High-throughput Fetal Fraction Amplification Increases Analytical Performance of Noninvasive Prenatal Screening

Overview

Journal Genet Med

Publisher Elsevier

Specialty Genetics

Date 2020 Nov 15

PMID 33190143

Citations 14

Authors

Noah C Welker

Albert K Lee

Rachel A S Kjolby

Helen Y Wan

Mark R Theilmann

Diana Jeon

James D Goldberg

Kevin R Haas

Dale Muzzey

Clement S Chu

Affiliations

Soon will be listed here.

Abstract

Purpose: The percentage of a maternal cell-free DNA (cfDNA) sample that is fetal-derived (the fetal fraction; FF) is a key driver of the sensitivity and specificity of noninvasive prenatal screening (NIPS). On certain NIPS platforms, >20% of women with high body mass index (and >5% overall) receive a test failure due to low FF (<4%).

Methods: A scalable fetal fraction amplification (FFA) technology was analytically validated on 1264 samples undergoing whole-genome sequencing (WGS)-based NIPS. All samples were tested with and without FFA.

Results: Zero samples had FF < 4% when screened with FFA, whereas 1 in 25 of these same patients had FF < 4% without FFA. The average increase in FF was 3.9-fold for samples with low FF (2.3-fold overall) and 99.8% had higher FF with FFA. For all abnormalities screened on NIPS, z-scores increased 2.2-fold on average in positive samples and remained unchanged in negative samples, powering an increase in NIPS sensitivity and specificity.

Conclusion: FFA transforms low-FF samples into high-FF samples. By combining FFA with WGS-based NIPS, a single round of NIPS can provide nearly all women with confident results about the broad range of potential fetal chromosomal abnormalities across the genome.

Citing Articles

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The performance evaluation of NIPT for fetal chromosome microdeletion/microduplication detection: a retrospective analysis of 68,588 Chinese cases.

Shen S, Qi H, Yuan X, Gan J, Chen J, Huang J Front Genet. 2024; 15:1390539.

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Application of non-invasive prenatal testing to 91,280 spontaneous pregnancies and 3477 pregnancies conceived by in vitro fertilization.

Wei R, Li J, Xia Y, Wang C, Lu X, Fang Y Mol Cytogenet. 2023; 16(1):25.

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White blood cell count affects fetal fraction and test failure rates in noninvasive prenatal screening.

Qiao L, Cao X, Tang H, Yu Z, Shi J, Xue Y Front Med (Lausanne). 2023; 10:1088745.

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Lower fetal fraction in clinical cell-free DNA screening results is associated with increased risk of hypertensive disorders of pregnancy.

Madala D, Maktabi M, Sabbagh R, Erfani H, Moon A, Van den Veyver I Prenat Diagn. 2022; 42(10):1253-1261.

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References

Chiu R, Chan K, Gao Y, Lau V, Zheng W, Leung T . Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci U S A. 2008; 105(51):20458-63. PMC: 2600580. DOI: 10.1073/pnas.0810641105. View

Fan H, Blumenfeld Y, Chitkara U, Hudgins L, Quake S . Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci U S A. 2008; 105(42):16266-71. PMC: 2562413. DOI: 10.1073/pnas.0808319105. View

Chiu R, Akolekar R, Zheng Y, Leung T, Sun H, Chan K . Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ. 2011; 342:c7401. PMC: 3019239. DOI: 10.1136/bmj.c7401. View

Palomaki G, Kloza E, Lambert-Messerlian G, Haddow J, Neveux L, Ehrich M . DNA sequencing of maternal plasma to detect Down syndrome: an international clinical validation study. Genet Med. 2011; 13(11):913-20. DOI: 10.1097/GIM.0b013e3182368a0e. View

Srinivasan A, Bianchi D, Huang H, Sehnert A, Rava R . Noninvasive detection of fetal subchromosome abnormalities via deep sequencing of maternal plasma. Am J Hum Genet. 2013; 92(2):167-76. PMC: 3567270. DOI: 10.1016/j.ajhg.2012.12.006. View

Hui L, Bianchi D . Fetal fraction and noninvasive prenatal testing: What clinicians need to know. Prenat Diagn. 2019; 40(2):155-163. PMC: 10040212. DOI: 10.1002/pd.5620. View

Wang E, Batey A, Struble C, Musci T, Song K, Oliphant A . Gestational age and maternal weight effects on fetal cell-free DNA in maternal plasma. Prenat Diagn. 2013; 33(7):662-6. DOI: 10.1002/pd.4119. View

Artieri C, Haverty C, Evans E, Goldberg J, Haque I, Yaron Y . Noninvasive prenatal screening at low fetal fraction: comparing whole-genome sequencing and single-nucleotide polymorphism methods. Prenat Diagn. 2017; 37(5):482-490. DOI: 10.1002/pd.5036. View

Hancock S, Ben-Shachar R, Adusei C, Oyolu C, Evans E, Kang H . Clinical experience across the fetal-fraction spectrum of a non-invasive prenatal screening approach with low test-failure rate. Ultrasound Obstet Gynecol. 2019; 56(3):422-430. PMC: 7496885. DOI: 10.1002/uog.21904. View

10.

Advani H, Barrett A, Evans M, Choolani M . Challenges in non-invasive prenatal screening for sub-chromosomal copy number variations using cell-free DNA. Prenat Diagn. 2017; 37(11):1067-1075. DOI: 10.1002/pd.5161. View

11.

Pertile M, Halks-Miller M, Flowers N, Barbacioru C, Kinnings S, Vavrek D . Rare autosomal trisomies, revealed by maternal plasma DNA sequencing, suggest increased risk of feto-placental disease. Sci Transl Med. 2017; 9(405). PMC: 10040211. DOI: 10.1126/scitranslmed.aan1240. View

12.

Chen Y, Yu Q, Mao X, Lei W, He M, Lu W . Noninvasive prenatal testing for chromosome aneuploidies and subchromosomal microdeletions/microduplications in a cohort of 42,910 single pregnancies with different clinical features. Hum Genomics. 2019; 13(1):60. PMC: 6884830. DOI: 10.1186/s40246-019-0250-2. View

13.

Liang D, Cram D, Tan H, Linpeng S, Liu Y, Sun H . Clinical utility of noninvasive prenatal screening for expanded chromosome disease syndromes. Genet Med. 2019; 21(9):1998-2006. DOI: 10.1038/s41436-019-0467-4. View

14.

Grati F, Gross S . Noninvasive screening by cell-free DNA for 22q11.2 deletion: Benefits, limitations, and challenges. Prenat Diagn. 2019; 39(2):70-80. DOI: 10.1002/pd.5391. View

15.

Mainardi P . Cri du Chat syndrome. Orphanet J Rare Dis. 2006; 1:33. PMC: 1574300. DOI: 10.1186/1750-1172-1-33. View

16.

Yu D, Zhang K, Han M, Pan W, Chen Y, Wang Y . Noninvasive prenatal testing for fetal subchromosomal copy number variations and chromosomal aneuploidy by low-pass whole-genome sequencing. Mol Genet Genomic Med. 2019; 7(6):e674. PMC: 6565572. DOI: 10.1002/mgg3.674. View

17.

Ravi H, McNeill G, Goel S, Meltzer S, Hunkapiller N, Ryan A . Validation of a SNP-based non-invasive prenatal test to detect the fetal 22q11.2 deletion in maternal plasma samples. PLoS One. 2018; 13(2):e0193476. PMC: 5825123. DOI: 10.1371/journal.pone.0193476. View

18.

Hui L . Cell-free DNA testing for 22q11.2 deletion syndrome: appraising the viability, effectiveness and appropriateness of screening. Ultrasound Obstet Gynecol. 2016; 47(2):137-41. DOI: 10.1002/uog.15845. View

19.

Schmid M, Wang E, Bogard P, Bevilacqua E, Hacker C, Wang S . Prenatal Screening for 22q11.2 Deletion Using a Targeted Microarray-Based Cell-Free DNA Test. Fetal Diagn Ther. 2017; 44(4):299-304. PMC: 6390460. DOI: 10.1159/000484317. View

20.

Van Opstal D, van Maarle M, Lichtenbelt K, Weiss M, Schuring-Blom H, Bhola S . Origin and clinical relevance of chromosomal aberrations other than the common trisomies detected by genome-wide NIPS: results of the TRIDENT study. Genet Med. 2017; 20(5):480-485. PMC: 5929118. DOI: 10.1038/gim.2017.132. View