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

Hestand, Matthew S.; Bessem, Mark; Rijn, Peter van; Menezes, Renée X. de; Sie, Daoud; Bakker, Ingrid; Boon, Elles M. J.; Sistermans, Erik A.; Weiss, Marjan M.

doi:10.1038/s41431-018-0271-7

Cited by 45 publications

(54 citation statements)

References 21 publications

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“…However, the methods used to measure FF vary considerably and are not directly comparable, leading to calls for industry standardization in methods and reporting . While Y chromosome‐based methods appear to be the closest to an accepted “gold standard" in this field, these are obviously limited by their applicability to only those pregnancies with a male fetus. Some advocate using a combination of methods to check for the presence of fetal cfDNA and FF calculation for female and male bearing pregnancies .…”

Section: Clinical Laboratory Aspects Of Ffmentioning

confidence: 99%

“…They have been previously thoroughly reviewed by Peng and colleagues . Several attempts to compare different FF algorithms have been published that highlight the significant variation between methods . It is now apparent that individual clinical laboratories should optimize their platform‐specific FF methods according to their lower LOD, and not rely on arbitrary FF cutoff values for quality control.…”

Section: Clinical Laboratory Aspects Of Ffmentioning

confidence: 99%

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

2019

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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

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Section: Clinical Laboratory Aspects Of Ffmentioning

confidence: 99%

Section: Clinical Laboratory Aspects Of Ffmentioning

confidence: 99%

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

2019

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“…The responses are summarized in Table 4 below. Two respondents indicated that they would offer termination of pregnancy for a very high risk [1,7] on FTS.…”

Section: Recommendations At Various Fts Risk Levelsmentioning

confidence: 99%

“…For instance, a foetal fraction of at least 4% is essential for a reportable result. A low foetal fraction is more likely in certain populations such as obese women and those with certain aneuploidies [6][7][8], and these facts need to be incorporated into pre and post-test counselling.…”

Section: Introductionmentioning

confidence: 99%

Prenatal screening in the era of non-invasive prenatal testing: a Nationwide cross-sectional survey of obstetrician knowledge, attitudes and clinical practice

Yang

Tan

2020

BMC Pregnancy Childbirth

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Background Non-invasive prenatal testing (NIPT) has revolutionized the prenatal screening landscape with its high accuracy and low false positive rate for detecting Trisomy 21, 18 and 13. Good understanding of its benefits and limitations is crucial for obstetricians to provide effective counselling and make informed decisions about its use. This study aimed to evaluate obstetrician knowledge and attitudes regarding NIPT for screening for the common trisomies, explore how obstetricians integrated NIPT into first-line and contingent screening, and determine whether expanded use of NIPT to screen for sex chromosome aneuploidies (SCAs) and microdeletion/microduplication syndromes (CNVs) was widespread. Methods A questionnaire was designed and administered with reference to the CHERRIES criteria for online surveys. Doctors on the Obstetrics & Gynaecology trainee and specialist registers were invited to participate. Medians and 95% confidence intervals (CI) were reported for confidence and knowledge scores. Results 94/306 (30.7%) doctors responded to the survey. First trimester screening (FTS) remained the main method offered to screen for the common trisomies. 45.7% (43/94) offered NIPT as an alternative first-line screen for singletons and 30.9% (29/94) for monochorionic diamniotic twins. A significant proportion offered concurrent NT and NIPT (25/94, 26.6%), or FTS and NIPT (33/94, 35.1%) in singletons. Varying follow up strategies were offered at intermediate, high and very-high FTS risk cut-offs for Trisomy 21. Respondents were likely to offer screening for SCAs and CNVs to give patients autonomy of choice (53/94, 56.4% SCAs, 47/94, 50% CNVs) at no additional cost (52/94, 55.3% SCAs, 39/94, 41.5% CNVs). Median clinical knowledge scores were high (10/12) and did not differ significantly between specialists (95% CI 10–11) and non-specialists (95% CI 9.89–11). Lower scores were observed for scenarios in which NIPT would be more likely to fail. Conclusions Our findings show the diversity of clinical practice with regard to the incorporation of NIPT into prenatal screening algorithms, and suggest that the use of NIPT both as a first-line screening tool in the general obstetric population, and to screen for SCAs and CNVs, is becoming increasingly prevalent. Clear guidance and continuing educational support are essential for providers in this rapidly evolving field.

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“…While z scores are used for evacuating risk of aneuploidy of chromosome 13, 18 and 21, fetal fraction (FF) of cell free DNA is also considered critical to the results [7,8]. FF is based on the sequencing results of NIPS and is calculated using chrY concentration or algorithms of generalized linear regression such as seqFF [9]. It is conformed that FF lower than 3.5%-4% is a key factor may cause no-call reports or false positive and negative results [10,11].…”

Section: Introductionmentioning

confidence: 99%

A comprehensive predictive method for low fetal fraction in noninvasive prenatal screening

Hu¹,

Pei²,

Luo³

et al. 2020

Preprint

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BackgroundThe study was a retrospective cohort analysis based on the results of noninvasive prenatal screening (NIPS), complete blood count, thyroxin test and Down's syndrome screening in first or second trimester from 14043 pregnant women. Random forests algorithm was applied to predict the low fetal fraction of cell free DNA (with FF lower than 10th percentile) through individual and laboratory information. Performance of the model was evaluated and compared to prediction using maternal weight.To investigate factors associated with lower FF in the NIPS and to develop a new predictive method for low FF before NIPS. ResultsOf 14043 cases, maternal weight, RBC, HGB and free T3 were significantly negative correlated with FF while gestation age, free T4, PAPP-A, AFP, uE3 and β-hCG were significantly positive correlated with FF. Compared to prediction using maternal weight as isolated parameter, the model has a higher area under curve(AUC) of Receiver Operating Characteristic (ROC) and overall accuracy. ConclusionsThe comprehensive predictive method based on combined multiple factors was more effective than single-factor model in low FF status prediction. This method can provide more information for clinical choice and pre-test quality control of NIPS.

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

Cited by 45 publications

References 21 publications

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

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

Prenatal screening in the era of non-invasive prenatal testing: a Nationwide cross-sectional survey of obstetrician knowledge, attitudes and clinical practice

A comprehensive predictive method for low fetal fraction in noninvasive prenatal screening

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