Novel Driver Strength Index highlights important cancer genes in TCGA PanCanAtlas patients
Background Cancer driver genes are usually ranked by mutation frequency, which does not necessarily reflect their driver strength. We hypothesize that driver strength is higher for genes preferentially mutated in patients with few driver mutations overall, because these few mutations should be stron...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2022-08-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/13860.pdf |
| _version_ | 1827607067953725440 |
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| author | Aleksey V. Belikov Alexey D. Vyatkin Sergey V. Leonov |
| author_facet | Aleksey V. Belikov Alexey D. Vyatkin Sergey V. Leonov |
| author_sort | Aleksey V. Belikov |
| collection | DOAJ |
| description | Background Cancer driver genes are usually ranked by mutation frequency, which does not necessarily reflect their driver strength. We hypothesize that driver strength is higher for genes preferentially mutated in patients with few driver mutations overall, because these few mutations should be strong enough to initiate cancer. Methods We propose formulas for the Driver Strength Index (DSI) and the Normalized Driver Strength Index (NDSI), the latter independent of gene mutation frequency. We validate them using TCGA PanCanAtlas datasets, established driver prediction algorithms and custom computational pipelines integrating SNA, CNA and aneuploidy driver contributions at the patient-level resolution. Results DSI and especially NDSI provide substantially different gene rankings compared to the frequency approach. E.g., NDSI prioritized members of specific protein families, including G proteins GNAQ, GNA11 and GNAS, isocitrate dehydrogenases IDH1 and IDH2, and fibroblast growth factor receptors FGFR2 and FGFR3. KEGG analysis shows that top NDSI-ranked genes comprise EGFR/FGFR2/GNAQ/GNA11–NRAS/HRAS/KRAS–BRAF pathway, AKT1–MTOR pathway, and TCEB1–VHL–HIF1A pathway. Conclusion Our indices are able to select for driver gene attributes not selected by frequency sorting, potentially for driver strength. Genes and pathways prioritized are likely the strongest contributors to cancer initiation and progression and should become future therapeutic targets. |
| first_indexed | 2024-03-09T06:49:15Z |
| format | Article |
| id | doaj.art-60465b5c66214236a8d4cb5e449b9373 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:49:15Z |
| publishDate | 2022-08-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-60465b5c66214236a8d4cb5e449b93732023-12-03T10:30:27ZengPeerJ Inc.PeerJ2167-83592022-08-0110e1386010.7717/peerj.13860Novel Driver Strength Index highlights important cancer genes in TCGA PanCanAtlas patientsAleksey V. BelikovAlexey D. VyatkinSergey V. LeonovBackground Cancer driver genes are usually ranked by mutation frequency, which does not necessarily reflect their driver strength. We hypothesize that driver strength is higher for genes preferentially mutated in patients with few driver mutations overall, because these few mutations should be strong enough to initiate cancer. Methods We propose formulas for the Driver Strength Index (DSI) and the Normalized Driver Strength Index (NDSI), the latter independent of gene mutation frequency. We validate them using TCGA PanCanAtlas datasets, established driver prediction algorithms and custom computational pipelines integrating SNA, CNA and aneuploidy driver contributions at the patient-level resolution. Results DSI and especially NDSI provide substantially different gene rankings compared to the frequency approach. E.g., NDSI prioritized members of specific protein families, including G proteins GNAQ, GNA11 and GNAS, isocitrate dehydrogenases IDH1 and IDH2, and fibroblast growth factor receptors FGFR2 and FGFR3. KEGG analysis shows that top NDSI-ranked genes comprise EGFR/FGFR2/GNAQ/GNA11–NRAS/HRAS/KRAS–BRAF pathway, AKT1–MTOR pathway, and TCEB1–VHL–HIF1A pathway. Conclusion Our indices are able to select for driver gene attributes not selected by frequency sorting, potentially for driver strength. Genes and pathways prioritized are likely the strongest contributors to cancer initiation and progression and should become future therapeutic targets.https://peerj.com/articles/13860.pdfCancerDriverGenesMutationsPathways |
| spellingShingle | Aleksey V. Belikov Alexey D. Vyatkin Sergey V. Leonov Novel Driver Strength Index highlights important cancer genes in TCGA PanCanAtlas patients PeerJ Cancer Driver Genes Mutations Pathways |
| title | Novel Driver Strength Index highlights important cancer genes in TCGA PanCanAtlas patients |
| title_full | Novel Driver Strength Index highlights important cancer genes in TCGA PanCanAtlas patients |
| title_fullStr | Novel Driver Strength Index highlights important cancer genes in TCGA PanCanAtlas patients |
| title_full_unstemmed | Novel Driver Strength Index highlights important cancer genes in TCGA PanCanAtlas patients |
| title_short | Novel Driver Strength Index highlights important cancer genes in TCGA PanCanAtlas patients |
| title_sort | novel driver strength index highlights important cancer genes in tcga pancanatlas patients |
| topic | Cancer Driver Genes Mutations Pathways |
| url | https://peerj.com/articles/13860.pdf |
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