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P087: Retrospective analysis of comprehensive cancer panel sequencing at Fox Chase Cancer Center to evaluate the QIAGEN Clinical Insight Interpret database
Guo, Tingwei Baldwin, Don Tan, Yinfei Gong, Yulan Huang, Min Mackrides, Nicholas Nejati, Reza Wang, Yue Lynn Wasik, Mariusz
Guo, Tingwei
Baldwin, Don
Tan, Yinfei
Gong, Yulan
Huang, Min
Mackrides, Nicholas
Nejati, Reza
Wang, Yue Lynn
Wasik, Mariusz
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Journal article
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2024-03-08
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https://doi.org/10.1016/j.gimo.2024.100968
Abstract
Introduction
As the utilization of next-generation sequencing panels for tumor genomic profiling expands, there is an increasing volume of somatic variants identified, but interpretation of these variants poses a challenge for clinical molecular oncology labs. The Association for Molecular Pathology (AMP), American Society of Clinical Oncology (ASCO), and College of American Pathologists (CAP) published guidelines for the interpretation and reporting of sequence variants in 2017. These guidelines classify the clinical relevance of somatic variants using a four-tiered system. Assignment to a tier and assessing the clinical implications of these variants remains tedious. QIAGEN Clinical Insight Interpret (QCI, previously N-Of-One) streamlines variant interpretation by applying a framework based on AMP/ASCO/CAP cancer actionability guidelines and ACMG/AMP sequence variant interpretation guidelines. The resulting database is queried with a list of variants for each patient case, and an automated pipeline returns any available classifications and associated molecular mechanisms, therapies, and clinical trials. If a queried variant has not been curated in the QCI database, expert investigation and annotation is available for an additional fee, but this service was not evaluated in this study.
Methods
We conducted a retrospective analysis of 3,089 cancer cases with solid tumor and hematological malignancies tested by the Molecular Diagnostics Laboratory at Fox Chase Cancer Center-Temple Health from 2020 to September 2023. Tumor and matched normal DNA were used for multiplex amplification with gene-specific primers targeting the coding exons and exon flanking regions of 275 cancer-related genes using the QIAseq Human Comprehensive Cancer Panel (Qiagen). Next-generation sequencing was performed using the NextSeq500 (Illumina) and analyzed with CLC Genomics Workbench (Qiagen). Variants with low call quality or significant strand bias were excluded. The remaining variants were filtered based on variant allele frequency (VAF >= 5%), mutation databases, and population-based reference datasets including gnomAD, ClinVar, and COSMIC. Variants that were clearly benign were removed. The final lists of reportable variants were then uploaded to query QCI along with tumor type and context for further interpretation.
Results
Of the 275 genes targeted, 201 genes had at least one Tier 1 or 2 variant in our case cohort. Out of 3,089 cases, 986 (32%) had at least one Tier 1 variant with strong clinical significance, 1,431 (46%) had Tier 2 variants with potential clinical significance, 421 (14%) had Tier 3 variants of unknown clinical significance, and 4 (0.1%) had Tier 4 benign or likely benign variants. On average, 8.3 variants (range: 1 to 124) were submitted to QCI, with an average of 3.6 variants (range: 0 to 49) classified using the four-tiered system. An average of 4.7 variants (range: 0 to 165) remained uninterpreted by QCI, necessitating manual curation by our clinical lab. One notable case involved a 69-year-old male with melanoma. Sequencing of the tumor and adjacent normal tissue revealed 44 somatic variants (tumor mutation burden TMB = 56.4 muts/Mb). No Tier 1 variants were found, but two Tier 2 variants in NF1 (R1870) and KRAS (K117N) were identified. Twenty-seven of the 44 variants were not curated by QCI. Among these, a PMS1 stop-gain mutation Gln437* was manually curated as a likely pathogenic Tier 2 variant, possibly serving as a driver mutation explaining the high TMB.
Conclusion
QIAseq Human Comprehensive Cancer Panel and QIAGEN Clinical Insight Interpret software combined to be a sensitive and specific approach for detecting and interpreting clinically significant variants in both solid tumors and hematological malignancies. However, manual investigation, in addition to QCI, is necessary to interpret variants not yet curated by QCI and achieve highest diagnostic rates.
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Citation
Tingwei Guo, Don Baldwin, Yinfei Tan, Yulan Gong, Min Huang, Nicholas Mackrides, Reza Nejati, Yue Lynn Wang, Mariusz Wasik,
P087: Retrospective analysis of comprehensive cancer panel sequencing at Fox Chase Cancer Center to evaluate the QIAGEN Clinical Insight Interpret database,
Genetics in Medicine Open,
Volume 2, Supplement 1,
2024,
100968,
ISSN 2949-7744,
https://doi.org/10.1016/j.gimo.2024.100968.
(https://www.sciencedirect.com/science/article/pii/S2949774424001146)
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Elsevier
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Genetics in Medicine Open, Vol. 2
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