Biomaterial Database

Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing. 2014

Stephanie C Y Yu, and K C Allen Chan, and Yama W L Zheng, and Peiyong Jiang, and Gary J W Liao, and Hao Sun, and Ranjit Akolekar, and Tak Y Leung, and Attie T J I Go, and John M G van Vugt, and Ryoko Minekawa, and Cees B M Oudejans, and Kypros H Nicolaides, and Rossa W K Chiu, and Y M Dennis Lo

Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China;Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong SAR, China;

Noninvasive prenatal testing using fetal DNA in maternal plasma is an actively researched area. The current generation of tests using massively parallel sequencing is based on counting plasma DNA sequences originating from different genomic regions. In this study, we explored a different approach that is based on the use of DNA fragment size as a diagnostic parameter. This approach is dependent on the fact that circulating fetal DNA molecules are generally shorter than the corresponding maternal DNA molecules. First, we performed plasma DNA size analysis using paired-end massively parallel sequencing and microchip-based capillary electrophoresis. We demonstrated that the fetal DNA fraction in maternal plasma could be deduced from the overall size distribution of maternal plasma DNA. The fetal DNA fraction is a critical parameter affecting the accuracy of noninvasive prenatal testing using maternal plasma DNA. Second, we showed that fetal chromosomal aneuploidy could be detected by observing an aberrant proportion of short fragments from an aneuploid chromosome in the paired-end sequencing data. Using this approach, we detected fetal trisomy 21 and trisomy 18 with 100% sensitivity (T21: 36/36; T18: 27/27) and 100% specificity (non-T21: 88/88; non-T18: 97/97). For trisomy 13, the sensitivity and specificity were 95.2% (20/21) and 99% (102/103), respectively. For monosomy X, the sensitivity and specificity were both 100% (10/10 and 8/8). Thus, this study establishes the principle of size-based molecular diagnostics using plasma DNA. This approach has potential applications beyond noninvasive prenatal testing to areas such as oncology and transplantation monitoring.

UI	MeSH Term	Description	Entries
D009006	Monosomy	The condition in which one chromosome of a pair is missing. In a normally diploid cell it is represented symbolically as 2N-1.	Monosomies
D011247	Pregnancy	The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.	Gestation,Pregnancies
D011296	Prenatal Diagnosis	Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth.	Diagnosis, Prenatal,Fetal Diagnosis,Fetal Imaging,Fetal Screening,Intrauterine Diagnosis,Antenatal Diagnosis,Antenatal Screening,Diagnosis, Antenatal,Diagnosis, Intrauterine,Prenatal Screening,Antenatal Diagnoses,Antenatal Screenings,Diagnosis, Fetal,Fetal Diagnoses,Fetal Imagings,Fetal Screenings,Imaging, Fetal,Intrauterine Diagnoses,Prenatal Diagnoses,Prenatal Screenings,Screening, Antenatal,Screening, Fetal,Screening, Prenatal
D002882	Chromosomes, Human, Pair 13	A specific pair of GROUP D CHROMOSOMES of the human chromosome classification.	Chromosome 13
D002887	Chromosomes, Human, Pair 18	A specific pair of GROUP E CHROMOSOMES of the human chromosome classification.	Chromosome 18
D004247	DNA	A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).	DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D004314	Down Syndrome	A chromosome disorder associated either with an extra CHROMOSOME 21 or an effective TRISOMY for chromosome 21. Clinical manifestations include HYPOTONIA, short stature, BRACHYCEPHALY, upslanting palpebral fissures, epicanthus, Brushfield spots on the iris, protruding tongue, small ears, short, broad hands, fifth finger clinodactyly, single transverse palmar crease, and moderate to severe INTELLECTUAL DISABILITY. Cardiac and gastrointestinal malformations, a marked increase in the incidence of LEUKEMIA, and the early onset of ALZHEIMER DISEASE are also associated with this condition. Pathologic features include the development of NEUROFIBRILLARY TANGLES in neurons and the deposition of AMYLOID BETA-PROTEIN, similar to the pathology of ALZHEIMER DISEASE. (Menkes, Textbook of Child Neurology, 5th ed, p213)	Mongolism,Trisomy 21,47,XX,+21,47,XY,+21,Down Syndrome, Partial Trisomy 21,Down's Syndrome,Partial Trisomy 21 Down Syndrome,Trisomy 21, Meiotic Nondisjunction,Trisomy 21, Mitotic Nondisjunction,Trisomy G,Downs Syndrome,Syndrome, Down,Syndrome, Down's
D005260	Female		Females
D005315	Fetal Diseases	Pathophysiological conditions of the FETUS in the UTERUS. Some fetal diseases may be treated with FETAL THERAPIES.	Embryopathies,Disease, Fetal,Diseases, Fetal,Embryopathy,Fetal Disease
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man