PREFACE: In silico pipeline for accurate cell-free fetal DNA fraction prediction.
Cell-Free Nucleic Acids
/ analysis
Chromosome Disorders
/ diagnosis
Cohort Studies
Computational Biology
/ methods
Computer Simulation
Female
Fetus
/ metabolism
Genetic Testing
/ methods
High-Throughput Nucleotide Sequencing
/ methods
Humans
Infant, Newborn
Male
Noninvasive Prenatal Testing
/ methods
Pregnancy
Principal Component Analysis
/ methods
Prognosis
Reproducibility of Results
Retrospective Studies
Sequence Analysis, DNA
/ methods
Sex Factors
Software
Journal
Prenatal diagnosis
ISSN: 1097-0223
Titre abrégé: Prenat Diagn
Pays: England
ID NLM: 8106540
Informations de publication
Date de publication:
09 2019
09 2019
Historique:
received:
11
02
2019
revised:
16
05
2019
accepted:
15
06
2019
pubmed:
21
6
2019
medline:
2
7
2020
entrez:
21
6
2019
Statut:
ppublish
Résumé
During routine noninvasive prenatal testing (NIPT), cell-free fetal DNA fraction is ideally derived from shallow-depth whole-genome sequencing data, preventing the need for additional experimental assays. The fraction of aligned reads to chromosome Y enables proper quantification for male fetuses, unlike for females, where advanced predictive procedures are required. This study introduces PREdict FetAl ComponEnt (PREFACE), a novel bioinformatics pipeline to establish fetal fraction in a gender-independent manner. PREFACE combines the strengths of principal component analysis and neural networks to model copy number profiles. For sets of roughly 1100 male NIPT samples, a cross-validated Pearson correlation of 0.9 between predictions and fetal fractions according to Y chromosomal read counts was noted. PREFACE enables training with both male and unlabeled female fetuses. Using our complete cohort (n Allowing individual institutions to generate optimized models sidelines between-laboratory bias, as PREFACE enables user-friendly training with a limited amount of retrospective data. In addition, our software provides the fetal fraction based on the copy number state of chromosome X. We show that these measures can predict mixed multiple pregnancies, sex chromosomal aneuploidies, and the source of observed aberrations.
Identifiants
pubmed: 31219182
doi: 10.1002/pd.5508
pmc: PMC6771918
doi:
Substances chimiques
Cell-Free Nucleic Acids
0
Types de publication
Journal Article
Validation Study
Langues
eng
Sous-ensembles de citation
IM
Pagination
925-933Informations de copyright
© 2019 The Authors. Prenatal Diagnosis Published by John Wiley & Sons Ltd.
Références
Prenat Diagn. 2018 Oct;38(11):841-848
pubmed: 30068017
J Stat Softw. 2010;33(1):1-22
pubmed: 20808728
Prenat Diagn. 2019 Sep;39(10):925-933
pubmed: 31219182
Nat Commun. 2017 Nov 6;8(1):1324
pubmed: 29109393
Nucleic Acids Res. 2019 Feb 28;47(4):1605-1614
pubmed: 30566647
Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8583-8
pubmed: 24843150
Clin Chem. 2010 Oct;56(10):1627-35
pubmed: 20729299
Prenat Diagn. 2015 Aug;35(8):810-5
pubmed: 25967380
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Sci Rep. 2016 Dec 05;6:38359
pubmed: 27917919
Orphanet J Rare Dis. 2010 May 29;5:15
pubmed: 20509956
Fetal Diagn Ther. 2018;44(2):85-90
pubmed: 28873375
Eur J Hum Genet. 2010 Mar;18(3):265-71
pubmed: 19568271
Biostatistics. 2014 Jul;15(3):427-41
pubmed: 24478395
Proc Natl Acad Sci U S A. 2007 Aug 7;104(32):13116-21
pubmed: 17664418
Sci Transl Med. 2010 Dec 8;2(61):61ra91
pubmed: 21148127
Prenat Diagn. 2016 Jul;36(7):614-21
pubmed: 26996738
Clin Chem. 2011 Jan;57(1):92-101
pubmed: 21078840
Prenat Diagn. 2017 Dec;37(12):1265
pubmed: 29271029
PLoS One. 2016 Jul 14;11(7):e0159233
pubmed: 27415003
Orphanet J Rare Dis. 2006 Oct 24;1:42
pubmed: 17062147
Nucleic Acids Res. 2012 May;40(10):e72
pubmed: 22323520
PLoS One. 2014 Dec 12;9(12):e113800
pubmed: 25503062
Prenat Diagn. 2016 Apr;36(4):304-11
pubmed: 26815144
Prenat Diagn. 2016 Aug;36(8):699-707
pubmed: 27176606
Clin Chem. 2006 Dec;52(12):2211-8
pubmed: 17068167
Prenat Diagn. 2018 Mar;38(4):258-266
pubmed: 29388226
Curr Genomics. 2007 Apr;8(2):129-36
pubmed: 18660847
Eur J Hum Genet. 2015 Oct;23(10):1286-93
pubmed: 25585704
Bioinformatics. 2012 Nov 15;28(22):2883-90
pubmed: 22962347
NPJ Genom Med. 2016 May 11;1:16013
pubmed: 29263813
Genet Med. 2011 Nov;13(11):913-20
pubmed: 22005709
Genet Med. 2012 Mar;14(3):296-305
pubmed: 22281937
Prenat Diagn. 2010 Dec;30(12-13):1226-9
pubmed: 21072784
J Int Med Res. 2017 Apr;45(2):621-630
pubmed: 28357876
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Ultrasound Obstet Gynecol. 2015 May;45(5):530-8
pubmed: 25598039
Nucleic Acids Res. 2014 Mar;42(5):e31
pubmed: 24170809
Prenat Diagn. 2017 Aug;37(8):769-773
pubmed: 28561435
Eur J Obstet Gynecol Reprod Biol. 2018 Jul;226:35-39
pubmed: 29804026