FetalQuantSD: accurate quantification of fetal DNA fraction by shallow-depth sequencing of maternal plasma DNA

Jiang, Peiyong; Peng, Xianlu L.; Su, Xiaoxi; Sun, Kun; Yu, Stephanie C Y; Chu, Weng In; Leung, Tak Yeung; Sun, Hao; Chiu, Rossa W.̉K.; Lo, Y.M. Dennis; Chan, K C Allen

doi:10.1038/npjgenmed.2016.13

Cited by 33 publications

(31 citation statements)

References 36 publications

(51 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Methods including SANEFALCON [ 27 ], which makes use of nucleosome profiling to assess fetal fraction, and SEQFF [ 24 ], which uses a high dimensional regression model of existing NIPT sequencing data, can be used to assess fetal fraction in pregnancies with a fetus of either sex. FetalQuant SD has been recently developed for fetal fraction quantification, based on shallow-depth WGS, using SNPs absent from the maternal genome at regions where the mother is homozygous for the alternative allele [ 41 ] However, all of these methods are based on whole genome sequencing; we wanted to develop a relatively inexpensive targeted amplicon-based approach which could be used in conjunction with our RMD assays for single-gene disorders, such as β-thalassaemia. Whole genome sequencing to assess the fetal fraction in these instances would be prohibitively expensive, whereas we can multiplex our targeted indel panel onto a run with the single-gene disorder samples with little impact on the number of reads that we obtain for the β-thalassaemia targets.…”

Section: Discussionmentioning

confidence: 99%

Measurement of fetal fraction in cell-free DNA from maternal plasma using a panel of insertion/deletion polymorphisms

et al. 2017

View full text Add to dashboard Cite

ObjectiveCell-free DNA from maternal plasma can be used for non-invasive prenatal testing for aneuploidies and single gene disorders, and also has applications as a biomarker for monitoring high-risk pregnancies, such as those at risk of pre-eclampsia. On average, the fractional cell-free fetal DNA concentration in plasma is approximately 15%, but can vary from less than 4% to greater than 30%. Although quantification of cell-free fetal DNA is straightforward in the case of a male fetus, there is no universal fetal marker; in a female fetus measurement is more challenging. We have developed a panel of multiplexed insertion/deletion polymorphisms that can measure fetal fraction in all pregnancies in a simple, targeted sequencing reaction.MethodsA multiplex panel of primers was designed for 35 indels plus a ZFX/ZFY amplicon. cfDNA was extracted from plasma from 157 pregnant women, and maternal genomic DNA was extracted for 20 of these samples for panel validation. Sixty-one samples from pregnancies with a male fetus were subjected to whole genome sequencing on the Ion Proton sequencing platform, and fetal fraction derived from Y chromosome counts was compared to fetal fraction measured using the indel panel. A total of 157 cell-free DNA samples were sequenced using the indel panel, and informativity was assessed, along with the proportion of fetal DNA.ResultsUsing gDNA we optimised the indel panel, removing amplicons giving rise to PCR bias. Good correlation was found between fetal fraction using indels and using whole genome sequencing of the Y chromosome (Spearmans r = 0.69). A median of 12 indels were informative per sample. The indel panel was informative in 157/157 cases (mean fetal fraction 14.4% (±0.58%)).ConclusionsUsing our targeted next generation sequencing panel we can readily assess the fetal DNA percentage in male and female pregnancies.

show abstract

Section: Discussionmentioning

confidence: 99%

Measurement of fetal fraction in cell-free DNA from maternal plasma using a panel of insertion/deletion polymorphisms

et al. 2017

View full text Add to dashboard Cite

show abstract

“…10,11 A recent method only genotyped the mother. 12 It first identified maternal homozygous loci, tallied and computed nonmaternal allele fractions at these loci from low-coverage sequencing data of maternal plasma, and used these to train a linear model to predict FF. High-depth targeted sequencing of maternal plasma was successfully used to determine FF.…”

Section: Introductionmentioning

confidence: 99%

Inferring fetal fractions from read heterozygosity empowers the noninvasive prenatal screening

Dang

Zhang³

et al. 2020

Genetics in Medicine

View full text Add to dashboard Cite

Purpose: Fetal fraction (FF) is the percent of cell-free DNA (cfDNA) in the mother's peripheral blood that is of fetal origin, which plays a pivotal role in noninvasive prenatal screening (NIPS). We present a method that can reliably estimate FFs by examining autosome single-nucleotide polymorphisms (SNPs).Methods: Even at a very low sequencing depth, there are plenty of SNPs covered by more than one read. At those SNPs, we define read heterozygosity and demonstrate that the percent of read heterozygosity is a function of FF, which allows FF to be inferred. Results:We first demonstrated the effectiveness of our method in inferring FF. Then we used the inferred FF as an informative alternative prior to computing Bayes factors to test for aneuploidy, and observed better power than the Z-test. In analysis of clinical samples, we were able to identify female-male twins thanks to the accurate FF inference.Conclusion: Knowing FF improves efficacy of NIPS. It brings a powerful Bayesian method, allows "no call" for samples with small FFs, renders screening for XXY syndrome simpler, and permits an adaptive design to sequence at a higher depth for samples with small FFs.Genetics in Medicine (2020) 22:301-308; https://doi.

show abstract

“…In the existing approaches used to determine the fetal fraction, the Y chromosomal sequence‐based approach calculated from the proportion of Y chromosome is simple and accurate, but only for male fetuses . Single‐nucleotide polymorphism (SNP)–based approach depends on the analysis of fetal‐specific alleles inherited from the father being direct, but it requires at least the prior maternal genotype information to identify the informative SNP loci . The methylation‐based method depends on the fetal‐specific epigenetic changes and is generally less accurate, requiring a separate processing step involving methylation‐sensitive restriction enzymes digestion.…”

Section: Introductionmentioning

confidence: 99%

Validation of fetal DNA fraction estimation and its application in noninvasive prenatal testing for aneuploidy detection in multiple pregnancies

Chen

Jiang

Guo³

et al. 2019

Prenatal Diagnosis

View full text Add to dashboard Cite

Objective To analyze the fetal fraction, fetal sex, and chromosomal aneuploidy in multiple pregnancies using noninvasive prenatal testing (NIPT). Method A total of 362 pregnant women including 203 singleton pregnancies, 69 twins, and 90 higher‐order multiple pregnancies were recruited. Fetal fractions estimated by size ratio‐based and Y chromosome‐based approaches in singleton pregnancies with male fetus were used as source data to establish the model. The model was then applied to multiple pregnancies for fetal fraction estimation. By comparing the fetal fractions estimated by size ratio to those estimated by Y chromosome or autosomal chromosomes, fetal sex and chromosomal aneuploidy can be analyzed. Results The size ratio‐based approach has been well established in estimating fetal fractions for twin and higher‐order multiple pregnancies. Fetal fraction had a positive correlation with gestational age in twin and triplet pregnancies. Fetal sex was determined with accuracies of 98.6% (95% CI, 92.19%‐99.96%) in twins and 97.6% (95% CI, 91.76%‐99.71%) in triplet pregnancies. Four trisomy 21, one trisomy 18, and one trisomy 13 cases were detected by NIPT. Two trisomy 21 singleton pregnancies and one trisomy 21 twin pregnancy were confirmed by karyotyping. Conclusion Fetal sex and chromosomal aneuploidy in multiple pregnancies can be determined using NIPT.

show abstract

FetalQuantSD: accurate quantification of fetal DNA fraction by shallow-depth sequencing of maternal plasma DNA

Cited by 33 publications

References 36 publications

Measurement of fetal fraction in cell-free DNA from maternal plasma using a panel of insertion/deletion polymorphisms

Measurement of fetal fraction in cell-free DNA from maternal plasma using a panel of insertion/deletion polymorphisms

Inferring fetal fractions from read heterozygosity empowers the noninvasive prenatal screening

Validation of fetal DNA fraction estimation and its application in noninvasive prenatal testing for aneuploidy detection in multiple pregnancies

Contact Info

Product

Resources

About