NSCLC Digital PCR Panel Returns Low-Input Sample Results Where Sequencing Fails
Molecular diagnostics has drastically improved the survival rate of patients diagnosed with non-small cell lung cancer (NSCLC) over the last 10 years. Despite advancements in molecular testing, targeted therapies, and national guideline recommendations, more than half of NSCLC patients in the United...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-01-01
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| Series: | Diagnostics |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2075-4418/14/3/243 |
| _version_ | 1797318928691625984 |
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| author | Leah Rowland Herdt Paige Berroteran Malini Rajagopalan Bradley A. Brown Jerrod J. Schwartz |
| author_facet | Leah Rowland Herdt Paige Berroteran Malini Rajagopalan Bradley A. Brown Jerrod J. Schwartz |
| author_sort | Leah Rowland Herdt |
| collection | DOAJ |
| description | Molecular diagnostics has drastically improved the survival rate of patients diagnosed with non-small cell lung cancer (NSCLC) over the last 10 years. Despite advancements in molecular testing, targeted therapies, and national guideline recommendations, more than half of NSCLC patients in the United States either never receive testing or patient care is not informed via molecular testing. Here, we sought to explore the relationship between DNA/RNA input, the molecular testing method, and test success rates. On a shared set of low-input reference test materials (<i>n</i> = 3), we ran both a hybrid capture-based, next-generation sequencing (NGS) assay and a multiplexed digital PCR (dPCR) panel. The dPCR panel was highly sensitive and specific for low-input samples in dilution studies ranging from 40 to 1 ng DNA and from 20 to 2.5 ng RNA, while NGS had up to an 86% loss in sensitivity as contrived sample inputs were serially diluted. The dPCR panel also demonstrated a high PPA (>95%) at diluted inputs as low as 15/7.5 ng DNA/RNA on 23 banked clinical samples with the same NGS hybrid capture assay at a high input. These data suggest that digital PCR is an accurate and effective way of identifying clinically relevant NSCLC mutations at low nucleotide input and quality. |
| first_indexed | 2024-03-08T03:59:33Z |
| format | Article |
| id | doaj.art-613d124d33e749bda436c88fbb836185 |
| institution | Directory Open Access Journal |
| issn | 2075-4418 |
| language | English |
| last_indexed | 2024-03-08T03:59:33Z |
| publishDate | 2024-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diagnostics |
| spelling | doaj.art-613d124d33e749bda436c88fbb8361852024-02-09T15:09:56ZengMDPI AGDiagnostics2075-44182024-01-0114324310.3390/diagnostics14030243NSCLC Digital PCR Panel Returns Low-Input Sample Results Where Sequencing FailsLeah Rowland Herdt0Paige Berroteran1Malini Rajagopalan2Bradley A. Brown3Jerrod J. Schwartz4ChromaCode Inc., 2330 Faraday Ave, Carlsbad, CA 92008, USAChromaCode Inc., 2330 Faraday Ave, Carlsbad, CA 92008, USAChromaCode Inc., 2330 Faraday Ave, Carlsbad, CA 92008, USAChromaCode Inc., 2330 Faraday Ave, Carlsbad, CA 92008, USAChromaCode Inc., 2330 Faraday Ave, Carlsbad, CA 92008, USAMolecular diagnostics has drastically improved the survival rate of patients diagnosed with non-small cell lung cancer (NSCLC) over the last 10 years. Despite advancements in molecular testing, targeted therapies, and national guideline recommendations, more than half of NSCLC patients in the United States either never receive testing or patient care is not informed via molecular testing. Here, we sought to explore the relationship between DNA/RNA input, the molecular testing method, and test success rates. On a shared set of low-input reference test materials (<i>n</i> = 3), we ran both a hybrid capture-based, next-generation sequencing (NGS) assay and a multiplexed digital PCR (dPCR) panel. The dPCR panel was highly sensitive and specific for low-input samples in dilution studies ranging from 40 to 1 ng DNA and from 20 to 2.5 ng RNA, while NGS had up to an 86% loss in sensitivity as contrived sample inputs were serially diluted. The dPCR panel also demonstrated a high PPA (>95%) at diluted inputs as low as 15/7.5 ng DNA/RNA on 23 banked clinical samples with the same NGS hybrid capture assay at a high input. These data suggest that digital PCR is an accurate and effective way of identifying clinically relevant NSCLC mutations at low nucleotide input and quality.https://www.mdpi.com/2075-4418/14/3/243NSCLCdPCRNGSQNS |
| spellingShingle | Leah Rowland Herdt Paige Berroteran Malini Rajagopalan Bradley A. Brown Jerrod J. Schwartz NSCLC Digital PCR Panel Returns Low-Input Sample Results Where Sequencing Fails Diagnostics NSCLC dPCR NGS QNS |
| title | NSCLC Digital PCR Panel Returns Low-Input Sample Results Where Sequencing Fails |
| title_full | NSCLC Digital PCR Panel Returns Low-Input Sample Results Where Sequencing Fails |
| title_fullStr | NSCLC Digital PCR Panel Returns Low-Input Sample Results Where Sequencing Fails |
| title_full_unstemmed | NSCLC Digital PCR Panel Returns Low-Input Sample Results Where Sequencing Fails |
| title_short | NSCLC Digital PCR Panel Returns Low-Input Sample Results Where Sequencing Fails |
| title_sort | nsclc digital pcr panel returns low input sample results where sequencing fails |
| topic | NSCLC dPCR NGS QNS |
| url | https://www.mdpi.com/2075-4418/14/3/243 |
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