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gpt-3.5-turbo_2shot.json
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gpt-3.5-turbo_2shot.json
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{
"results": [
{
"prompt": "As an intelligent assistant, your task is to extract, process, and structure biomarkers from the clinical trials input that starts after the word \"INPUT:\". You must maintain the logical connections (AND, OR) between biomarkers and follow the provided instructions using Chain of Thought, reasoning, and common sense.\n\nINSTRUCTIONS: \nReturn a JSON in the following format: {{\"inclusion_biomarker\": [], \"exclusion_biomarker\": []}}. Each key contains a list of lists of strings, where each inner list represents a set of genomic biomarkers required for patient inclusion or exclusion in the trial.\n\nExtract biomarkers from the input only and avoid any information from the instructions. Focus on extracting biomarkers in the following categories: gene alteration (single mutation, fusion, rearrangement, copy number alteration, deletion, insertion, translocation), pathway alteration, gene expression, protein expression, path-way expression, HLA, TMB (tumor molecular burden, TMB-H or TMB-L), MSI (microsatellite instability, MSI-H, MSI-L, MSS, microsatellite stable) status, gene pathway alterations like dMMR (deficient Mismatch Repair Pathway) or pMMR (proficient Mismatch Repair), protein status, and HER2, ER, PgR, PD-L1 positive or negative status. Ignore any items that don't fall into these categories. Place the extracted biomarkers under the appropriate key, \"inclusion_biomarker\" or \"exclusion_biomarker\", based on whether they are required for patient inclusion or exclusion in the trial.\n\nOmit information related to age, medical condition, potential pregnancy, stage or phase of disease, allergies, treatment history, histology, specific cancer type, diseases or conditions, HIV, and infections. Disregard data about levels, scores, doses, or ratio of expression, as well as any illnesses. Do not extract biomarkers associated with model experimental animals or historical data or previous studies.\n\nPreserve the logical connection (AND, OR) between biomarkers in the input. Group biomarkers connected by 'AND' in the same list and place biomarkers connected by 'OR' in separate lists. Treat each main bullet in the \"Inclusion Criteria\" section as AND logic (unless specified as OR or different ARM/cohort) and main bullets in the \"Exclusion Criteria\" section as OR logic (unless explicitly stated otherwise). Handle ambiguous (AND, OR) logic by considering it as OR .\n\nProcess the biomarkers to ensure each one presents the gene name followed by the variant. Remove the words \"gene\", \"allele\", and \"status\" from the biomarker. Remove the term \"mutation\" from the biomarker when there's has a specific variant in the string (e.g CCND1 P287T mutation becomes CCND1 P287T). Make sure the variant is singular and noun-based (e.g \"translocated\" becomes \"translocation\"). Replace \"mutant\" with \"mutation\". Insert a space between the gene name and its variant, and also between the status and the hormone name. Replace the expression \"positive expression\" with just \"expression\". Replace symbols \"-\" and \"+\" with \"negative\" and \"positive\" respectlively, unless it's in the MSI status or known fusions separated by \"-\". When \"germline\" or \"somatic\" terms are mentioned in the input, place them in parentheses at the end of the corresponding biomarker. Ignore any biomarker mentioned as an \"exception\" or after \"other than\". Handle synonyms found in parentheses by extracting the biomarker but ignoring the synonym. Extract each biomarker once. Make sure to expand the biomarkers when needed.\n\nBefore returning the JSON output, remove any empty lists and stray empty lists caused by having no biomarkers in a category, ensuring that the keys \"inclusion_biomarker\" and \"exclusion_biomarker\" have just an empty list [] if there are no biomarkers in that category.\n\nBelow is only an example used for demonstration.\nEXAMPLE 1: {example}\nBelow is only an example used for demonstration.\nEXAMPLE 2: {example2}\n\nINPUT: {trial}\nJSON:",
"Model": "gpt-3.5-turbo",
"predicted_size": 50,
"failed_size": 0,
"Precited": [
{
"inclusion_biomarker": [],
"exclusion_biomarker": [
"HIV",
"HBV",
"HCV"
]
},
{
"inclusion_biomarker": [
[
"NPM1 alteration"
],
[
"KMT2A alteration"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"ALK translocation"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"DNMT inhibitor"
],
[
"DLBCL"
],
[
"DLBCL",
"relapsed"
],
[
"DLBCL",
"refractory"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"IDH1 R132H"
],
[
"TMZ"
],
[
"TP53 mutation"
],
[
"ASXL1 mutation"
],
[
"EZH2 mutation"
],
[
"RUNX1 mutation"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"PD-1 inhibitor",
"CTLA-4 inhibitor",
"IDH1 R132H"
],
[
"PD-1 inhibitor",
"CTLA-4 inhibitor",
"BRAF mutation"
],
[
"PD-1 inhibitor",
"CTLA-4 inhibitor",
"BRAF/MEK combination therapy"
]
],
"exclusion_biomarker": [
"autoimmune disease",
"CNS metastases",
"systemic infections",
"HIV infection",
"chronic hepatitis B or C"
]
},
{
"inclusion_biomarker": [
[
"CD30 expression"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"CD19 mutation"
],
[
"DLBCL"
],
[
"PMLBCL"
],
[
"TFL"
],
[
"HGBCL"
],
[
"CD19 mutation",
"DLBCL"
],
[
"CD19 mutation",
"PMLBCL"
],
[
"CD19 mutation",
"TFL"
],
[
"CD19 mutation",
"HGBCL"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"PIK3CA mutation"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"PD-1"
],
[
"LAG-3"
],
[
"PD-1",
"LAG-3"
],
[
"PD-L1"
],
[
"PD-1",
"PD-L1"
],
[
"PD-L1",
"PD-1"
],
[
"PD-1",
"LAG-3"
],
[
"PD-L1",
"LAG-3"
],
[
"PD-1",
"PD-L1",
"LAG-3"
]
],
"exclusion_biomarker": [
"Pregnancy",
"lactation",
"breastfeeding",
"CNS metastases",
"second malignancy",
"HIV",
"hepatitis B",
"hepatitis C",
"autoimmune disease",
"immune deficiency",
"CAR-T therapies",
"immunosuppressive therapy",
"EGFR mutation",
"ALK rearrangement",
"ROS1 translocation",
"BRAFV600E mutation",
"NTRK translocation",
"immunomodulatory agents",
"neo-adjuvant anti-PD-1 therapy"
]
},
{
"inclusion_biomarker": [],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"CD19 expression"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"PIK3CA mutation"
],
[
"PIK3CB mutation"
],
[
"PIK3CD mutation"
],
[
"PIK3CG mutation"
],
[
"PIK3R1 mutation"
],
[
"PIK3R2 mutation"
],
[
"PIK3R3 mutation"
],
[
"PIK3C2G mutation"
],
[
"PIK3C3 mutation"
],
[
"INPP4A mutation"
],
[
"INPP4B mutation"
],
[
"INPPL1 mutation"
],
[
"INPP5D mutation"
],
[
"PTEN mutation"
],
[
"AKT1 mutation"
],
[
"AKT2 mutation"
],
[
"AKT3 mutation"
],
[
"MTOR mutation"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"RET alteration"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"MTAP deletion"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"FGFR1 fusion"
],
[
"FGFR2 fusion"
],
[
"FGFR3 fusion"
],
[
"FGFR1 P150S"
],
[
"FGFR1 T340M"
],
[
"FGFR1 R445W"
],
[
"FGFR1 N546K"
],
[
"FGFR1 K656E"
],
[
"FGFR2 C62Y"
],
[
"FGFR2 A67V"
],
[
"FGFR2 N82K"
],
[
"FGFR2 D101Y"
],
[
"FGFR2 E160K"
],
[
"FGFR2 E163K"
],
[
"FGFR2 M186T"
],
[
"FGFR2 R203H"
],
[
"FGFR2 R210Q"
],
[
"FGFR2 Q212K"
],
[
"FGFR2 R251Q"
],
[
"FGFR2 S252W"
],
[
"FGFR2 P253R"
],
[
"FGFR2 P253L"
],
[
"FGFR2 A264T"
],
[
"FGFR2 W290C"
],
[
"FGFR2 K310R"
],
[
"FGFR2 Y328N"
],
[
"FGFR2 G364E"
],
[
"FGFR2 Y375C"
],
[
"FGFR2 C382R"
],
[
"FGFR2 A389T"
],
[
"FGFR2 V392A"
],
[
"FGFR2 R399Q"
],
[
"FGFR2 H416R"
],
[
"FGFR2 I422V"
],
[
"FGFR2 H544Q"
],
[
"FGFR2 N549H"
],
[
"FGFR2 N549K"
],
[
"FGFR2 N549D"
],
[
"FGFR2 N549S"
],
[
"FGFR2 L560F"
],
[
"FGFR2 K659E"
],
[
"FGFR2 K659N"
],
[
"FGFR2 R664W"
],
[
"FGFR2 E718K"
],
[
"FGFR2 S791T"
],
[
"FGFR3 G380E"
],
[
"FGFR3 G380R"
],
[
"FGFR3 A391E"
],
[
"FGFR3 K650T"
],
[
"FGFR3 K650E"
],
[
"FGFR3 K650Q"
],
[
"FGFR3 K650N"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"KK-LC-1 expression"
],
[
"HLA-A*01:01 allele"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"HER2 positive"
],
[
"TNBC"
],
[
"HR positive",
"HER2 negative"
]
],
"exclusion_biomarker": [
[
"central nervous system metastasis"
]
]
},
{
"inclusion_biomarker": [
[
"tPALB2 mutation"
]
],
"exclusion_biomarker": [
[
"VUS PALB2 variant"
],
[
"BRCA1 mutation"
],
[
"BRCA2 mutation"
]
]
},
{
"inclusion_biomarker": [
[
"AML"
],
[
"RECIST v1.1"
]
],
"exclusion_biomarker": [
"HIV",
"HBV",
"HCV"
]
},
{
"inclusion_biomarker": [],
"exclusion_biomarker": [
"TGF-\u03b2 antagonist",
"IL-15",
"TGF-\u03b2 antagonist",
"IL-15"
]
},
{
"inclusion_biomarker": [
[
"EGFR L858R"
],
[
"EGFR exon 19 deletion"
]
],
"exclusion_biomarker": [
"T790M"
]
},
{
"inclusion_biomarker": [
[
"EGFR p.L858R"
],
[
"EGFR del19"
]
],
"exclusion_biomarker": [
[
"MET amplification"
],
[
"EGFR mutations other than EGFR del19, p.L858R or p.T790M"
],
[
"brain metastases"
],
[
"HIV infection"
],
[
"hepatitis B"
],
[
"hepatitis C"
],
[
"interstitial lung disease"
],
[
"interstitial pneumonitis"
]
]
},
{
"inclusion_biomarker": [
[
"CD19 positive"
]
],
"exclusion_biomarker": [
"hepatitis B",
"hepatitis C",
"HIV"
]
},
{
"inclusion_biomarker": [
[
"HER2 exon 20 insYVMA"
],
[
"HER2 insGSP"
],
[
"HER2 insTGT"
],
[
"HER2 L755A"
],
[
"HER2 L755S"
],
[
"HER2 V777L"
],
[
"HER2 V659E"
],
[
"HER2 S310F"
],
[
"HER2 amplification"
],
[
"HER2 amplification"
],
[
"HER2 amplification"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"CD137"
],
[
"Pembrolizumab"
],
[
"MK-3475"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"PDGFRA exon 18 D842V"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"CCNE1 copy number amplification"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"B-cell malignancies"
],
[
"IDH1 R132H"
],
[
"WM"
],
[
"FL"
],
[
"MCL"
],
[
"MZL"
],
[
"DLBCL"
],
[
"HCL"
],
[
"CLL"
],
[
"IDH1 R132H",
"TP53 mutation"
],
[
"IDH1 R132H",
"ASXL1 mutation"
],
[
"IDH1 R132H",
"EZH2 mutation"
],
[
"IDH1 R132H",
"RUNX1 mutation"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"JAK2 V617F mutation"
],
[
"FLT3 kinase"
],
[
"CDK4/6"
],
[
"LCK"
],
[
"LN"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"CBFB-MYH11"
],
[
"RUNX1-RUNX1T1"
],
[
"FLT3 mutation"
],
[
"NPM1 mutation"
],
[
"CEBPa mutation"
],
[
"AML with myelodysplasia-related changes"
]
],
"exclusion_biomarker": [
"t(9;22)"
]
},
{
"inclusion_biomarker": [
[
"BCR-ABL"
],
[
"IDH1 R132H"
],
[
"Ph chromosome"
],
[
"IDH1 R132H",
"BCR-ABL"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"ALK positive"
],
[
"ALK inhibitor naive"
],
[
"ALK positive",
"IDH1 R132H mutation"
]
],
"exclusion_biomarker": [
[
"pancreatitis"
],
[
"diabetes mellitus"
],
[
"interstitial lung disease"
],
[
"uncontrolled heart disease"
],
[
"hypersensitivity to LDK378 excipients"
],
[
"GI disease"
],
[
"CYP3A4/5 inhibitors"
],
[
"QT prolonging medications"
],
[
"warfarin sodium"
],
[
"corticosteroids"
],
[
"major surgery"
],
[
"enzyme-inducing anticonvulsants"
],
[
"pregnant"
],
[
"nursing"
],
[
"child-bearing potential"
]
]
},
{
"inclusion_biomarker": [
[
"EGFR mutation"
],
[
"EGFR C797S mutation"
],
[
"T790M mutation"
],
[
"19del mutation"
],
[
"21L858R mutation"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"PD-1/PD-L1 antibodies",
"cutaneous melanoma"
],
[
"PD-1/PD-L1 antibodies",
"non-small cell lung cancer"
],
[
"PD-1/PD-L1 antibodies",
"small cell lung cancer"
],
[
"PD-1/PD-L1 antibodies",
"renal cell carcinoma"
],
[
"PD-1/PD-L1 antibodies",
"head and neck squamous cell cancer"
],
[
"PD-1/PD-L1 antibodies",
"microsatellite instability-high/mismatch repair deficient cancer"
],
[
"PD-1/PD-L1 antibodies",
"gastric cancer"
],
[
"PD-1/PD-L1 antibodies",
"esophageal cancer"
],
[
"PD-1/PD-L1 antibodies",
"cervical cancer"
],
[
"PD-1/PD-L1 antibodies",
"merkel cell carcinoma"
],
[
"PD-1/PD-L1 antibodies",
"endometrial carcinoma"
],
[
"PD-1/PD-L1 antibodies",
"tumor mutation burden-high"
],
[
"PD-1/PD-L1 antibodies",
"cutaneous squamous cell carcinoma"
],
[
"PD-1/PD-L1 antibodies",
"triple-negative breast cancer"
],
[
"HER2+",
"breast cancer",
"trastuzumab",
"pertuzumab"
],
[
"HER2+",
"gastric cancer",
"trastuzumab"
],
[
"HER2+",
"solid tumor",
"HER2 status",
"U.S. Food and Administration approved test"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"PIK3CA mutation"
],
[
"PTEN loss"
]
],
"exclusion_biomarker": []
},
{
"inclusion_biomarker": [
[
"ABL F317L"
],
[
"ABL F317V"
],
[
"ABL F317I"
],
[
"ABL F317C"
],
[
"ABL V299L"
],
[
"ABL T315A"
],
[
"ABL Y253H"
],
[
"ABL E255K"
],
[
"ABL E255V"
],
[
"ABL F359C"
],
[
"ABL F359V"
],
[
"ABL F359I"
],
[
"ABL T315I"
]
],
"exclusion_biomarker": [
[
"T315I"
],
[
"Y253F"
],
[
"Y253H"
],