Noninvasive prenatal detection of trisomy 21 by an epigenetic-genetic chromosome-dosage approach.
BACKGROUND
The use of fetal DNA in maternal plasma for noninvasive prenatal diagnosis of trisomy 21 (T21) is an actively researched area. We propose a novel method of T21 detection that combines fetal-specific epigenetic and genetic markers.


METHODS
We used combined bisulfite restriction analysis to search for fetal DNA markers on chromosome 21 that were differentially methylated in the placenta and maternal blood cells and confirmed any target locus with bisulfite sequencing. We then used methylation-sensitive restriction endonuclease digestion followed by microfluidics digital PCR analysis to investigate the identified marker. Chromosome-dosage analysis was performed by comparing the dosage of this epigenetic marker with that of the ZFY (zinc finger protein, Y-linked) gene on chromosome Y.


RESULTS
The putative promoter of the HLCS (holocarboxylase synthetase) gene was hypermethylated in the placenta and hypomethylated in maternal blood cells. A chromosome-dosage comparison of the hypermethylated HLCS and ZFY loci could distinguish samples of T21 and euploid placental DNA. Twenty-four maternal plasma samples from euploid pregnancies and 5 maternal plasma samples from T21 pregnancies were analyzed. All but 1 of the euploid samples were correctly classified.


CONCLUSIONS
The epigenetic-genetic chromosome-dosage approach is a new method for noninvasive prenatal detection of T21. The epigenetic part of the analysis can be applied to all pregnancies. Because the genetic part of the analysis uses paternally inherited, fetal-specific genetic markers that are abundant in the genome, broad population coverage should be readily achievable. This approach has the potential to become a generally usable technique for noninvasive prenatal diagnosis.
Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China.
Yu K
YK
Tong
Shengnan
S
Jin
Rossa W K
RW
Chiu
Chunming
C
Ding
K C Allen
KC
Chan
Tak Y
TY
Leung
Ling
L
Yu
Tze K
TK
Lau
Y M Dennis
YM
Lo
D019731:Carbon-Nitrogen Ligases / Q000235:genetics*; D002891:Chromosomes, Human, Pair 21; D018899:CpG Islands; D019175:DNA Methylation; D004314:Down Syndrome / Q000175:diagnosis*; D044127:Epigenesis, Genetic; D018628:Gene Dosage; D006801:Humans; D051741:Kruppel-Like Transcription Factors / Q000235:genetics; D011296:Prenatal Diagnosis / Q000379:methods*; D025521:Tumor Suppressor Proteins / Q000235:genetics
D051741:Kruppel-Like Transcription Factors; C411762:RASSF1 protein, human; D025521:Tumor Suppressor Proteins; C054430:ZFY protein, human; D019731:Carbon-Nitrogen Ligases; C023312:holocarboxylase synthetases