Accurate Pan-Cancer Molecular Diagnosis of Microsatellite Instability by Single-Molecule Molecular Inversion Probe Capture and High-Throughput Sequencing
| Autor: | Nahum Smith, Ronald J. Hause, Eric Q. Konnick, Colin C. Pritchard, Stephen J. Salipante, Adam Waalkes, Kelsi Penewit, Jennifer A. Hempelmann |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Clinical Biochemistry Computational biology Biology Molecular Inversion Probe Polymerase Chain Reaction Article DNA sequencing 03 medical and health sciences Limit of Detection Prostate Neoplasms medicine Humans Typing Pan cancer Biochemistry (medical) High-Throughput Nucleotide Sequencing Reproducibility of Results Cancer Microsatellite instability medicine.disease 030104 developmental biology medicine.anatomical_structure Molecular Diagnostic Techniques Microsatellite Microsatellite Instability |
| Zdroj: | Clinical Chemistry. 64:950-958 |
| ISSN: | 1530-8561 0009-9147 |
| DOI: | 10.1373/clinchem.2017.285981 |
| Popis: | BACKGROUND Microsatellite instability (MSI) is an emerging actionable phenotype in oncology that informs tumor response to immune checkpoint pathway immunotherapy. However, there remains a need for MSI diagnostics that are low cost, highly accurate, and generalizable across cancer types. We developed a method for targeted high-throughput sequencing of numerous microsatellite loci with pan-cancer informativity for MSI using single-molecule molecular inversion probes (smMIPs). METHODS We designed a smMIP panel targeting 111 loci highly informative for MSI across cancers. We developed an analytical framework taking advantage of smMIP-mediated error correction to specifically and sensitively detect instability events without the need for typing matched normal material. RESULTS Using synthetic DNA mixtures, smMIPs were sensitive to at least 1% MSI-positive cells and were highly consistent across replicates. The fraction of identified unstable microsatellites discriminated tumors exhibiting MSI from those lacking MSI with high accuracy across colorectal (100% diagnostic sensitivity and specificity), prostate (100% diagnostic sensitivity and specificity), and endometrial cancers (95.8% diagnostic sensitivity and 100% specificity). MSI-PCR, the current standard-of-care molecular diagnostic for MSI, proved equally robust for colorectal tumors but evidenced multiple false-negative results in prostate (81.8% diagnostic sensitivity and 100% specificity) and endometrial (75.0% diagnostic sensitivity and 100% specificity) tumors. CONCLUSIONS smMIP capture provides an accurate, diagnostically sensitive, and economical means to diagnose MSI across cancer types without reliance on patient-matched normal material. The assay is readily scalable to large numbers of clinical samples, enables automated and quantitative analysis of microsatellite instability, and is readily standardized across clinical laboratories. |
| Databáze: | OpenAIRE |
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