araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 70-year-old male with gastrointestinal stromal tumor; genetic feature: KIT (V654A)

Clinical trial: Magnetic Resonance Imaging Screening in Li Fraumeni Syndrome

Summary: This study is aimed at exploring the use of whole body MRI for early cancer detection in TP53 mutation carriers and population controls, with the hypothesis that more cancers will be detected in the TP53 mutation carrier group. A secondary end-point will be the number of incidental findings detected and subsequent investigations required. A series of questionnaires will be used to assess the psychological impact of screening on both the study and control group.


Eligibility: Inclusion Criteria:
  -  Carrier of germline TP53 mutation which, in the view of the geneticist, is not known to be low penetrance OR non-related individual with no personal history of malignancy and no first degree relatives diagnosed with malignancy under the age of 50 years
  -  Please note, TP53 carrier cohort is complete and no longer open to recruitment
  -  Age between 18 and 60
  -  Able to give informed consent
  Exclusion Criteria:
  -  Individual with low penetrance TP53 mutation
  -  Individual with TP53 variant of unknown significance.
  -  Previous malignancy diagnosed < 5 years ago in TP53 carriers (except non-melanomatous skin cancer or cervical CIS) Previous history of malignancy in non-related controls (except non-melanomatous skin cancer or cervical CIS)
  -  Current symptoms suggestive of malignancy
  -  Contraindication to MRI (such as non-MR compatible metal implants) as specified by the standard MR safety checklist
  -  Claustrophobia
  -  ECOG performance status >2

Relevance to patient case: not relevant
Patient case: 70-year-old male with gastrointestinal stromal tumor; genetic feature: KIT (V654A)

Clinical trial: Trial to Assess the Efficacy of Midostaurin (PKC412) in Patients With c-KIT or FLT3-ITD Mutated t(8;21) AML

Summary: To assess the efficacy of tyrosine-kinase inhibitor midostaurin in c-KIT or FLT3-ITD mutated t(8;21) AML. To assess the efficacy of midostaurin depending on the type of c-KIT mutation

Detailed description: AML patients displaying t(8;21) have a relatively favourable outcome. Nevertheless, only approximately 50% of patients carrying this cytogenetic aberration are alive at 5 years. This suggests that some patients have more aggressive leukemic phenotypes and indicates the need for treatment optimization with novel therapies.
  The mutated KIT gene as well as the FLT3-ITD mutation have recently been identified as factors most likely to explain the heterogeneous clinical outcomes within the group of t(8;21) AML. The FLT3 and c-KIT genes encode type III receptor tyrosine kinases (RTK) with important and partly redundant functions in early hematopoietic stem cells. Various activating mutations have been described for both genes. For c-KIT, the incidence ranges from 17 to 48% depending on the source population and type of mutations determined. It has been consistently shown that in AMLs with t(8;21), mutated c-KIT is associated with a dramatically increased risk of relapse and reduced overall survival compared to their unmutated counterparts. The FLT3-ITD mutation has a similar negative effect on prognosis in the patient group of t(8;21) mutated AMLs as c-KIT.
  PKC412 (midostaurin) is known to inhibit the c-KIT RTK activity as well as the FLT3 kinase, both in patients with ITD and TKD mutations. It should therefore be possible to abrogate the negative impact of pathologically increased c-KIT or FLT3-ITD activity on relapse and overall survival by using midostaurin in this patient population. Aim of the proposed clinical trial is to prove the efficacy of midostaurin in c-KIT or FLT3-ITD mutated t(8;21)- AMLs in an open-label one-arm design.

Eligibility: Inclusion Criteria:
  -  Diagnosis of c-KIT mutated t(8;21) AML i.e.
  1. >20% myeloid blasts in bone marrow and/or peripheral blood at initial diagnosis
  2. Plus cytogenetic diagnosis of aberration t(8;21)/AML1-ETO
  3. Plus mutation of c-KIT gene (mut-KIT17 or mut-KIT8) or FLT3-ITD mutation or both c-KIT and FLT3-ITD mutations
  -  Chemoresponsive disease as determined by early bone marrow assessment on day 14-16 after first cycle of induction therapy with cytarabine in combination with daunorubicine or idarubicine, or mitoxantrone- Fit for further intensive chemotherapy
  -  Age 18-65 years
  -  ECOG performance status of 0-2
  -  Life expectancy of at least 12 weeks
  Exclusion Criteria:
  -  Primary refractory or previously relapsed AML
  -  Non-eligibility for high-dose cytarabine based consolidation, e.g. intolerance to cytarabine
  -  Inability to swallow oral medications
  -  Symptomatic congestive heart failure
  -  Bilirubin >2.5 x upper limit of normal

Relevance to patient case: not relevant
Patient case: 70-year-old male with gastrointestinal stromal tumor; genetic feature: KIT (V654A)

Clinical trial: XL999 Administered Intravenously to a Subject With Advanced Malignancies

Summary: Cancer is a worldwide clinical and economic problem. Conventional approaches to treating cancer include surgery, radiotherapy, and cytotoxic chemotherapy as single modalities or as combined therapies. Recently, targeted therapies including antibodies and small molecule inhibitors have also demonstrated clinical benefit. It is now possible to study different genetic lesions involved in cancer types due to advances in genomic methodologies. The investigational drug in this study, XL999 inhibits multiple receptor tyrosine kinases, including VEGF receptor (VEGFR2/KDR), platelet derived growth factor receptors (PDGFRβ), fms-like tyrosine kinase receptor 3 (FLT3), fibroblast growth factor receptors (FGFR1, FGFR3), RET, and KIT, and thus, interferes with multiple cellular processes simultaneously and will likely have effects on the integrity of tumor neovasculature and angiogenesis. Together with the ability to induce a novel cell cycle arrest, the spectrum of activities that XL999 exhibits may reduce both tumor cell proliferation and angiogenesis in the clinic.
  The rationale and purpose of this maintenance study is to allow a subject receiving clinical benefit from XL999 to continue treatment.


Eligibility: Inclusion Criteria:
  -  The subject is eligible to continue to receive XL999 in the absence of progressive disease and unacceptable XL999-related toxicity.
  Exclusion Criteria:
  -  Progressive disease.

Relevance to patient case: not relevant
Patient case: 70-year-old male with gastrointestinal stromal tumor; genetic feature: KIT (V654A)

Clinical trial: The Oncopanel Pilot (TOP) Study

Summary: The BCCA Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes.
  The purpose of this pilot study is to assess the feasibility and effect on clinical-decision-making of the Oncopanel test. Eligible patients are those with advanced lung, colorectal, melanoma and GIST cancers and patients with diagnosed malignancies being considered for clinical trials.

Detailed description: Somatic mutations in solid tumors represent an established means of characterizing malignancies for prognostic, diagnostic and therapeutic purposes. Mutations in EGFR, KRAS, BRAF, and KIT and PDGFRA genes direct therapy in patients with advanced lung, colorectal, melanoma, and GIST tumors, respectively. Known or novel mutations in other genes may also be of clinical significance but are not identified by current genotyping offered to BC Cancer Agency (BCCA) patients. Furthermore, numerous candidate genes have been implicated as potential prognostic and predictive biomarkers in patients with solid tumours. As such, the Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes. The following clinically relevant set of genes and exons are included in the Oncpanel: KRAS, EGFR, BRAF, NRAS and HRAS, PIK3CA Signal Transduction Pathway Genes, RAS-RAF-MEK-MAPK Pathway, HER2, IDH1 and IDH2, ALK, TP53, c-KIT, STAT1&3 and PDGFRA. Additional testing on the tumour material will also include analysis of specific gene variants associated with adverse events or response to therapy.
  Numerous studies have documented the presence of circulating tumour DNA (ctDNA) among patients with advanced and early stage malignancies (20-22). The ability to diagnose standard cancer mutations with a blood-based assay (a "liquid biopsy") has not yet been established but presents obvious advantages. The emergence of "resistance" mutations arising in the metastatic tumor or throughout the course of therapy is well documented (21, 22). A blood biopsy may represent more accurate determination of the tumor's genetic features than archival DNA specimen. Adequate tissue specimens can be difficult to obtain from some patients with diagnosed malignancies, particularly lung cancer. A blood biopsy may represent a less invasive and timelier means of diagnosing both standard and translational cancer mutations.

Eligibility: Patients with archival tumor tissue and a known history of invasive malignancies are eligible if they meet one or more of the following criteria:
  -  Advanced colorectal cancer and eligible for standard KRAS testing,
  -  Advanced non-small cell lung cancer and eligible for standard EGFR testing,
  -  Advanced melanoma and eligible for standard BRAF testing,
  -  Gastrointestinal stromal tumors (GISTs) eligible for standard c-KIT and PDGFRA testing,
  -  Being considered for potential eligibility in clinical trial.

Relevance to patient case: not relevant
Patient case: 70-year-old male with gastrointestinal stromal tumor; genetic feature: KIT (V654A)

Clinical trial: Prospective Cohort Study of the Clinical Applications for the Pathologic Type, Staging, and Grading of GIST

Summary: Evaluate the reliability of morphology standards for GIST pathologic type, staging and grading by retrospective analyzing clinical data; on this basis, establish a GIST standardized and individualized treatment mode to maximum benefit GIST patients, avoid under- and over-treatment.

Detailed description: 1. Retrospective analysis of GIST cases in the recent five years: the GIST clinical data of Fudan University Zhongshan Hospital from 2007 January to 2012 December were collected. By reviewing the HE slides, GIST was evaluated by 12 indicators, NIH scheme and WHO standard. Accomplish the gene sequencing of KIT, PDGFRA, B-raf, and SDH. Follow up the patients about their treatment and prognosis. Analyze and compare the advantages and disadvantages of the histomorphology indicators, NIH scheme, and WHO standard.
  2. Organize the first prospective cohort study of GIST individualized treatment based on the histomorphology. Obtain the evidence of histological assessment for GIST by following up patients for 3 years.
  3. Establish an evaluation criteria based on the morphology of GIST. Make objective evaluations about GIST tumor size, tumor location and gene mutation status in the prognosis estimate. Make rules to effectively guide individualized treatment of GIST.

Eligibility: All patients pathologically diagnosed with GIST during the period from 2013 to 2015

Relevance to patient case: definitely relevant
Patient case: 70-year-old male with gastrointestinal stromal tumor; genetic feature: KIT (V654A)

Clinical trial: Circulating Cell-free Tumor DNA in the Plasma of Patients With Gastrointestinal Stromal Tumors (GIST)

Summary: This observational study is proposed to evaluate if the trend in the levels of cf-DNA evaluated on a sample of peripheral blood may be related to different clinical behaviors of the disease monitored by radiological investigations conducted.

Detailed description: Demetri and colleagues presented, at the AACR and ASCO Annual Meeting 2013, an exploratory analysis to assess GIST genotypes on patients in the GRID study. Mutations in the KIT gene were detected in 58 percent of the blood samples compared with 66 percent of the tumor tissue samples (31). However, when focusing their analysis on secondary KIT mutations, which are the mutations that drive resistance to targeted therapies like imatinib and sunitinib, the researchers found mutations in 47 percent of blood samples compared with only 12 percent of tissue samples. In addition, nearly half of blood samples in which secondary KIT mutations were found, harbored multiple secondary mutations. Therefore, cf-DNA may become an efficient marker of mutational GIST status and disease itself.
  On this basis, this trial aims to evaluate whether tumor DNA carrying mutations (for KIT, PDGFRα, BRAF, RAS, SDH) can be detected and quantified in the plasma of patients with GISTs, either with active disease or during follow-up, and whether detection can be correlated with the disease status.

Eligibility: -  Male or female patients aged >= 18 years
  -  Histologically confirmed diagnosis of GIST of any anatomical location either by biopsy or surgical specimen
  -  Available archival tumor tissue
  -  Signed informed consent form
  Exclusion Criteria:
  -  Impossibility to ensure adequate clinical and serum sample follow-up
  -  Serious psychiatric disease that precludes informed consent or limits compliance

Relevance to patient case: not relevant
Patient case: 70-year-old male with gastrointestinal stromal tumor; genetic feature: KIT (V654A)

Clinical trial: Patients With Refractory, Metastatic Cancer Harboring KIT Mutation or Amplification to Investigate the Clinical Efficacy and Safety of Imatinib Therapy

Summary: KIT is a receptor tyrosine kinase that binds to stem-cell factor (SCF), activating a series of downstream effector pathways. KIT is an established therapeutic target in cancer with activating mutations of KIT, such as gastrointestinal stromal tumors (GIST), and significant benefit is achieved with various small molecule inhibitors of KIT such as imatinib mesylate. Moreover, there is increasing evidence implicating KIT mutations as tractable therapeutic targets in melanoma. Additional information is required to characterize the functional role of low-frequency mutations in KIT and to determine whether amplification of wild type KIT is a real driver that can be targeted therapeutically. Except GIST and melanoma, other solid cancers were reported to have KIT mutation even in low frequency. A molecular profiling of the tumors of patients referred to the phase I clinic at the M.D. Anderson Cancer Center showed KIT mutation in 7 patients in total of 431 patients (2%).
  Hence, the investigators planned this study to apply the molecularly targeted agent, imatinib to various types of cancers harboring KIT mutation or amplification.


Eligibility: Inclusion Criteria:
  1. age ≥ 20
  2. advanced, refractory cancer patients who failed standard of care (SOC)
  3. KIT aberration: defined as mutation in exons 9, 11, 13, 17 or 18, or nanostring CNV by quantitative PCR (greater than 3 copies) or subject with specific sensitivity (Z-score<-1) to imatinib by Avatar scan whose disease has progressed following standard therapy or that has not responded to standard therapy or for which there is no standard therapy
  4. ECOG performance status of 0~2
  5. measurable or evaluable lesion per RECIST 1.1 criteria
  6. adequate marrow, hepatic, renal and cardiac functions
  -  Serum aspartate transaminase (AST) and serum alanine transaminase (ALT) ≤ 2.5 x upper limit of normal (ULN), or AST and ALT ≤ 5 x ULN if liver function abnormalities are due to underlying malignancy
  -  Total serum bilirubin ≤ 1.5 x ULN
  -  Absolute neutrophil count(ANC) ≥ 1,500/uL
  -  Platelets ≥ 100,0000/uL
  -  Hemoglobin ≥ 9.0 g/dL
  7. provision of a signed written informed consent
  Exclusion Criteria:
  1. severe co-morbid illness and/or active infections
  2. pregnant or lactating women
  3. history of major surgery or radiotherapy within 4 weeks
  4. active CNS metastases not controllable with radiotherapy or corticosteroids (however, CNS metastases (except for leptomeningeal seeding) are allowed if controlled by gamma knife surgery or surgery or radiotherapy or steroid)
  5. known history of hypersensitivity to study drugs

Relevance to patient case: possibly relevant
Patient case: 70-year-old male with gastrointestinal stromal tumor; genetic feature: KIT (V654A)

Clinical trial: Non Invasive Detection of IDH1/2 Mutation in Gliomas

Summary: This trial develops a non invasive diagnostic approach of IDH1 mutated gliomas combining mutation detection from free plasmatic DNA, D-2HG dosage in urine samples, and D-2HG detection by Brain Spectro MRI.
  In group 1 (25 patients), patients with presumed grade II-III gliomas candidate to surgery will undergo spectro MRI, plasma, urine dosages. Results will then be confronted to tumor mutational status and D-2HG.
  In group 2 (15 patients), patients with known IDH1 mutation will undergo spectro MRI, plasma, urine dosages overtime in order to correlate results with the response to treatment.

Detailed description: The aim of this trial is to develop and validate a non invasive diagnostic approach of IDH1 mutated gliomas. It will evaluate the specificity and sensitivity of D-2HG detection by Brain Spectro MRI. This approach will be coupled with mutation detection from free plasmatic DNA and D-2HG dosage in urine samples.
  The primary end-point is the quantification of D-2HG by spectro-MRI, and the correlation with the dosage of D-2HG in the tumor fragment, and the mutational status (group 1: 25 patients).
  The secondary endpoints include:
  1. longitudinal analysis Spectro-MRI overtime (12 months) correlation with radiological evolution and the response to treatment (group 2: 15 patients)
  2. Differentiation of tumor recurrence from radiation induced changes
  3. Confrontation of Spectro-MRI, D-2HG dosages and IDH mutation detection from plasma DNA, and elaboration of a combined score of prediction

Eligibility: Inclusion criteria
  1. Affiliation to a social security system
  2. Patient≥ 18 years old
  3. Written informed consent
  4. One of the two situations:
  -  presumed grade II-III glioma candidate to surgery (group 1)
  -  IDH1/IDH2 mutated grade II-III gliomas, candidate to chemotherapy or radiotherapy treatment, or simple follow-up (group 2)
  5. Evaluable tumoral mass min diameter >2 cm (FLAIR)
  6. PKPS > 60
  Exclusion criteria
  1. Contra-indication to MRI
  2. Patient unable to give an written Informed Consent
  3. Patient under guardianship or deprived of freedom
  4. For group 2: patient already included in group 1

Relevance to patient case: not relevant
Patient case: 70-year-old male with gastrointestinal stromal tumor; genetic feature: KIT (V654A)

Clinical trial: [18F]FLT PET/CT in Rb+ Metastatic Breast Cancer

Summary: In this study positron emission tomography (PET/CT) imaging will be used to evaluate proliferative activity in sites of metastatic disease using the investigational radiotracer [18F]fluorothymidine (FLT).

Detailed description: This protocol is designed to develop relationships between parameters determined from imaging biomarker studies and ones used for determination of therapeutic response to combined CDK4 Inhibitor and chemotherapy regimens. Imaging will occur prior to starting therapy on the separate therapeutic protocol UPCC 06115. Patients may undergo a second FLT PET/CT scan following a 3-day run of ribociclib (LEE011) (day -6 to -4) and a third FLT PET/CT scan on cycle 1 day 12 following two treatments of weekly Paclitaxel to compare changes in FLT uptake measures.

Eligibility: Inclusion Criteria:
  1. At least 18 years of age
  2. History of histologically or cytologically confirmed breast cancer, any ER, PR or HER2 status is allowed as long as it expresses the Rb protein.
  3. At least one site of metastatic breast cancer that is outside of the liver and bone that is identified by standard imaging (e.g. CT, MRI, FDG PET/CT, ultrasound, x-ray)
  4. Participants must be informed of the investigational nature of this study and provide written informed consent in accordance with institutional and federal guidelines prior to study-specific procedures.
  5. Patients must be candidates to receive treatment on the therapeutic trial UPCC06115, a Phase I study of ribociclib (LEE011) and weekly paclitaxel.
  Exclusion Criteria:
  1. Females who are pregnant at the time of screening will not be eligible for this study, urine pregnancy test will be performed at screening in women of child-bearing potential.
  2. Inability to tolerate imaging procedures in the opinion of an investigator or treating physician
  3. Serious or unstable medical or psychological conditions that, in the opinion of the investigator, would compromise the subject's safety or successful participation in the study.
  4. Ineligible for the therapeutic trial UPCC 06115

Relevance to patient case: not relevant
Patient case: 70-year-old male with gastrointestinal stromal tumor; genetic feature: KIT (V654A)

Clinical trial: A Study to Evaluate the Efficacy of Venetoclax in Relapsed/Refractory Participants With Chronic Lymphocytic Leukemia (CLL) Including Those With 17p Deletion or TP53 Mutation or Those Who Have Received a Prior B-cell Receptor Inhibitor.

Summary: The purpose of this open-label, single-arm study is to evaluate the efficacy of venetoclax monotherapy in approximately 250 participants with relapsed/refractory CLL including those with the 17p deletion or TP53 mutation (assessed by local lab) OR those who have received prior treatment with a B-cell receptor inhibitor. The starting dose of venetoclax is 20 mg once daily. The dose must be gradually increased over a period of 5 weeks up to the daily dose of 400 mg. Participants may continue receiving venetoclax for up to 2 years. After the treatment period, participants may continue on into a 2-year follow-up period.


Eligibility: Inclusion Criteria:
  -  Participant has Eastern Cooperative Oncology Group (ECOG) performance score of less than or equal to 2
  -  Participant has relapsed/refractory disease (received at least 1 prior therapy)
  -  Participant has diagnosis of CLL that meets published 2008 Modified IWCLL NCI-WG Guidelines and:
  -  has an indication for treatment according to the 2008 Modified IWCLL NCI-WG criteria
  -  has clinically measurable disease (lymphocytosis greater than 5 × 109/L and/or palpable and measurable nodes by physical exam and/or organomegaly assessed by physical exam)
  -  In addition, participants:
  -  with or without 17p deletion or TP53 mutation, assessed by a local laboratory in bone marrow or peripheral blood AND/OR
  -  may have been previously treated with a prior B-cell receptor inhibitor
  -  Participant must have adequate bone marrow function, coagulation profile, renal, and hepatic function, per laboratory reference range at Screening
  Exclusion Criteria:
  -  Participant has developed Richter's transformation or Prolymphocytic leukemia
  -  Participant has previously received venetoclax
  -  History of active malignancies other than CLL within the past 2 years prior to first dose of venetoclax, with the exception of:
  -  adequately treated in situ carcinoma of the cervix uteri
  -  adequately treated basal cell carcinoma or localized squamous cell carcinoma of the skin
  -  previous malignancy confined and surgically resected (or treated with other modalities) with curative intent
  -  Participant has active and uncontrolled autoimmune cytopenias (for 2 weeks prior to Screening), including autoimmune hemolytic anemia and idiopathic thrombocytopenic purpura despite low dose corticosteroids
  -  Participant has undergone an allogeneic stem cell transplant grade 2:
  -  Any anti-cancer therapy including chemotherapy, or radiotherapy;
  -  Investigational therapy, including targeted small molecule agents
  -  Participant is human immunodeficiency virus (HIV) positive
  -  Participant has known allergy to both xanthine oxidase inhibitors and rasburicase

Relevance to patient case: not relevant