Prenatal diagnostic testing can be a risky business. Common invasive tests, such as amniocentesis and chorionic villus sampling, identify fetal chromosomal abnormalities, including Down syndrome (trisomy 21), but pose the risk of miscarriage. Now, two research groups report noninvasive techniques to diagnose fetal chromosome abnormalities in recent articles in Nature Medicine and the Lancet.
Maternal plasma contains a small amount of cell-free fetal DNA. Approximately 3-6% of DNA in maternal plasma is derived from the fetus. Both research groups determined the copy number of fetal chromosome 21 from ratios of fetal-derived single nucleotide polymorphisms (SNPs) in maternal blood.
Lo et al. identified a placental gene located on chromosome 21, PLAC4, that is expressed in the plasma of pregnant, but not nonpregnant women. They found four SNPs in expressed regions of PLAC4 DNA, the most variable of which was SNP rs8130833. They genotyped PLAC4 DNA from placental tissue and the 'buffy coat' portion of maternal blood, which does not contain fetal DNA. Plasma RNA from mothers heterozygous at rs8130833 carrying fetuses homozygous at rs8130833 did not express the maternal-specific allele. Therefore, all PLAC4 alleles expressed in maternal plasma are fetal in origin.
The authors genotyped SNP rs8130833 in maternal plasma RNA by primer extension followed by mass spectrometry detection of heavy (G) and light (A) alleles. For heterozygous fetuses, they determined the ratio of the heavy to the light allele, which should be 1:1 in fetuses diploid, and 2:1 or 1:2 in fetuses triploid for chromosome 21. The authors correctly identified 90% of fetuses with and 96.5% of the fetuses without trisomy 21. Analysis of additional SNPs will increase accuracy and allow the diagnosis of fetuses that are homozygous at SNP rs8130833, according to the authors.
Dhallan et al. also analyzed heterozygous SNPs on chromosome 21. They treated maternal plasma with formaldehyde to prevent maternal cell lysis, thereby increasing the relative yield of cell-free fetal DNA. Then they genotyped the plasma along with maternal and paternal buffy coat samples for various SNPs on chromosome 21. They focused on SNPs for which the maternal buffy coat sample was homozygous, but the plasma sample was heterozygous. The ratio of the expression of the unique fetal allele to all other alleles should approach 1:3 for a fetus that is diploid, and 1:4 for a fetus that is triploid for chromosome 21. The authors correctly identified 66.7% of fetuses with and 98.2% of fetuses without trisomy 21.
Although both studies focused on trisomy 21, these techniques could be modified to detect other aneuploidies, like trisomy 18 (Edward syndrome) and trisomy 13 (Patau syndrome), which are usually fatal before or just after birth. These techniques might also be modified to detect chromosomal deletions, including 22q and 13q syndromes.