araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 57-year-old male with lung adenocarcinoma; genetic feature: KRAS (G12V), high tumor mutational burden

Clinical trial: A Study to Evaluate Rucaparib in Combination With Nivolumab in Patients With Selected Solid Tumors (ARIES)

Summary: This is an open label Phase 2, 2-stage, 2-cohort study to evaluate rucaparib in combination with nivolumab in patients with high-grade serous or endometroid ovarian cancer, or locally advanced unresectable/metastatic transitional cell urothelial carcinoma.
  Patients entering the following cohorts must have BRCA mutational status confirmed by a central lab:
  -  Cohort A1: No BRCA mutation in tumor; high level of LOH (loss of heterozygosity)
  -  Cohort A2: BRCA mutation in tumor
  Patients entering the following cohort must have a sample of tumor tissue available for mutational analysis:
  -  Cohort B: Urothelial Cancer


Eligibility: General Inclusion Criteria:
  -  ≥ 18 years of age
  -  Adequate organ function
  -  Life expectancy ≥ 16 weeks
  -  Women of childbearing potential must have a negative serum pregnancy test
  Cohort A1 and A2 Ovarian Cancer-Only Inclusion Criteria
  -  High-grade serous or endometrioid epithelial ovarian, fallopian tube, or primary peritoneal cancer
  -  Received 1 or 2 prior regimens, including ≥ 1 prior platinum-based therapy and have platinum-sensitive disease
  -  Relapsed/progressive disease (confirmed by radiologic assessment)
  -  Willing and able to have a biopsy of tumor at screening and after 4 weeks of treatment.
  -  Measurable disease (RECIST v1.1)- Cohort A1 only
  -  ECOG performance status of 0 to 1
  Cohort B Urothelial Cancer-Only Inclusion Criteria
  -  Locally advanced unresectable or metastatic transitional cell carcinoma of the urothelium (including renal pelvis, ureter, urinary bladder, or urethra). Mixed transitional/non-transitional cell histologies are allowed.
  -  Not eligible to receive cisplatin chemotherapy and have declined carboplatin chemotherapy OR had disease progression during or after platinum-containing chemotherapy.
  -  Measurable disease (RECIST v1.1)
  -  Have a sample of tumor tissue available for analysis.
  -  ECOG performance status ≤ 2 (cisplatin ineligible patients) or ECOG performance status ≤ 1 (prior platinum patients)
  General Exclusion Criteria (All patients)
  -  Active second malignancy
  -  Central nervous system brain metastases
  -  Evidence of interstitial lung disease, active pneumonitis, myocarditis, or history of myocarditis.
  -  Active, known or suspected autoimmune disease (eg, autoimmune hepatitis).
  -  Condition requiring systemic treatment with either corticosteroids
  -  Prior treatment with a PARP inhibitor or immune checkpoint inhibitor.
  Cohort A1 and A2 Ovarian Cancer-Only Exclusion Criteria
  -  Non-epithelial tumors (pure sarcomas) or ovarian tumors with low malignant potential (ie, borderline tumors) or mucinous tumors. Mixed Mullerian tumors/carcinosarcomas are allowed.

Relevance to patient case: not relevant
Patient case: 57-year-old male with lung adenocarcinoma; genetic feature: KRAS (G12V), high tumor mutational burden

Clinical trial: K-RAS and EGFR in Lung Cancer

Summary: Retrospective analysis where patients with histologically confirmed Non-small cell lung cancer (NSCLC) were centrally evaluated for the presence of KRAS and EGFR mutations.

Detailed description: A retrospective analysis, performed by the Hellenic Co-operative Oncology Group (HeCOG), in samples from patients with histologically confirmed NSCLC, who had been treated within HeCOG-affiliated centres from March 2000 through December 2012, were centrally evaluated for the presence of KRAS and EGFR mutations. All patients had available clinicopathological data at diagnosis. Formalin-fixed, paraffin-embedded tissue blocks were retrospectively retrieved from the HeCOG tumor repository. Cytologic material was prospectively submitted for genotyping in more recent years (2010-2012).

Eligibility: Inclusion Criteria:
  -  Patients with histologically confirmed NSCLC
  -  Signed and dated written informed consent
  -  Age 18 years
  -  Available cytological material
  Exclusion Criteria: -

Relevance to patient case: possibly relevant
Patient case: 57-year-old male with lung adenocarcinoma; genetic feature: KRAS (G12V), high tumor mutational burden

Clinical trial: INST 1204: PIK3CA Mutations as Biomarkers for Metastasis in Colon Cancer

Summary: This proposal seeks to further understand the contribution of the PIK3CA mutations in colon cancer, by correlating the type of hotspot mutation with the development of metastases in stage II and stage Ill patients.
  In order to do this, DNA will be extracted from either frozen or paraffin embedded colon cancer tissues to sequence PIK3CA, KRAS and BRAF. Clinical outcome data will be gathered to include metastases and survival to correlate with PIK3CA, KRAS and BRAF mutational status. Patients with stage II and stage Ill colon cancers will be identified in the University of New Mexico Human Tissue Repository and the NIH PLCO prevention trial biorepository.
  Existing banked tissues of stage II and Ill colon cancers will be collected. There will be no direct contact with living individuals. Epidemiological factors such as age, race, gender and outcome data of metastases and survival will be collected.

Detailed description: This proposal aims to identify PIK3CA mutations as a biomarker for metastasis.
  In order to do this, DNA will be extracted from either frozen or paraffin embedded colon cancer tissues to sequence PIK3CA, KRAS and BRAF. Clinical outcome data will be gathered to include metastases and survival to correlate with PIK3CA, KRAS and BRAF mutational status. Patients with stage II and stage Ill colon cancers will be identified in the University of New Mexico Human Tissue Repository and the NIH PLCO prevention trial biorepository.
  Existing banked tissues of stage II and Ill colon cancers will be collected. There will be no direct contact with living individuals. Epidemiological factors such as age, race, gender and outcome data of metastases and survival will be collected.
  Specific Aims:
  1. To develop and standardize methods for high throughput DNA extraction and analysis from colon tumors of patients with stage II and stage III disease harboring PIK3CA exon 9 and exon 20 mutations.
  2. To determine the correlation between wild type and PIK3CA, PIK3CA exon 9 and PIK3CA exon 20 mutations and development of metastatic disease and overall survival in stage II and stage III patients with colorectal cancer.

Eligibility: Inclusion Criteria:
  -  Specimen from patients with stage II and stage III colon cancer.
  Exclusion Criteria:
  -  Any other stage or type of disease outside of stage II and stage III colon cancer.

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Safety Study of PLX4032 in Patients With Solid Tumors

Summary: The primary objective of this FIH study is to assess the safety and pharmacokinetics of PLX4032 in patients with solid tumors. The secondary objective is to assess the pharmacodynamic activity in paired biopsy specimens obtained from patients with malignant melanoma who have the V600E BRAF oncogenic mutation.

Detailed description: Activating mutations of the BRAF gene have been observed in a variety of cancers, including 55-68% of malignant melanomas. In general, oncogenic mutations of BRAF correlate with a poor outcome. PLX4032 is a compound that selectively inhibits oncogenic B-Raf kinase.
  Two extension cohorts of patients with confirmed V600E mutations will be recruited, consisting of advanced melanoma and metastatic colorectal carcinoma.

Eligibility: Inclusion Criteria:
  -  Solid tumors confirmed histologically whose tumors are refractory to standard therapy, or for whom standard or curative therapy does not exist
  -  Patients from whom paired melanoma biopsies are planned must have a V600E+ BRAF mutation confirmed prior to the administration of PLX4032
  -  Previous chemotherapy, immunotherapy, or radiation therapy must have been completed at least 2 weeks prior to starting PLX4032 therapy, and all associated toxicity must be resolved prior to administration of PLX4032
  -  Patients in the Extension cohorts (melanoma or adenocarcinoma of the colon or rectum) must have both a V600E+ BRAF mutation and measurable disease (by RECIST V 1.0 criteria) prior to the administration of PLX4032. All patients enrolled must provide archival or fresh melanoma tumor biopsy for confirmation of V600E+ BRAF mutation status by TaqMan assay
  -  ECOG performance status 0 or 1
  -  Life expectancy ≥ 3 months
  -  Adequate hematologic, hepatic, and renal function
  Exclusion Criteria:
  -  Brain metastases that are progressing or have been documented to be stable for less than 3 months, or for which systemic corticosteroids are required
  -  Investigational drug use within 28 days of the first dose of PLX4032
  -  Uncontrolled intercurrent illness
  -  Refractory nausea and vomiting, malabsorption, or significant bowel resection that would preclude adequate absorption

Relevance to patient case: possibly relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Prognostic Significance of Fine-Needle Aspiration Cytology Features in Papillary Thyroid Carcinoma

Summary: The purpose of this study is to investigate the relationship between prognosis and fine needle aspiration cytology character of papillary thyroid cancer.

Detailed description: Papillary thyroid carcinoma is the most common thyroid malignancy worldwide. The influence of clinicopathologic features on prognosis has been examined, but the relationship between cytologic features obtained by fine-needle aspiration (FNA) and prognosis has been minimally studied. We retrospectively studied the cytologic features with computerized morphometry in 83 patients with usual-type papillary thyroid cancer and followed them for more than 10 years except for one with metastasis at diagnosis. The cytologic features of FNA and recurrence of cancer were examined statistically.

Eligibility: Inclusion Criteria:
  -  Papillary thyroid cancer diagnosed in NTUH from 1977 to 2000
  Exclusion Criteria:
  -  Patient without complete medical record

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Pyrosequencing of the BRAFV600E Mutation

Summary: To investigate the diagnostic efficiency of pyrosequencing for the mutant BRAF allele in ultrasound (US)-guided fine needle aspiration biopsies (FNAB) of thyroid incidentalomas.


Eligibility: Inclusion Criteria:
  -  Patients with thyroid nodule larger than 1 cm, or nodule smaller than 1 cm that required further evaluation because of suspicious ultrasound findings
  Exclusion Criteria:
  -  Patients who refuse participation.

Relevance to patient case: possibly relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Prophylactic Central Lymph Node Dissection in Papillary Thyroid Microcarcinoma

Summary: The purpose of this study is to determine whether the prophylactic ipsilateral central lymph node dissection is equally effective in the management of papillary thyroid microcarcinoma(PTMC) to the bilateral central lymph node dissection.

Detailed description: The extent, the advantage and disadvantage of prophylactic central lymph node dissection was not fully established up to now in papillary thyroid microcarcinoma.
  Prophylactic bilateral central lymph node dissection can give a important clinical information about the status of lymph nodes, and possibly guide a further adjuvant treatment. However, it causes high postoperative morbidity, including hypocalcemia and hoarseness. In this respect, some advocate no central lymph node dissection in prophylactic settings.
  Thus, we aimed to prove the efficacy of prophylactic ipsilateral central lymph node dissection in thyroid papillary microcarcinoma, compared to the bilateral dissection and no dissection.
  Type of Study design: Prospective randomized, controlled double-blinded (to subjects and observers) study.
  Group I: Limited/ipsilateral central lymph node dissection (UniCND) Group II: Comprehensive/bilateral central lymph node dissection (BiCND) Group III: No central lymph node dissection (NoCND)
  Outcomes: vocal cord palsy, hypocalcemia, locoregional recurrence, distant metastasis

Eligibility: Inclusion Criteria:
  -  Age: 18 to 70
  -  Sonographically node-negative cytology confirmed thyroid papillary carcinoma
  -  Tumor size less than 1 cm in sonography
  -  Tumor confined to the one lobe of the thyroid gland
  -  One who provides the informed consent
  Exclusion Criteria:
  -  History of radiation treatment to head and neck area
  -  History of other malignancy except thyroid cancer
  -  Poor performance status (ECOG 3-4)

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: A Study of Vemurafenib in Previously Treated Patients With Metastatic Melanoma

Summary: This open-label single arm study will assess the efficacy, safety and tolerability of Vemurafenib in previously treated patients with metastatic melanoma. Patients will receive oral Vemurafenib [RG7204; PLEXXIKON: PLX4032] at a dose of 960 mg b.i.d. continuously until disease progression or withdrawal from study and will be assessed at regular intervals for tumour response and tolerability. Target sample size is <100 patients.


Eligibility: Inclusion Criteria:
  -  adult patients >/=18 years of age
  -  histologically confirmed metastatic melanoma (Stage IV, AJCC)
  -  patients must have completed and failed at least one prior standard of care regimen (e.g. DTIC, temozolomide, etc.)
  -  BRAF V600E positive mutation (by Roche CoDx BRAF mutation assay)
  -  measurable disease by RECIST criteria
  -  negative pregnancy test and, for fertile men and women, effective contraception during treatment and for 6 months after completion
  Exclusion Criteria:
  -  active CNS metastases on CT/MRI within 28 days prior to enrollment
  -  history of or known carcinomatous meningitis
  -  previous treatment with BRAF (sorafenib allowed) or MEK inhibitor
  -  cardiac dysrhythmias >2 NCI CTCAE or treatment with drugs with dysrhythmic potential
  -  uncontrolled hypertension(>150/100mmHg) despite optimal medical therapy
  -  infectious disease including HIV, HBV and HCV

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Nexavar® Versus Placebo in Locally Advanced/Metastatic RAI-Refractory Differentiated Thyroid Cancer

Summary: Trial of sorafenib versus placebo in the treatment of locally advanced or metastatic differentiated thyroid cancer refractory to radioiodine

Detailed description: Eligible subjects were randomized 1:1 to sorafenib 800 mg daily or matching placebo. Progression was assessed every 8 weeks by modified RECIST criteria. Subjects had the option to unblind study treatment after progression and to receive open label sorafenib regardless of initial treatment assignment. Following discontinuation of study treatment, subjects were followed for survival every 3 months in long-term follow-up. Subjects who terminated study treatment (either double only or double blind and open label) for reasons other than death, lost to follow-up or consent withdrawn entered long-term follow up

Eligibility: Inclusion Criteria:
  -  Locally advanced or metastatic differentiated thyroid cancer (papillary, follicular and Hurthle cell)
  -  Poorly differentiated and other thyroid variants (e.g. insular, tall cell, etc.) are eligible provided that the histology has no medullary differentiation nor anaplastic features
  -  Progression within 14 months (RECIST [Response Evaluation Criteria in Solid Tumors] should be used as a basis for the assessment of disease progression)
  -  RAI (radioactive iodine) refractory
  Exclusion Criteria:
  -  Histologic subtypes of thyroid cancer other than differentiated (i.e. like anaplastic and medullary carcinoma, lymphoma or sarcoma)
  -  Prior anti-cancer treatment with tyrosine kinase inhibitors, monoclonal antibodies (licensed or investigational) that target VEGF (vascular endothelial growth factor) or VEGF Receptors or other targeted agents
  -  Prior anti-cancer treatment for thyroid cancer with use of chemotherapy (low dose chemotherapy for radiosensitization is allowed) or Thalidomide or any of its derivatives

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: A Study of Vemurafenib (RO5185426) in Comparison With Dacarbazine in Previously Untreated Patients With Metastatic Melanoma (BRIM 3)

Summary: This randomized, open-label study evaluated the efficacy, safety and tolerability of vemurafenib (RO5185426) as compared to dacarbazine in previously untreated patients with metastatic melanoma. Patients were randomized to receive either vemurafenib 960 mg orally twice daily or dacarbazine 1000 mg/m2 intravenously every 3 weeks. Study treatment was continued until disease progression or unacceptable toxicity occurred. The data and safety monitoring board recommended that patients in the dacarbazine group be allowed to cross over to receive vemurafenib, and the protocol was amended accordingly on January 14, 2011, as both overall survival and progression-free survival endpoints had met the prespecified criteria for statistical significance in favor of vemurafenib.


Eligibility: Inclusion Criteria:
  -  adults, >/=18 years of age
  -  metastatic melanoma, stage IIIC or IV (AJCC)
  -  treatment-naïve (no prior systemic anticancer therapy)
  -  positive for BRAF V600E mutation
  -  measurable disease by RECIST criteria
  -  negative pregnancy test and, for fertile men and women, effective contraception during treatment and for 6 months after completion
  Exclusion Criteria:
  -  active central nervous system metastases
  -  history of carcinomatous meningitis
  -  severe cardiovascular disease within 6 months prior to study drug administration
  -  previous malignancy within 5 years prior to study, except for basal or squamous cell carcinoma of the skin, melanoma in-situ, or carcinoma in-situ of the cervix

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Safety and Efficacy Study of BMS-908662 Alone or in Combination With Cetuximab in Subjects With K-RAS or B-RAF Mutation Positive Advanced or Metastatic Colorectal Cancer

Summary: The purpose of the study is to identify a safe and tolerable dose of BMS-908662 in combination with cetuximab; and then to evaluate the tumor response to BMS-908662 when administered alone or in combination with cetuximab

Detailed description: Phase 1: Single Arm Study
  Phase 2: Randomized Controlled, Parallel

Eligibility: Inclusion Criteria:
  -  Subjects with K-RAS (codon 12 or 13) or B -RAF (V600E) mutation positive advanced or metastatic colorectal cancer who have relapsed or are refractory to 2 or more standard systemic anticancer regimes for metastatic disease, or are intolerant to existing therapies.
  -  Histologic or cytologic confirmation of the diagnosis.
  -  Eastern Cooperative Oncology Group (ECOG) ≤ 1
  -  Adequate organ & marrow function.
  Exclusion Criteria:
  -  Uncontrolled or significant cardiovascular disease.
  -  Phase 2: Prior therapy with a RAF inhibitor.

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: Prophylactic Selective Lateral Neck Dissection in Patients With Papillary Thyroid Carcinoma

Summary: The purpose of this study is to prospectively analyze the incidence of occult lateral neck metastasis (LNM) and to elucidate the factors that predict LNM in papillary thyroid carcinoma (PTC) with central neck metastasis (CNM) by performing prophylactic selective lateral neck dissection (SND).

Detailed description: The lymphatic drainage pattern of the thyroid is uniform and consistent, and therefore, metastatic patterns are relatively predictable. Initial nodal metastasis in PTC usually occurs in the paratracheal and pretracheal nodes in level VI of the central compartment of the ipsilateral neck and spreads to the lateral cervical lymph nodes. Macroscopic skip metastases to the lateral compartment of the neck in the absence of central disease are uncommon.

Eligibility: Inclusion Criteria:
  -  Papillary thyroid carcinoma with central neck metastasis
  -  No evidence of lateral neck metastasis as determined by high-resolution neck ultrasonography and computed tomography
  Exclusion Criteria:
  -  History of previous thyroid operation
  -  Isthmic thyroid lesion

Relevance to patient case: not relevant
Patient case: 51-year-old female with papillary thyroid carcinoma; genetic feature: BRAF (V600E)

Clinical trial: A Pharmacokinetic/Pharmacodynamic Study of RO5185426 in Previously Treated Patients With Metastatic Melanoma

Summary: This open-label study will assess the pharmacokinetics, efficacy and safety of RO5185426 administered as 240mg tablets in previously treated patients with metastatic melanoma. Patients will be randomized to receive one of four dose-levels of RO5185426 [RG7204; PLEXXIKON; PLX4032] orally twice daily on days 1 to 15 (morning dose). Starting on day 22, treatment with RO5185426 may be resumed at a dose of 960 mg twice daily and continued until disease progression. Target sample size is <100 patients.


Eligibility: Inclusion Criteria:
  -  adult patients, >/=18 years of age
  -  histologically confirmed metastatic melanoma, stage IIIc or IV (AJCC)
  -  failure of at least one prior standard of care regimen
  -  positive for BRAF V600E mutation (by Roche CoDx BRAF mutation assay)
  -  ECOG performance status 0 or 1
  -  adequate hematologic, renal and liver function
  Exclusion Criteria:
  -  active CNS lesions on CT/MRI within 28 days prior to enrollment
  -  history of spinal cord compression o carcinomatous meningitis
  -  anticipated or ongoing anti-cancer therapies other than those administered in this study
  -  previous treatment with BRAF inhibitor (sorafenib allowed) or MEK inhibitor
  -  severe cardiovascular disease within 6 months prior to study
  -  previous malignancy within the past 5 years except for basal or squamous cell carcinoma of the skin, melanoma in-situ and carcinoma in-situ of the cervix

Relevance to patient case: not relevant