scholarly journals Circulating Fetal Cell-Free DNA Fractions Differ in Autosomal Aneuploidies and Monosomy X

2014 ◽  
Vol 60 (1) ◽  
pp. 243-250 ◽  
Author(s):  
Richard P Rava ◽  
Anupama Srinivasan ◽  
Amy J Sehnert ◽  
Diana W Bianchi
Keyword(s):  
Massively Parallel Sequencing ◽  
Prenatal Testing ◽  
Maternal Blood ◽  
Maternal Plasma ◽  
Maternal Body Mass Index ◽  
Cell Free Dna ◽  
Monosomy X ◽  
Free Dna ◽  
Human Genome Assembly ◽  
Diagnostic Sensitivity And Specificity

Abstract BACKGROUND Noninvasive prenatal testing based on massively parallel sequencing (MPS) of cell-free DNA in maternal plasma has become rapidly integrated into clinical practice for detecting fetal chromosomal aneuploidy. We directly determined the fetal fraction (FF) from results obtained with MPS tag counting and examined the relationships of FF to such biological parameters as fetal karyotype and maternal demographics. METHODS FF was determined from samples previously collected for the MELISSA (Maternal Blood Is Source to Accurately Diagnose Fetal Aneuploidy) study. Samples were resequenced, analyzed blindly, and aligned to the human genome (assembly hg19). FF was calculated in pregnancies with male or aneuploid fetuses by means of an equation that incorporated the ratio of the tags in these samples to those of a euploid training set. RESULTS The mean (SD) FF from euploid male pregnancies was 0.126 (0.052) (n = 160). Weak but statistically significant correlations were found between FF and the maternal body mass index (r2 = 0.18; P = 2.3 × 10−8) and between FF and gestational age (r2 = 0.02; P = 0.047). No relationship with maternal ethnicity or age was observed. Mean FF values for trisomies 21 (n = 90), 18 (n = 38), and 13 (n = 16) and for monosomy X (n = 20) were 0.135 (0.051), 0.089 (0.039), 0.090 (0.062), and 0.106 (0.045), respectively. CONCLUSIONS MPS tag-count data can be used to determine FF directly and accurately. Compared with male euploid fetuses, the FF is higher in maternal plasma when the fetus has trisomy 21 and is lower when the fetus has trisomy 18, 13, or monosomy X. The different biologies of these aneuploidies have practical implications for the determination of cutoff values, which in turn will affect the diagnostic sensitivity and specificity of the test.

scholarly journals Cell-Free DNA Analysis of Targeted Genomic Regions in Maternal Plasma for Non-Invasive Prenatal Testing of Trisomy 21, Trisomy 18, Trisomy 13, and Fetal Sex

2016 ◽  
Vol 62 (6) ◽  
pp. 848-855 ◽  
Author(s):  
George Koumbaris ◽  
Elena Kypri ◽  
Kyriakos Tsangaras ◽  
Achilleas Achilleos ◽  
Petros Mina ◽  
...  
Keyword(s):  
Trisomy 21 ◽  
Dna Analysis ◽  
Prenatal Testing ◽  
Cost Effective ◽  
Maternal Plasma ◽  
Trisomy 13 ◽  
Cell Free Dna ◽  
Free Dna ◽  
Genomic Regions ◽  
Fetal Fraction

Abstract BACKGROUND There is great need for the development of highly accurate cost effective technologies that could facilitate the widespread adoption of noninvasive prenatal testing (NIPT). METHODS We developed an assay based on the targeted analysis of cell-free DNA for the detection of fetal aneuploidies of chromosomes 21, 18, and 13. This method enabled the capture and analysis of selected genomic regions of interest. An advanced fetal fraction estimation and aneuploidy determination algorithm was also developed. This assay allowed for accurate counting and assessment of chromosomal regions of interest. The analytical performance of the assay was evaluated in a blind study of 631 samples derived from pregnancies of at least 10 weeks of gestation that had also undergone invasive testing. RESULTS Our blind study exhibited 100% diagnostic sensitivity and specificity and correctly classified 52/52 (95% CI, 93.2%–100%) cases of trisomy 21, 16/16 (95% CI, 79.4%–100%) cases of trisomy 18, 5/5 (95% CI, 47.8%–100%) cases of trisomy 13, and 538/538 (95% CI, 99.3%–100%) normal cases. The test also correctly identified fetal sex in all cases (95% CI, 99.4%–100%). One sample failed prespecified assay quality control criteria, and 19 samples were nonreportable because of low fetal fraction. CONCLUSIONS The extent to which free fetal DNA testing can be applied as a universal screening tool for trisomy 21, 18, and 13 depends mainly on assay accuracy and cost. Cell-free DNA analysis of targeted genomic regions in maternal plasma enables accurate and cost-effective noninvasive fetal aneuploidy detection, which is critical for widespread adoption of NIPT.

scholarly journals The fragmentation patterns of maternal plasma cell‐free DNA and its applications in non‐invasive prenatal testing

2020 ◽  
Vol 40 (8) ◽  
pp. 911-917 ◽  
Author(s):  
Min Pan ◽  
Pingsheng Chen ◽  
Jiafeng Lu ◽  
Zhiyu Liu ◽  
Erteng Jia ◽  
...  
Keyword(s):  
Plasma Cell ◽  
Prenatal Testing ◽  
Maternal Plasma ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Fragmentation Patterns

Non-invasive prenatal testing for fetal aneuploidy by massively parallel DNA sequencing of maternal plasma: the future has arrived today/Nicht-invasiver Pränatal-Test auf fetale Aneuploidie mittels massiv-paralleler DNA-Sequenzanalyse im mütterlichen Plasma: in der Zukunft angekommen

2012 ◽  
Vol 36 (5) ◽  
Author(s):  
Amy Swanson ◽  
Christin Coffeen ◽  
Amy J. Sehnert
Keyword(s):  
Massively Parallel Sequencing ◽  
Prenatal Testing ◽  
The United States ◽  
Maternal Blood ◽  
Maternal Plasma ◽  
Massively Parallel ◽  
Clinical Implementation ◽  
Maternal Cell ◽  
Non Invasive ◽  
Fetal Aneuploidy

AbstractAfter decades of research, non-invasive prenatal testing (NIPT) using maternal blood to determine fetal chromosome status has found its way from the research laboratory into clinical practice, triggering a long-awaited paradigm shift in prenatal care. A variety of methods using sequencing of maternal cell-free DNA (cfDNA) have now been studied, primarily demonstrating their ability to detect the most common fetal aneuploidy, trisomy 21 (T21). The focus of this article is on massively parallel sequencing (MPS) with optimized sequence tag mapping and chromosome quantification, which accurately detects T21 as well as multiple other aneuploidies across the genome. The power of this technique resides in its high precision and reduction of variation within and between sequencing runs. Using MPS, classification of aneuploidy status for a given sample can be reliably assigned from the genetic information alone without the need to factor in other maternal pre-test risk or other clinical variables. Performance of this method has been prospectively demonstrated in a rigorous, blinded, multi-center study in the United States. The findings suggest that MPS can be incorporated into existing prenatal screening algorithms to reduce unnecessary invasive procedures. This technology and key considerations for clinical implementation are discussed.

Non-invasive prenatal testing for whole chromosome abnormalities/Nicht invasives pränatales Testen auf Chromosomenstörungen

2012 ◽  
Vol 36 (5) ◽  
Author(s):  
Zachary Demko ◽  
Bernhard Zimmermann ◽  
Matthew Rabinowitz
Keyword(s):  
Prenatal Testing ◽  
Maternal Plasma ◽  
Chromosome Abnormalities ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna

AbstractAfter decades of anticipation, non-invasive prenatal testing for aneuploidy is now a reality. Three published methods, described herein, are able to test for certain whole-chromosome abnormalities in the fetus by sequencing and analyzing cell-free DNA in maternal plasma, a fraction of which is fetal.

scholarly journals Performance of cell-free DNA sequencing-based non-invasive prenatal testing: experience on 36,456 singleton and multiple pregnancies

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Marco La Verde ◽  
Luigia De Falco ◽  
Annalaura Torella ◽  
Giovanni Savarese ◽  
Pasquale Savarese ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Retrospective Analysis ◽  
False Negative ◽  
Screening Method ◽  
Prenatal Testing ◽  
Maternal Blood ◽  
Cell Free Dna ◽  
Detection Rates ◽  
Non Invasive ◽  
Free Dna

Abstract Background This paper describes the clinical practice and performance of cell-free DNA sequencing-based non-invasive prenatal testing (NIPT) as a screening method for fetal trisomy 21, 18, and 13 (T21, T18, and T13) and sex chromosome aneuploidies (SCA) in a general Italian pregnancy population. Methods The AMES-accredited laboratory offers NIPT in maternal blood as a screening test for fetal T21, T18, T13 and SCA. Samples were sequenced on a NextSeq 550 (Illumina) using the VeriSeq NIPT Solution v1 assay. Results A retrospective analysis was performed on 36,456 consecutive maternal blood samples, including 35,650 singleton pregnancies, 800 twin pregnancies, and 6 triplet pregnancies. Samples were tested between April 2017 and September 2019. The cohort included 46% elevated-risk and 54% low-risk patients. A result indicative of a classic trisomy was found in 356 (1%) of singleton or twin samples: 254 T21, 69 T18, and 33 T13. In addition, 145 results (0.4%) were indicative of a SCA. Of the combined 501 screen-positive cases, 484 had confirmatory diagnostic testing. NIPT results were confirmed in 99.2% (247/249) of T21 cases, 91.2% (62/68) of T18 cases, 84.4% (27/32) of T13 cases, and 86.7% (117/135) of SCA cases. In the 35,955 cases reported as unaffected by a classic trisomy or SCA, no false negative cases were reported. Assuming that false negative results would be reported, the sensitivity of NIPT was 100.00% for T21 (95% Cl 98.47–100.0), T18 (95% Cl 94.17–100.0), and T13 (95% Cl 87.54–100.0). The specificities were 99.99% (95% Cl 99.98–100.0), 99.98% (95% Cl 99.96–100.0), 99.99% (95% Cl 99.97–100.0), and 99.95% (95% Cl 99.92–99.97) for T21, T18, T13, and SCA, respectively. Conclusion This retrospective analysis of a large cohort of consecutive patients who had whole-genome sequencing-based NIPT for classic trisomies and SCA shows excellent detection rates and low false positive rates.

scholarly journals Cancer Diagnoses Following Abnormal Noninvasive Prenatal Testing: A Case Series, Literature Review, and Proposed Management Model

2021 ◽  
pp. 1001-1012
Author(s):  
Eryn Dow ◽  
Alison Freimund ◽  
Kortnye Smith ◽  
Rodney J. Hicks ◽  
Peter Jurcevic ◽  
...  
Keyword(s):  
Case Series ◽  
Prenatal Testing ◽  
High Sensitivity ◽  
Maternal Blood ◽  
Noninvasive Prenatal Testing ◽  
Cell Free Dna ◽  
Single Center Experience ◽  
Cancer Breast ◽  
Free Dna ◽  
Positron Emission

Noninvasive prenatal testing (NIPT) is a screening test for fetal chromosomal aneuploidy using cell-free DNA derived from maternal blood. It has been rapidly accepted into obstetric practice because of its application from 10-weeks' gestation, and its high sensitivity and specificity. NIPT results can be influenced by several factors including placental or maternal mosaicism and co-twin demise; cell-free DNA from a maternal origin can also complicate interpretation, with evidence that NIPT can detect previously unsuspected malignancies. This study aimed to develop management guidelines for women with NIPT results suspicious of maternal malignancy. The Peter MacCallum Cancer Center's experience of seven cases where abnormal NIPT results led to investigation for maternal malignancy between 2016 and 2019 were reviewed, along with the published literature. Six of the seven women (86%) referred for investigation were diagnosed with advanced malignancies, including colorectal cancer, breast cancer, melanoma, and Hodgkin lymphoma. Based on our single-center experience, as well as the available literature, guidelines for the investigation of women with NIPT results suspicious of malignancy are proposed, including utilization of fluorodeoxyglucose positron emission tomography-computed tomography, which had a high concordance with other investigations and diagnoses. These guidelines include maternal and fetal investigations, as well as consideration of the complex medical, psychologic, social, and ethical needs of these patients and their families.

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