Application of risk score analysis to low-coverage whole genome sequencing data for the noninvasive detection of trisomy 21, trisomy 18, and trisomy 13.
OBJECTIVE
Clinical performance of a low coverage, low cost, massively parallel sequencing (MPS)-based assay to stratify risk of trisomy 21, 18, and 13 pregnancies was determined.


METHODS
The study included 1100 samples with birth outcome or karyotype results, comprising low-risk patients (84.2%) negative for risk indications from maternal age, serum screening, ultrasound, or family history, and high-risk patients (15.8%) with at least one of the aforementioned indications. Cell free DNA (cfDNA) was extracted from maternal plasma. Library preparation incorporated 96 index barcodes to enable sequencing on a HiSeq 2000 or 2500. Risk scores were calculated using chromosomal representation, fetal fraction, and maternal age at the estimated date of delivery. A risk score greater than or equal to 1 in 100 was used to stratify samples as high risk for trisomy 21, trisomy 18, or trisomy 13.


RESULTS
Sensitivity and specificity were calculated based on risk group stratification. Trisomy 21, trisomy 18, and trisomy 13 were detected with greater than 99% sensitivity and 99.9% specificity. Fetal sex classification accuracy was 99.3%.


CONCLUSIONS
We conclude that simplified MPS can be used to stratify the risk of pregnancies for trisomy 21, trisomy 18, and trisomy 13 and accurately determine fetal sex. © 2015 John Wiley & Sons, Ltd.
Sequenom Laboratories, San Diego, CA, USA.
J A
JA
Tynan
Sequenom Laboratories, San Diego, CA, USA.
S K
SK
Kim
Sequenom Laboratories, San Diego, CA, USA.
A R
AR
Mazloom
Sequenom Laboratories, San Diego, CA, USA.
C
C
Zhao
Sequenom, Inc., San Diego, CA, USA.
G
G
McLennan
Sequenom Laboratories, San Diego, CA, USA.
R
R
Tim
Sequenom Laboratories, San Diego, CA, USA.
L
L
Liu
Sequenom Laboratories, San Diego, CA, USA.
G
G
Hannum
School of Medicine, University of California, San Diego, CA, USA.
A
A
Hull
Sequenom, Inc., San Diego, CA, USA.|School of Medicine, University of California, San Diego, CA, USA.
A T
AT
Bombard
Sequenom Laboratories, San Diego, CA, USA.
P
P
Oeth
Sequenom, Inc., San Diego, CA, USA.
T
T
Burcham
Sequenom, Inc., San Diego, CA, USA.
D
D
van den Boom
Sequenom, Inc., San Diego, CA, USA.
M
M
Ehrich
D000328:Adult; D025063:Chromosome Disorders / Q000175:diagnosis* / Q000235:genetics; D002882:Chromosomes, Human, Pair 13 / Q000235:genetics; D002887:Chromosomes, Human, Pair 18 / Q000235:genetics; D003661:Decision Support Techniques; D004314:Down Syndrome / Q000175:diagnosis* / Q000235:genetics; D005260:Female; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008423:Maternal Age; D062145:Maternal Serum Screening Tests; D008875:Middle Aged; D011247:Pregnancy; D012189:Retrospective Studies; D018570:Risk Assessment; D012307:Risk Factors; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D014314:Trisomy / Q000175:diagnosis* / Q000235:genetics; D000073839:Trisomy 13 Syndrome; D000073842:Trisomy 18 Syndrome; D016216:Ultrasonography, Prenatal