Cell-Free DNA Analysis of Targeted Genomic Regions in Maternal Plasma for Non-Invasive Prenatal Testing of Trisomy 21, Trisomy 18, Trisomy 13, and Fetal Sex.
There is great need for the development of highly accurate cost effective technologies that could facilitate the widespread adoption of noninvasive prenatal testing (NIPT).



We developed an assay based on the targeted analysis of cell-free DNA for the detection of fetal aneuploidies of chromosomes 21, 18, and 13. This method enabled the capture and analysis of selected genomic regions of interest. An advanced fetal fraction estimation and aneuploidy determination algorithm was also developed. This assay allowed for accurate counting and assessment of chromosomal regions of interest. The analytical performance of the assay was evaluated in a blind study of 631 samples derived from pregnancies of at least 10 weeks of gestation that had also undergone invasive testing.



Our blind study exhibited 100% diagnostic sensitivity and specificity and correctly classified 52/52 (95% CI, 93.2%-100%) cases of trisomy 21, 16/16 (95% CI, 79.4%-100%) cases of trisomy 18, 5/5 (95% CI, 47.8%-100%) cases of trisomy 13, and 538/538 (95% CI, 99.3%-100%) normal cases. The test also correctly identified fetal sex in all cases (95% CI, 99.4%-100%). One sample failed prespecified assay quality control criteria, and 19 samples were nonreportable because of low fetal fraction.



The extent to which free fetal DNA testing can be applied as a universal screening tool for trisomy 21, 18, and 13 depends mainly on assay accuracy and cost. Cell-free DNA analysis of targeted genomic regions in maternal plasma enables accurate and cost-effective noninvasive fetal aneuploidy detection, which is critical for widespread adoption of NIPT.
NIPD Genetics, Ltd, Nicosia, Cyprus;
George
G
Koumbaris
NIPD Genetics, Ltd, Nicosia, Cyprus;
Elena
E
Kypri
NIPD Genetics, Ltd, Nicosia, Cyprus;
Kyriakos
K
Tsangaras
NIPD Genetics, Ltd, Nicosia, Cyprus;
Achilleas
A
Achilleos
NIPD Genetics, Ltd, Nicosia, Cyprus;
Petros
P
Mina
The Cyprus Institute of Neurology and Genetics;
Maria
M
Neofytou
NIPD Genetics, Ltd, Nicosia, Cyprus;
Voula
V
Velissariou
NIPD Genetics, Ltd, Nicosia, Cyprus;
Georgia
G
Christopoulou
AAK Ultrasound and Fetal Medicine Center, Nicosia, Cyprus;
Ioannis
I
Kallikas
Andros Day Surgery Clinic, Reproductive Medicine Unit. Palermo, Italy;
Alicia
A
González-Liñán
Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania;
Egle
E
Benusiene
Center for Medical Genetics Genesis, Poznan, Poland;
Anna
A
Latos-Bielenska
Gynecology and Obstetrics, Poznan University of Medical Sciences, Poland;
Pietryga
P
Marek
Clinical Genetics, Childhood Hospital Materno-Infantil, Las Palmas GC, Canary Islands, Spain;
Alfredo
A
Santana
Department of Medical Genetics, University of Szeged, Szeged, Hungary;
Nikoletta
N
Nagy
Department of Medical Genetics, University of Szeged, Szeged, Hungary;
Márta
M
Széll
Department of Perinatology and Obstetrics Medical University of Bialystok, Poland.
Piotr
P
Laudanski
NIPD Genetics, Ltd, Nicosia, Cyprus;
Elisavet A
EA
Papageorgiou
NIPD Genetics, Ltd, Nicosia, Cyprus;
Marios
M
Ioannides
NIPD Genetics, Ltd, Nicosia, Cyprus; The Cyprus Institute of Neurology and Genetics; p.patsalis@nipd.com.
Philippos C
PC
Patsalis
D025063:Chromosome Disorders / Q000097:blood / Q000235:genetics*; D002882:Chromosomes, Human, Pair 13 / Q000235:genetics; D002887:Chromosomes, Human, Pair 18 / Q000235:genetics; D004247:DNA / Q000097:blood / Q000235:genetics*; D004314:Down Syndrome / Q000097:blood / Q000235:genetics*; D005260:Female; D005333:Fetus / Q000378:metabolism*; D006801:Humans; D011247:Pregnancy; D011296:Prenatal Diagnosis; D017422:Sequence Analysis, DNA; D012732:Sex Determination Analysis / Q000379:methods*; D014314:Trisomy / Q000235:genetics*; D000073839:Trisomy 13 Syndrome; D000073842:Trisomy 18 Syndrome
D004247:DNA