An Advanced Model to Precisely Estimate the Cell-Free Fetal DNA Concentration in Maternal Plasma.
BACKGROUND
With the speedy development of sequencing technologies, noninvasive prenatal testing (NIPT) has been widely applied in clinical practice for testing for fetal aneuploidy. The cell-free fetal DNA (cffDNA) concentration in maternal plasma is the most critical parameter for this technology because it affects the accuracy of NIPT-based sequencing for fetal trisomies 21, 18 and 13. Several approaches have been developed to calculate the cffDNA fraction of the total cell-free DNA in the maternal plasma. However, most approaches depend on specific single nucleotide polymorphism (SNP) allele information or are restricted to male fetuses.


METHODS
In this study, we present an innovative method to accurately deduce the concentration of the cffDNA fraction using only maternal plasma DNA. SNPs were classified into four maternal-fetal genotype combinations and three boundaries were added to capture effective SNP loci in which the mother was homozygous and the fetus was heterozygous. The median value of the concentration of the fetal DNA fraction was estimated using the effective SNPs. A depth-bias correction was performed using simulated data and corresponding regression equations for adjustments when the depth of the sequencing data was below 100-fold or the cffDNA fraction is less than 10%.


RESULTS
Using our approach, the median of the relative bias was 0.4% in 18 maternal plasma samples with a median sequencing depth of 125-fold. There was a significant association (r = 0.935) between our estimations and the estimations inferred from the Y chromosome. Furthermore, this approach could precisely estimate a cffDNA fraction as low as 3%, using only maternal plasma DNA at the targeted region with a sequencing depth of 65-fold. We also used PCR instead of parallel sequencing to calculate the cffDNA fraction. There was a significant association (r = 98.2%) between our estimations and those inferred from the Y chromosome.
BGI Education Center, University of Chinese Academy of Science, Shenzhen 518083, China.
Xiongbin
X
Kang
BGI Education Center, University of Chinese Academy of Science, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
Jun
http://orcid.org/0000-0002-5382-1545
J
Xia
BGI-Shenzhen, Shenzhen 518083, China.
Yicong
Y
Wang
BGI-Shenzhen, Shenzhen 518083, China.
Huixin
H
Xu
BGI-Shenzhen, Shenzhen 518083, China.
Haojun
H
Jiang
BGI-Shenzhen, Shenzhen 518083, China.
Weiwei
W
Xie
BGI-Shenzhen, Shenzhen 518083, China.|Shenzhen Birth Defects Screening Project Lab, BGI-Shenzhen, Shenzhen, China.
Fang
F
Chen
BGI-Shenzhen, Shenzhen 518083, China.
Peng
P
Zeng
BGI-Shenzhen, Shenzhen 518083, China.
Xuchao
X
Li
BGI Education Center, University of Chinese Academy of Science, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
Yifan
Y
Xie
BGI Education Center, University of Chinese Academy of Science, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
Hongtai
H
Liu
BGI-Shenzhen, Shenzhen 518083, China.
Guodong
G
Huang
BGI Education Center, University of Chinese Academy of Science, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
Dayang
D
Chen
BGI-Shenzhen, Shenzhen 518083, China.
Ping
P
Liu
BGI-Shenzhen, Shenzhen 518083, China.
Hui
H
Jiang
BGI Education Center, University of Chinese Academy of Science, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
Xiuqing
X
Zhang
Bioinformatics. 2009 Dec 15;25(24):3207-12
19808877
Bioinformatics. 2012 Nov 15;28(22):2883-90
22962347
Bioinformatics. 2009 Aug 1;25(15):1966-7
19497933
Genet Med. 2012 Mar;14(3):296-305
22281937
Clin Chem. 2008 Oct;54(10):1664-72
18703764
BMJ. 2008 Apr 12;336(7648):816-8
18390496
Sci Transl Med. 2010 Dec 8;2(61):61ra91
21148127
PLoS One. 2013 Jun 28;8(6):e67464
23840709
Clin Chem. 2011 Jan;57(1):92-101
21078840
Blood. 2011 Mar 31;117(13):3684-91
21263151
BMC Genomics. 2012 Jul 24;13:341
22827831
Prenat Diagn. 2012 Aug;32(8):730-4
22585317
Am J Obstet Gynecol. 2005 Aug;193(2):421-5
16098864
Am J Hum Genet. 1998 Apr;62(4):768-75
9529358
Bioinformatics. 2010 Mar 15;26(6):730-6
20130035
Prenat Diagn. 2010 Dec;30(12-13):1226-9
21072784
Bioinformatics. 2012 Apr 1;28(7):907-13
22285562
Clin Chem. 2006 Dec;52(12):2211-8
17068167
N Engl J Med. 1998 Dec 10;339(24):1734-8
9845707
Bioinformatics. 2009 May 15;25(10):1244-50
19307238
N Engl J Med. 2011 Nov 10;365(19):1847-8
22070496
Am J Obstet Gynecol. 2011 Mar;204(3):205.e1-11
21310373
Transfusion. 2013 Sep;53(9):1956-64
23320950
Proc Natl Acad Sci U S A. 2007 Aug 7;104(32):13116-21
17664418
Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16266-71
18838674
Genome Res. 2009 Jun;19(6):1124-32
19420381
J Comput Biol. 1995 Summer;2(2):291-306
7497130
Lancet. 1997 Aug 16;350(9076):485-7
9274585
Am J Obstet Gynecol. 2012 Apr;206(4):319.e1-9
22464072
Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14753-8
16203989
Fetal Diagn Ther. 2014;35(3):199-203
24356438
N Engl J Med. 2002 May 9;346(19):1502
12000828
Genome Res. 2002 Nov;12(11):1679-86
12421754
Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20458-63
19073917
PLoS One. 2011;6(7):e21791
21755002
Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19920-5
19060211
Genet Med. 2011 Nov;13(11):913-20
22005709
PLoS One. 2010 May 03;5(5):e10439
20454671