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January 17, 2025 14:58
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vs vanilla with examples adhoc-api
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| >>> can you run code to get gene panel data? | |
| To help you with getting gene panel data, I need more information about the specific source or API you want to use to retrieve this data. Could you please provide more details or specify the API or database you are interested in? | |
| >>> I'm just doing early exploration, I don't know what I want. | |
| thought: Since the user is exploring options for obtaining gene panel data, I | |
| will list the available APIs to see if any are relevant to their needs. | |
| tool: list_apis | |
| tool_input: {} | |
| observation: {'cbioportal': {'description': "The cBioPortal for Cancer Genomics | |
| was originally developed at \nMemorial Sloan Kettering Cancer Center (MSK). The | |
| public cBioPortal \nsite is hosted by the Center for Molecular Oncology at MSK. | |
| The \ncBioPortal software is now available under an open source license \nvia | |
| GitHub. The software is now developed and maintained by a \nmulti-institutional | |
| team, consisting of MSK, the Dana Farber Cancer \nInstitute, Princess Margaret | |
| Cancer Centre in Toronto, Children's \nHospital of Philadelphia, Caris Life | |
| Sciences, The Hyve and SE4BIO \nin the Netherlands, and Bilkent University in | |
| Ankara, Turkey.\n"}} | |
| One available API for exploring gene panel data is the cBioPortal for Cancer Genomics. It provides access to a wide range of cancer genomics data and is developed by a multi-institutional team. If you're interested in exploring gene panel data related to cancer genomics, this could be a good starting point. | |
| Would you like to explore how to use the cBioPortal API to get gene panel data? | |
| >>> run code to get gene panel data | |
| thought: Using the cBioPortal API to fetch gene panel data will provide a good | |
| starting point for exploration. | |
| tool: use_api | |
| tool_input: {'api': 'cbioportal', 'goal': 'Retrieve gene panel data for | |
| exploration purposes.'} | |
| INFO {'api': 'cbioportal', 'WRITE_CODE': 'Retrieve gene panel data for exploration purposes.'} | |
| observation: import requests | |
| url = "https://www.cbioportal.org/api/gene-panels" | |
| response = requests.get(url) | |
| if response.status_code == 200: | |
| gene_panels = response.json() | |
| for panel in gene_panels: | |
| print(f"Gene Panel ID: {panel['genePanelId']}") | |
| print(f"Description: {panel.get('description', 'No description | |
| available')}") | |
| print(f"Number of Genes: {len(panel.get('genes', []))}") | |
| print("-" * 80) | |
| thought: Calling tool 'run' | |
| tool: run | |
| tool_input: {'code': 'import requests\n\nurl = | |
| "https://www.cbioportal.org/api/gene-panels"\nresponse = requests.get(url)\n\nif | |
| response.status_code == 200:\n gene_panels = response.json()\n for panel | |
| in gene_panels:\n print(f"Gene Panel ID: {panel[\'genePanelId\']}")\n | |
| print(f"Description: {panel.get(\'description\', \'No description | |
| available\')}")\n print(f"Number of Genes: {len(panel.get(\'genes\', | |
| []))}")\n print("-" * 80)'} | |
| observation: Gene Panel ID: ACYC_FMI_27 | |
| Description: Targeted (27 cancer genes) sequencing of adenoid cystic carcinomas | |
| on Illumina HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: Agilent | |
| Description: Targeted panel of 232 genes. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: AmpliSeq | |
| Description: Targeted panel of 8 genes. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: ARCHER-HEME-CV1 | |
| Description: ARCHER-HEME gene panel (199 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: ARCHER-SOLID-CV1 | |
| Description: ARCHER-SOLID Gene Panel (62 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: bait_v3 | |
| Description: Targeted sequencing of various tumor types via bait v3. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: bait_v4 | |
| Description: Targeted sequencing of various tumor types via bait v4. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: bait_v5 | |
| Description: Targeted sequencing of various tumor types via bait v5. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: bcc_unige_2016_cancer_panel | |
| Description: Targeted panel of 387 cancer-related genes. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: HemePACT_v3 | |
| Description: Research (CMO) IMPACT-Heme gene panel version 3. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: ctDx_lung_panel | |
| Description: Targeted sequencing of 18 genes via Resolution ctDx Lung assay. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: DFCI_504 | |
| Description: Targeted sequencing of 503 cancer-associated genes on Illumina | |
| HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: FMI-D2 | |
| Description: FoundationOne Heme gene panel targets the entire coding sequence of | |
| 406 genes, selected introns of 31 genes involved in rearrangements and utilizes | |
| RNA sequencing to interrogate 265 genes | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: FMI-R2 | |
| Description: FoundationOne Heme gene panel targets the entire coding sequence of | |
| 406 genes, selected introns of 31 genes involved in rearrangements and utilizes | |
| RNA sequencing to interrogate 265 genes | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: FMI-T4b | |
| Description: Foundation Medicine T4b gene panel (214 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: FMI-T5a | |
| Description: Foundation Medicine T5a gene panel (323 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: FMI-T7 | |
| Description: Foundation Medicine T7 gene panel (429 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: gbm_tcga_pub_cancer_panel | |
| Description: Targeted panel of 600 genes. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: glioma_dfci_2020_DFCI-ONCOPANEL-1 | |
| Description: DFCI-ONCOPANEL-1 (304 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: glioma_dfci_2020_DFCI-ONCOPANEL-2 | |
| Description: DFCI-ONCOPANEL-2 (326 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: glioma_dfci_2020_DFCI-ONCOPANEL-3 | |
| Description: DFCI-ONCOPANEL-3 (447 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: glioma_mskcc_2019_fmi_t5 | |
| Description: Foundation Medicine T5 gene panel (326 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: glioma_mskcc_2019_fmi_t7 | |
| Description: Foundation Medicine T7 gene panel (434 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: grail_cfdna_508 | |
| Description: High-intensity targeted sequencing assay by GRAIL covering 508 | |
| genes. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: GUARDANT_73 | |
| Description: Targeted variant analysis from 73 cancer genes by Next-Generation | |
| (NGS)/Massively parallel sequencing (MPS). | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: IMPACT-HEME-400 | |
| Description: Targeted (400 cancer genes) sequencing of various tumor types via | |
| MSK-IMPACT Heme on Illumina HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: IMPACT-HEME-468 | |
| Description: Targeted (467 cancer genes) sequencing of various tumor types via | |
| MSK-IMPACT Heme on Illumina HiSeq sequencers. Originally 468 genes with | |
| CDKN2Ap14ARF and CDKN2Ap16INK4A, merged into CDKN2A. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: IMPACT-HEME-HS | |
| Description: Hotspot sequencing panel for MSK-IMPACT Heme on Illumina HiSeq | |
| sequencers (204 genes). | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: IMPACT230 | |
| Description: Targeted sequencing of urcc tumor via MSK-IMPACT. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: IMPACT279 | |
| Description: Targeted (279 cancer genes) sequencing of various tumor types via | |
| MSK-IMPACT on Illumina HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: IMPACT300 | |
| Description: Targeted (300 cancer genes) sequencing of bladder urothelial | |
| carcinomas via MSK-IMPACT on Illumina HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: IMPACT341 | |
| Description: Targeted (341 cancer genes) sequencing of various tumor types via | |
| MSK-IMPACT on Illumina HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: IMPACT410 | |
| Description: Targeted (410 cancer genes) sequencing of various tumor types via | |
| MSK-IMPACT on Illumina HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: IMPACT468 | |
| Description: Targeted (468 cancer genes) sequencing of various tumor types via | |
| MSK-IMPACT on Illumina HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: IMPACT505 | |
| Description: Targeted (505 cancer genes) sequencing of various tumor types via | |
| MSK-IMPACT on Illumina HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: MDSIWG152 | |
| Description: Targeted (152 genes) sequencing of MDS samples from the | |
| International Working Group (IWG) for the prognosis of MDS | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: Papaemmanuil_NEJM_2016_MDS_2013_panel | |
| Description: Targeted NGS of AML/MDs Samples. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: METABRIC_173 | |
| Description: Targeted (173 cancer genes) sequencing of breast cancers on | |
| Illumina HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: ACCESS129 | |
| Description: Targeted (129 genes) sequencing of cfDNA via MSK-ACCESS on Illumina | |
| HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: MSKCC_BLCA_15 | |
| Description: Targeted sequencing of 15 oncogenes and tumor suppressor genes, | |
| selected for their potential as predictive biomarkers of response to targeted | |
| agents by Sanger sequencing. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: MYB-IMPACT341 | |
| Description: Targeted (343 cancer genes, IMPACT341 plus MYB and NFIB) sequencing | |
| of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: MYB-IMPACT410 | |
| Description: Targeted (412 cancer genes, IMPACT410 plus MYB and NFIB) sequencing | |
| of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: MYB-IMPACT468 | |
| Description: Targeted (470 cancer genes, IMPACT468 plus MYB and NFIB) sequencing | |
| of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: NSCLC_UNITO_2016_PANEL | |
| Description: Targeted NGS of NSCLC Samples. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: prad_mskcc_sanger | |
| Description: Targeted panel of 137 genes. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: prad_mskcc_sequenom_sanger | |
| Description: Targeted panel of 145 genes. (merge of prad_mskcc_sanger and | |
| prad_mskcc_sequenom) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: prad_mskcc_sequenom | |
| Description: Targeted panel of 21 genes. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: rbl_cfdna_msk_2020_panel | |
| Description: Targeted panel for cfDNA sequencing (2 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: RDTB49 | |
| Description: Targeted sequencing of clinical cases via Thunderbolts NGS Target | |
| Enrichment System, RainDance Technologies. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: RDTS30 | |
| Description: Targeted sequencing of clinical cases via ThunderStorm NGS Target | |
| Enrichment System, RainDance Technologies. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: RMG | |
| Description: A panel that's designed to target all exons of 262 genes that are | |
| recurrently mutated in de novo MDS/AML (â). | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: sarc_mskcc_panel | |
| Description: Targeted panel of 226 protein-coding genes. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: UCLA_1202 | |
| Description: Targeted deep sequencing (TDS) of 1202 genes on Illumina HiSeq2000 | |
| sequencers. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: WUSTL-DFCI_623 | |
| Description: DNA sequencing of 622 genes with known or potential relationships | |
| to cancer. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: NOVARTIS_BROAD_1651 | |
| Description: Targeted massively parallel sequencing of 4047 cancer genes. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: TERT-FMI-T7 | |
| Description: Foundation Medicine T7 gene panel (430 cancer genes, FMI-T7 plus | |
| TERT) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: FoundationOne | |
| Description: FoundationOne gene panel (317 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: DFCI-ONCOPANEL-3.1 | |
| Description: DFCI-ONCOPANEL-3.1, Number of Genes - 447 | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: DFCI-ONCOPANEL-3 | |
| Description: DFCI-ONCOPANEL-3, Number of Genes - 447 | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: DFCI-ONCOPANEL-1 | |
| Description: DFCI-ONCOPANEL-1, Number of Genes - 304 | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: DFCI-ONCOPANEL-2 | |
| Description: DFCI-ONCOPANEL-2, Number of Genes - 326 | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: ARCHER-SOLID-CV4 | |
| Description: ARCHER-SOLID-CV4 Gene Panel (123 genes) | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: MDAnderson_T200 | |
| Description: Targeted panel of 262 genes. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| Gene Panel ID: sarcoma_msk_2022_panel | |
| Description: Targeted panel of 476 cancer-related genes. | |
| Number of Genes: 0 | |
| -------------------------------------------------------------------------------- | |
| I retrieved gene panel data from the cBioPortal API. Here are some examples of the gene panels available: | |
| 1. **ACYC_FMI_27**: Targeted sequencing of adenoid cystic carcinomas (27 cancer genes). | |
| 2. **Agilent**: Targeted panel of 232 genes. | |
| 3. **AmpliSeq**: Targeted panel of 8 genes. | |
| 4. **ARCHER-HEME-CV1**: ARCHER-HEME gene panel (199 genes). | |
| 5. **ARCHER-SOLID-CV1**: ARCHER-SOLID Gene Panel (62 genes). | |
| These panels are used for targeted sequencing of various cancer types. If you need more detailed information about a specific panel or further exploration, feel free to ask! | |
| >>> |
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