226: Cell-free DNA fetal fraction and pregnancy outcome

Background: Follicular fluid considered as an important microenvironment for oocyte development, cell free-DNA (cfDNA) fragments that are found in this fluid and are released from cell apoptosis and/or necrosis, aimed to quantified the level of cf-DNA, in the follicular fluid and to assess any relation between the level of cf-DNA in this fluid with women’s age, duration of infertility, cause of infertility, her ovarian reserve values. Methods: Eighty-nine women were prospectively included in this study FF cf-DNA which was determined by conventional real time PCR-syber green detection approach which quantified by ALU-specific primers. Results: cell-free DNA (cfDNA) level in Follicular fluid samples of Iraqi women level was; cfDNA (Mean±SD, 0.916±0.106 ng/μl). there was no significant relation between cfDNA and pregnancy outcome, but very low level and very high level cf DNA were related to negative pregnancy outcome, cfDNA was second most important predictive factor of pregnancy outcome after fertilization rate, but both not statistically significant p value was (0.622 and 0.241) respectively. Conclusion: current study notice that cfDNA in the follicular fluid may mainly reflect the cellular activity and the balance between programed apoptosis and cell necrosis.

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An online tool for fetal fraction prediction based on direct size distribution analysis of maternal cell-free DNA

BioTechniques ◽

10.2144/btn-2020-0143 ◽

2020 ◽

Author(s):

Luca Bedon ◽

Josef Vuch ◽

Simeone Dal Monego ◽

Germana Meroni ◽

Vanna Pecile ◽

...

Keyword(s):

Size Distribution ◽

Prenatal Testing ◽

Distribution Analysis ◽

Blood Draw ◽

Noninvasive Prenatal Testing ◽

Cell Free Dna ◽

Maternal Cell ◽

Fetal Dna ◽

Free Dna ◽

Fetal Fraction

The discovery of circulating fetal DNA in the plasma of pregnant women has greatly promoted advances in noninvasive prenatal testing. Screening performance is enhanced with higher fetal fraction and analysis of samples whose fetal DNA fraction is lower than 4% are unreliable. Although current approaches to fetal fraction measurement are accurate, most of them are expensive and time consuming. Here we present a simple and cost-effective solution that provides a quick and reasonably accurate fetal fraction by directly evaluating the size distribution of circulating DNA fragments in the extracted maternal cell-free DNA. The presented approach could be useful in the presequencing stage of noninvasive prenatal testing to evaluate whether the sample is suitable for the test or a repeat blood draw is recommended.

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Impact of long‐term storage of plasma and cell‐free DNA on measured DNA quantity and fetal fraction

Vox Sanguinis ◽

10.1111/vox.12923 ◽

2020 ◽

Vol 115 (7) ◽

pp. 586-594 ◽

Cited By ~ 1

Author(s):

Frederik Banch Clausen ◽

Angela N. Barrett ◽

Henna V. Advani ◽

Mahesh Choolani ◽

Morten Hanefeld Dziegiel

Keyword(s):

Cell Free Dna ◽

Long Term Storage ◽

Free Dna ◽

Term Storage ◽

Fetal Fraction

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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

Clinical Chemistry ◽

10.1373/clinchem.2015.252502 ◽

2016 ◽

Vol 62 (6) ◽

pp. 848-855 ◽

Cited By ~ 29

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.

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Factors affecting cell-free DNA fetal fraction and the consequences for test accuracy

The Journal of Maternal-Fetal & Neonatal Medicine ◽

10.1080/14767058.2017.1330881 ◽

2017 ◽

Vol 31 (14) ◽

pp. 1865-1872 ◽

Cited By ~ 16

Author(s):

Fergus Perry Scott ◽

Melody Menezes ◽

Ricardo Palma-Dias ◽

Debbie Nisbet ◽

Philip Schluter ◽

...

Keyword(s):

Test Accuracy ◽

Cell Free Dna ◽

Factors Affecting ◽

Free Dna ◽

Fetal Fraction

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Cell-Free DNA (cfDNA) Fetal Fraction in Early- and Late-Onset Fetal Growth Restriction

Molecular Diagnosis & Therapy ◽

10.1007/s40291-018-0353-9 ◽

2018 ◽

Vol 22 (5) ◽

pp. 613-619 ◽

Cited By ~ 4

Author(s):

Danila Morano ◽

Stefania Rossi ◽

Cristina Lapucci ◽

Maria Carla Pittalis ◽

Antonio Farina

Keyword(s):

Fetal Growth ◽

Fetal Growth Restriction ◽

Late Onset ◽

Growth Restriction ◽

Cell Free Dna ◽

Free Dna ◽

Fetal Fraction

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Noninvasive Fetal Genotyping by Droplet Digital PCR to Identify Maternally Inherited Monogenic Diabetes Variants

Clinical Chemistry ◽

10.1093/clinchem/hvaa104 ◽

2020 ◽

Vol 66 (7) ◽

pp. 958-965 ◽

Cited By ~ 1

Author(s):

Richard C Caswell ◽

Tristan Snowsill ◽

Jayne A L Houghton ◽

Ali J Chakera ◽

Maggie H Shepherd ◽

...

Keyword(s):

At Risk ◽

Digital Pcr ◽

Monogenic Diabetes ◽

Droplet Digital Pcr ◽

High Birth Weight ◽

Cell Free Dna ◽

Pathogenic Variants ◽

Free Dna ◽

Increased Risk ◽

Fetal Fraction

Abstract Background Babies of women with heterozygous pathogenic glucokinase (GCK) variants causing mild fasting hyperglycemia are at risk of macrosomia if they do not inherit the variant. Conversely, babies who inherit a pathogenic hepatocyte nuclear factor 4α (HNF4A) diabetes variant are at increased risk of high birth weight. Noninvasive fetal genotyping for maternal pathogenic variants would inform pregnancy management. Methods Droplet digital PCR was used to quantify reference and variant alleles in cell-free DNA extracted from blood from 38 pregnant women heterozygous for a GCK or HNF4A variant and to determine fetal fraction by measurement of informative maternal and paternal variants. Droplet numbers positive for the reference/alternate allele together with the fetal fraction were used in a Bayesian analysis to derive probability for the fetal genotype. The babies’ genotypes were ascertained postnatally by Sanger sequencing. Results Droplet digital PCR assays for GCK or HNF4A variants were validated for testing in all 38 pregnancies. Fetal fraction of ≥2% was demonstrated in at least 1 cell-free DNA sample from 33 pregnancies. A threshold of ≥0.95 for calling homozygous reference genotypes and ≤0.05 for heterozygous fetal genotypes allowed correct genotype calls for all 33 pregnancies with no false-positive results. In 30 of 33 pregnancies, a result was obtained from a single blood sample. Conclusions This assay can be used to identify pregnancies at risk of macrosomia due to maternal monogenic diabetes variants.

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