Inferring fetal fractions from read heterozygosity empowers the noninvasive prenatal screening

Abstract

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.

Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review

“…Many studies have improved existing FF calculation methods. These improvements include enrichment of cffDNA, optimization of sequencing conditions, improvement of bioinformatics algorithms, and maximization of differences in maternal and fetal DNA fragment sizes (117,(124)(125)(126)(127)(128) NIPS to screen for and exclude shorter circulating cell-free DNA fragments from the total circulating cell-free DNA and then evaluated FF through Y-chromosome reads, which increased FF by 99-359% (128). After optimization, FF in a twin NIPS false-negative sample was increased by 23.1%.…”

Noninvasive prenatal diagnosis based on cell‐free DNA for tuberous sclerosis: A pilot study

“…In addition, gene amplification may produce allele dropout on account of highly fragmented cfDNA. Furthermore, we deduced fetal genotypes depended on SNP and SNP-based FF in this study, however, maternal inbreeding coefficient and sequencing error would affect the accuracy of inferring SNP and FF (Dang et al, 2019). To resolve this problem, we also detected wbcDNA besides cfDNA so that can improve the precision of FF estimation by inferring maternal inbreeding coefficient and combining reads from maternal wbcDNA and cfDNA.…”

Estimation of cell-free fetal DNA fraction from maternal plasma based on linkage disequilibrium information

“…Thirdly, in the prediction of monogenic disease, the FF is also a key parameter 5,6 to determine the statistical thresholds to ensure the statistical significance. Lastly, when FF is accurately known, a more powerful test to screen for fetal trisomy can be developed 28,33 and the fetal sex determination in twin pregnancies 34,35 also becomes a much simpler problem. The ability of measuring FF with high accuracy would make LDFF serve as a valuable tool to improve NIPT performance.…”

“…Another method calculates the distribution of reads starting around nucleosome positions based on the different DNA digestion between fetal and maternal cfDNA 26 , but its accuracy is relatively poor 27 . The third one makes use of the heterozygosity of single nucleotide polymorphisms (SNPs), however its accuracy might be limited for samples with sequencing depth <0.5x 28 .…”