CAP TODAY Pathology/Laboratory Medicine/Laboratory Management
Use of optical genome mapping for prenatal diagnostic testing
The rate of clinically recognized pregnancy loss is approximately 15 to 25 percent, with fetal anomalies occurring in another three to five percent. Chromosomal abnormalities often cause these adverse outcomes. Therefore, guidelines recommend that all pregnant women undergo prenatal genetic screening, regardless of maternal age, underlying clinical conditions, or stage of pregnancy. In many situations, noninvasive prenatal screening is offered at 10 to 12 weeks of gestation. Noninvasive screening, which analyzes fragments of fetal DNA circulating in maternal blood, is an exquisitely sensitive method of screening for chromosomal abnormalities. However, abnormal results should be confirmed with invasive diagnostic testing, such as chorionic villus sampling or amniocentesis. Fetal tissue obtained through one of these invasive procedures is traditionally analyzed by karyotyping, FISH, or chromosomal microarray. In many clinical situations, more than one of these diagnostic tests are performed since each method may have blind spots. Karyotyping involves visually inspecting G-banded chromosomes, and its resolution is limited to 5 to 10 Mb, as these are the smallest changes that can be viewed reliably under a light microscope. FISH requires fluorescent probes that hybridize to regions of interest, so it can only detect what is covered by the probe sets. Chromosomal microarray has high resolution for submicroscopic copy number alterations, but it cannot identify balanced translocations or determine the orientation or location of copy number changes. In contrast to these conventional methods, optical genome mapping (OGM), a next-generation cytogenomic technology, can assess all types of structural variants at high resolution across the entire genome. In this method, ultralong DNA molecules are labeled with a fluorescent marker at CTTAAG sequences. These sequences occur, on average, about every 5 kb, but they vary in frequency across the genome, allowing individual ultralong DNA molecules to be identified based on fluorescent pattern. The ultralong DNA molecules are loaded into a microfluidic device in which they are linearized and flow through parallel channels to undergo imaging via a high-resolution camera. Once the pattern of fluorescent markers is analyzed across all molecules, the genome can be assembled and any abnormalities identified. The authors of this study evaluated and clinically validated the use of OGM in prenatal diagnostic testing. Using OGM, they tested 114 samples harboring 101 aberrations identified by standard-of-care cytogenetic analysis. The test had 100 percent sensitivity compared with conventional methods. The chromosomal abnormalities included 29 interstitial/terminal deletions as small as 95 kb, 28 duplications, 26 aneuploidies, six absence-of-heterozygosity regions, three triploid genomes, four isochromosomes, three marker chromosomes, one chromosome with additional material, and one translocation. Because its resolution is higher than that of conventional methods, OGM also identified 64 structural variants that potentially would be reportable. Phenotypically normal control samples were assessed to test specificity. No false-positive pathogenic structural variants were identified using OGM, demonstrating 100 percent specificity. Reproducibility at the interrun, intrarun, and interinstrument levels was also 100 percent. This study demonstrates the feasibility of using OGM for diagnostic prenatal testing, one of the most important and high-volume applications of cytogenetic analysis.
Sahajpal NS, Mondal AK, Fee T, et al. Clinical validation and diagnostic utility of optical genome mapping in prenatal diagnostic testing. J Mol Diagn. 2023;25(4):234–246.
Correspondence: Dr. Ravindra Kolhe at rkolhe@augusta.edu