Next-generation sequencing (NGS) has overtaken Sanger sequencing as the dominant methodology in molecular pathology laboratory developed tests (LDTs), according to a review of data from New York State’s Clinical Laboratory Evaluation Program (CLEP). The analysis, covering more than 4,200 LDT submissions from 2010 to 2024, also shows increasing adoption of whole exome sequencing (WES), whole genome sequencing (WGS), and cell-free DNA assays.
The findings were presented at the 2025 annual meeting of the Association for Molecular Pathology (AMP) in Boston by a team from the New York State Department of Health, including Kate L. DeRosa, PhD, and colleagues from the Wadsworth Center and the Office of Information Technology Services. Dr. DeRosa and her coauthors analyzed LDT submissions from both constitutional genetics and oncology laboratories, evaluating methodology, specimen type, and assay trends over a 14-year period. According to the study, NGS has become the most common method overall, accounting for 33% of reviewed molecular pathology LDTs, whereas PCR-based methods represented 22.4% and Sanger sequencing represented 21.4%. NGS adoption began around 2012, coinciding with publication of CLEP guidance for NGS assays, and has increased steadily in both constitutional genetics and oncology.
“Constitutional LDTs tend to be screening panels, pharmacogenomics panels, and prenatal screening assays, while oncology LDTs are more diagnostic, prognostic, and predictive of therapy selection,” the authors note. The rate of adoption differs between the 2 categories, reflecting intended assay use.
Single-gene assays in constitutional genetics have largely been replaced by panel-based NGS tests, and submissions for WES and WGS have increased for both constitutional and oncology LDTs, though oncology adoption lagged several years. In parallel, the use of cell-free DNA (cfDNA) for molecular pathology—particularly in oncology—has risen sharply since 2016, likely reflecting technological advances in NGS and liquid biopsy assays.
The study also compared CLEP LDT submissions with US Food and Drug Administration (FDA) approved molecular assays from 2010 to 2024. CLEP received more than 45 times as many submissions requiring review as the FDA approved during the same period, highlighting the high volume of laboratory-developed tests in clinical use. PCR-based and NGS methods were the most frequently approved assay types, whereas no Sanger-based assays received FDA approval.
The authors conclude that NGS-based LDTs, including WES and WGS, are likely to continue expanding, whereas PCR-based assays remain popular due to cost-effectiveness and rapid turnaround. The data provide insight into how laboratory methodologies are evolving and may serve as a model for trends in molecular pathology testing nationally.
