth defects registry, this study examined the influence of prenatal diagnosis and elective termination of pregnancy on trisomy 13 and trisomy 18 prevalence in Hawaii between 1986 and 1997. The investigation also evaluated the impact of various demographic factors on risk for the aneuploidies. Forty-seven cases of trisomy 13 and 116 cases of trisomy 18 were identified. The total prevalence of trisomy 13 was 1.91 per 10,000 births and of trisomy 18 was 4.71 per 10,000 births. Elective terminations accounted for 38.3% of trisomy 13 cases and 48.3% of trisomy 13 cases. The 1-year mortality rate for trisomy 13 was 89.5% and for trisomy 18 was 74.3%. Rates for both aneuploidies increased during the time period. The racial/ethnic group with the highest prevalence of both anomalies was Far East Asian. The aneuploidies were more common in metropolitan Honolulu than the rest of Hawaii. Demographic factors demonstrated differences in risk for trisomies 13 and 18, although most of these differences appeared to be due, at least in part, to differences in maternal age distribution. For the secular trend, increased prenatal diagnosis of the anomalies also contributed to the observed increase.     

胎儿稽留流产与染色体异常的关系及其影响因素分析

目的：探讨B超联合FISH实验室诊断技术分析胎儿稽留流产与染色体非整倍体关系并对其他影响因素进行综合分析。方法：采用FISH技术对广西267例B超诊断为稽留流产孕妇的胎儿绒毛组织行13,16,18,21,22,X,Y染色体数目检测,荧光显微镜下观察结果;采用SPSS13．0对相关数据进行统计分析。结果：267例稽留流产胎儿绒毛组织中,染色体数目异常95例,异常率35．6％,数目异常以三体最常见,其次为四体,少见部分单体;异常病例样本中存在多种染色体混合嵌合体现象,如混合嵌合三体（2n＋1／2n）,混合嵌合四体（2n＋2／2n）,混合嵌合单倍体、三体、四体（2n-1／2n＋l／2n＋2／2n）等;稽留流产与患者年龄、流产史、孕周具有显著相关性。结论：染色体数目异常与染色体混合嵌合均是稽留流产的重要原因,同时稽留流产发生与患者高龄、多次流产史、早期妊娠密切关系。     

Lessons from 1950

Second-trimester maternal serum screening is a noninvasive means of identifying pregnant women at an increased risk for various conditions including a fetus with open spina bifida, fetal Down syndrome, trisomy 18, multiple gestation, and adverse pregnancy outcome. Combinations of several different markers are available for screening. These include alpha-fetoprotein, human chorionic gonadotropin, and unconjugated estriol. In this review, we discuss the benefits and limitations of the screening tests and the suggested protocols for the care of patients.     

The combined QF-PCR and cytogenetic approach in prenatal diagnosis

In this study, the importance of quantitative fluorescence polymerase chain reaction (QF-PCR) aneuploidy diagnosis test which provides earlier and easier results were discussed. The cell cultures and DNA isolations were performed on 100 amniotic fluids. DNA isolations were made from peripheral blood samples of mothers who had blood-stained amniotic fluid samples. The reasons of references of these pregnant women to our division were increased maternal age, positive double/triple screening test and fetal anomaly history. QF-PCR applied to 19 short tandem repeat markers in the chromosomes 13, 18, 21 and genes X and Y chromosomes. All electropherogram peaks were evaluated on ABI3130. Thirty two (32 %) samples have high maternal age, seven (7 %) have fetal anomaly and the others have double/triple screening test positivity. Ninety-nine (99 %) of the 100 amniotic fluid samples were resulted, but one (1 %) of them could not examined because of the culture failure. The maternal contamination rates were determined as 3 %. Of 100 samples, 2 had trisomy 21 (2 %), 1 had trisomy 13 (1 %), 1 had structural abnormalities (1 %) and the others (97 %) have not any aneuploidy. The results of QF-PCR were in compatible with the results of cell culture and chromosome analysis. Although QF-PCR is an easier and an earlier test, it has a limitation of not to able to scan full genome. It is also sensitive for maternal contamination, so it should be tested together with maternal blood samples. QF-PCR aneuploidy test is the fastest diagnostic test for prenatal diagnosis and so it provides less stressful period for pregnant women.     

Non-Invasive Prenatal Testing of Trisomy 18 by an Epigenetic Marker in First Trimester Maternal Plasma

Background

Quantification of cell-free fetal DNA by methylation-based DNA discrimination has been used in non-invasive prenatal testing of fetal chromosomal aneuploidy. The maspin (Serpin peptidase inhibitor, clade B (ovalbumin), member 5; SERPINB5) gene, located on chromosome 18q21.33, is hypomethylated in the placenta and completely methylated in maternal blood cells. The objective of this study was to evaluate the accuracy of non-invasive detection of fetal trisomy 18 using the unmethylated-maspin (U-maspin) gene as a cell-free fetal DNA marker and the methylated-maspin (M-maspin) gene as a cell-free total DNA marker in the first trimester of pregnancy.

Methodology/Principal Findings

A nested case-control study was conducted using maternal plasma collected from 66 pregnant women, 11 carrying fetuses with trisomy 18 and 55 carrying normal fetuses. Median U-maspin concentrations were significantly elevated in women with trisomy 18 fetuses compared with controls (27.2 vs. 6.7 copies/mL; P<0.001). Median M-maspin concentrations were also significantly higher in women with trisomy 18 fetuses than in controls (96.9 vs. 19.5 copies/mL, P<0.001). The specificities of U-maspin and M-maspin concentrations for non-invasive fetal trisomy 18 detection were 96.4% and 74.5%, respectively, with a sensitivity of 90.9%.

Conclusions

Our results suggest that U-maspin and M-maspin concentrations may be useful as potential biomarkers for non-invasive detection of fetal trisomy 18 in the first trimester of pregnancy, irrespective of the sex and genetic variations of the fetus.     

Plasma placental RNA allelic ratio permits noninvasive prenatal chromosomal aneuploidy detection

Current methods for prenatal diagnosis of chromosomal aneuploidies involve the invasive sampling of fetal materials using procedures such as amniocentesis or chorionic villus sampling and constitute a finite risk to the fetus. Here, we outline a strategy for fetal chromosome dosage assessment that can be performed noninvasively through analysis of placental expressed mRNA in maternal plasma. We achieved noninvasive prenatal diagnosis of fetal trisomy 21 by determining the ratio between alleles of a single-nucleotide polymorphism (SNP) in PLAC4 mRNA, which is transcribed from chromosome 21 and expressed by the placenta, in maternal plasma. PLAC4 mRNA in maternal plasma was fetal derived and cleared after delivery. The allelic ratios in maternal plasma correlated with those in the placenta. Fetal trisomy 21 was detected noninvasively in 90% of cases and excluded in 96.5% of controls.     

A Method to Quantify Cell-Free Fetal DNA Fraction in Maternal Plasma Using Next Generation Sequencing: Its Application in Non-Invasive Prenatal Chromosomal Aneuploidy Detection

Objective

The fraction of circulating cell-free fetal (cff) DNA in maternal plasma is a critical parameter for aneuploidy screening with non-invasive prenatal testing, especially for those samples located in equivocal zones. We developed an approach to quantify cff DNA fractions directly with sequencing data, and increased cff DNAs by optimizing library construction procedure.

Methods

Artificial DNA mixture samples (360), with known cff DNA fractions, were used to develop a method to determine cff DNA fraction through calculating the proportion of Y chromosomal unique reads, with sequencing data generated by Ion Proton. To validate our method, we investigated cff DNA fractions of 2,063 pregnant women with fetuses who were diagnosed as high risk of fetal defects. The z-score was calculated to determine aneuploidies for chromosomes 21, 18 and 13. The relationships between z-score and parameters of pregnancies were also analyzed. To improve cff DNA fractions in our samples, two groups were established as follows: in group A, the large-size DNA fragments were removed, and in group B these were retained, during library construction.

Results

A method to determine cff DNA fractions was successfully developed using 360 artificial mixture samples in which cff DNA fractions were known. A strong positive correlation was found between z-score and fetal DNA fraction in the artificial mixture samples of trisomy 21, 18 and 13, as well as in clinical maternal plasma samples. There was a positive correlation between gestational age and the cff DNA fraction in the clinical samples, but no correlation for maternal age. Moreover, increased fetal DNA fractions were found in group A compared to group B.

Conclusion

A relatively accurate method was developed to determine the cff DNA fraction in maternal plasma. By optimizing, we can improve cff DNA fractions in sequencing samples, which may contribute to improvements in detection rate and reliability.