From prenatal genomic diagnosis to fetal personalized medicine: progress and challenges

Abstract

Thus far, the focus of personalized medicine has been the prevention and treatment of conditions that affect adults. Although advances in genetic technology have been applied more frequently to prenatal diagnosis than to fetal treatment, genetic and genomic information is beginning to influence pregnancy management. Recent developments in sequencing the fetal genome combined with progress in understanding fetal physiology using gene expression arrays indicate that we could have the technical capabilities to apply an individualized medicine approach to the fetus. Here I review recent advances in prenatal genetic diagnostics, the challenges associated with these new technologies and how the information derived from them can be used to advance fetal care. Historically, the goal of prenatal diagnosis has been to provide an informed choice to prospective parents. We are now at a point where that goal can and should be expanded to incorporate genetic, genomic and transcriptomic data to develop new approaches to fetal treatment.

Figure 1

Outline of the three major current techniques for analyzing fetal chromosomes. (a) Fetal cells are cultured and analyzed during cell division in metaphase. Chromosomes are analyzed under the microscope for the presence of dark and light staining bands. The staining patterns are compared with normal reference standards. Only relatively large deviations from normal (~5–10 Mb) can be detected. (b,c) The DNA within the fetal chromosomes, rather than the fetal chromosome itself, is compared to reference genomes. The DNA can be isolated from fetal cells or cell-free amniotic fluid with or without prior cell culture. In array comparative genomic hybridization (cGH) (b), patient and reference DNA samples are labeled with competing fluorescent dyes and hybridized to an array that contains DNA probes. Each probe is known to map to a specific region of the human genome. When the array is read, areas of mismatch appear as red or green. Special software converts the signal to indicate the affected area of the genome. In the method shown in c, only the patient's DNA is hybridized to an array that contains oligonucleotides (~60 bp) with coverage across the human genome. Areas of mismatch between the patient's DNA and the reference sequence are identified as CNVs. BAC, bacterial artificial chromosome.

Figure 2

Cell-free DNA analysis to diagnose fetal disorders. Cell-free DNA from maternal plasma is a mixture of maternal and fetal DNA. When testing is being performed for the diagnosis of the presence or absence of a uniquely fetal gene, the relatively low-cost method of real-time quantitative PCR can be used (left). Primers and probes that map uniquely to the fetal genome can be used to amplify the gene of interest to allow, for example, the detection of the RHD gene. For diagnosing aneuploidies such as Down's syndrome, the total cell-free DNA in maternal plasma is sequenced (right). The DNA is fragmented and analyzed in 36-bp lengths known as reads. These 36-bp reads are aligned against the human genome sequence and counted. The amount of DNA in chromosomes of interest, for example, those involved in common fetal aneuploidies such as those of chromosomes 13, 18 and 21, is normalized against the DNA from other chromosomes to determine the relative number of reads present in a given sample. The lower right image shows an increased number of sequences derived from chromosome (chr) 21 (in red) plotted against what should normally be present, indicated by the dashed line slightly above 1.0. This result is consistent with a fetus that has trisomy 21.

Figure 3

A potential future diagnostic and treatment strategy for Down's syndrome. A comparison of the current two-tiered approach for the noninvasive diagnosis of fetal trisomy 21 with no fetal treatment options and a possible future approach in which sequencing of maternal plasma DNA may eliminate the need for invasive testing. Furthermore, advances in study of the fetal transcriptome may identify new treatments that could be administered to the pregnant woman as soon as the diagnosis is made.