araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Detection of IKZF1 Deletion Mutation in Patients With Acute Lymphoblastic Leukemia and Its Impact in Therapy

Summary: 1. To detect IKZF-1 deletion mutations in patients with ALL.
  2. To study the impact of IKZF-1 deletion mutation on therapy of ALL.
  3. To study the correlation between IKZF-1 deletion mutations and BCR-ABL.

Detailed description: Acute lymphoblastic leukemia (ALL) a malignant transformation and proliferation of lymphoid progenitor cells in the bone marrow, blood and extramedullary sites. While 80% of ALL occurs in children, it represents a devastating disease when it occurs in adults . predisposing factors include exposure to ionizing radiation, pesticides, certain solvents or viruses such as Epstein-Barr Virus and Human Immunodeficiency Virus. However, in the majority of cases, it appears as a de novo malignancy in previously healthy individuals. Chromosomal aberrations are the hallmark of ALL, but are not sufficient to generate leukemia. Characteristic translocations include t(12;21) [ETV6-RUNX1], t(1;19) [TCF3-PBX1], t(9;22) [BCR-ABL1] . More recently, a variant with a similar gene expression profile to (Philadelphia) Ph-positive ALL but without the BCR-ABL1 rearrangement has been identified. In more than 80% of cases of this so-called Ph-like ALL, the variant possesses deletions in key transcription factors involved in B-cell development including IKAROS family zinc finger 1 (IKZF1) . IKZF1 codes Ikaros, which is a member of a family of zinc- finger nuclear proteins that is required for the earliest stages of lymphoid lineage commitment and acts as tumor suppressor. Most IKZF1 mutations (94%) are deletion mutations, and there are rare point mutations resulting in loss of function of Ikaros .
  There are two major deletions occur in the IKZF1 gene:
  -  The first one was characterized by loss of exons 4 to 7 ( 4-7) with breakpoints occurring in introns 3 and 7 on chromosome 7p12.
  -  The second deletion involved exons 2 to 7 ( 2-7) with a variable pattern of breakpoints in intron 1 and intron 7 in the same region as those of the 4-7 deletion.
  IKZF1 mutations in cases of B-ALL are associated with poor prognosis and high risk of relapse. IKZF1 mutations are found in approximately 15% to 20% of pediatric B-ALL cases and in >75% of pediatric BCR-ABL positive ALL cases. The incidences of IKZF1 mutations in adults are approximately 50% in B-ALL cases and approximately 65% in BCR-ABL positive ALL cases .
  The presence of either IKZF1 mutation or BCR- ABL has been reported to be an independent risk factor of poor prognosis for patients with B-ALL .

Eligibility: Inclusion Criteria:
  -  Patients with acute lymphoblastic leukemia.
  Exclusion Criteria:
  -  patients with any other hematological malignancies.
  -  patients receiving chemotherapy.

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Advanced Refractory Solid Tumors With TP53 Mutations Register Study

Summary: The efficacy and safety of the PARP inhibitor in combination with the VEGFR inhibitor will be investigated in advanced refractory solid tumors patients with TP53 mutation .

Detailed description: TP53 is a well-known tumor suppressor gene. Multiple studies have demonstrated that TP53 mutations are poor prognostic factor in advanced solid tumor, the TP53 gene is frequently inactivated by mutation in a majority of human tumors. However, no effective TP53 -based therapy has been successfully translated into clinical cancer treatment. So, investigators intend to review and evaluate the efficacy and safety of the PARP inhibitor in combination with the VEGFR inhibitor for TP53 mutation in advanced refractory solid tumors patients from a real-world population.

Eligibility: Inclusion Criteria:
  1. Is equal to or greater than 18 years of age.
  2. Histologic or cytologic confirmation of advanced refractory solid tumors with no standard treatment options, including some patients with advanced disease in reduced general condition (Eastern Cooperative Oncology Group (ECOG) 3 and 4).
  3. Patients with measurable or evaluable disease per Response Evaluation Criteria In Solid Tumors (RECIST) version 1.1.
  4. Patients must be able to provide blood samples or tissue samples for NGS (Next Generation Sequencing) testing for understanding the TP53 gene status. The amount of blood and tissue samples should be able to meet the requirements of DNA extraction and quality control.
  5. Adequate baseline organ system function.
  6. Patients could receive treatment program from MTB (Molecular Tumor Board).
  7. No prior treatment with PARP combined with VEGFR inhibitions.
  8. Ability to understand and the willingness to provide a written informed consent document.
  Exclusion Criteria:
  1. Women who are pregnant or breastfeeding.
  2. Prior anti-cancer therapy or radiation therapy within 2 weeks prior to enrolment. Palliative radiotherapy to metastatic lesion(s) permitted providing that it has been completed at least 2 days prior to enrolment and no significant toxicity are expected.
  3. Clinically significant (active) cardiovascular disease: cerebral vascular accident/stroke or myocardial infarction within 6 months prior to study enrollment; unstable angina, congestive heart failure or a serious cardiac arrhythmia requiring medication.
  4. Active infection requiring systemic therapy.
  5. Patients unable to swallow orally administered medication.
  6. Prior treatment with PARP or VEGFR inhibitions.
  7. According to the investigator'judgment, there are serious, uncontrollable risks to patients'safety, or associated diseases (such as severe diabetes, thyroid disease, infection, spinal cord compression, superior vena cava syndrome, neurological or psychiatric disorders and so on) that affect the patients completion of the study.

Relevance to patient case: not relevant
Patient case: 64-year-old male with gastric cancer; genetic feature: ERBB2 amplification

Clinical trial: OSI-774 (Tarceva) in Treating Patients With Stage III or Stage IV Non-Small Cell Lung Cancer

Summary: The purpose of this study is to determine if OSI-774 will improve overall survival of patients with incurable stage IIIB/IV non-small cell lung cancer compared to standard of care. OSI-774 is a new type of drug under evaluation called an epidermal growth factor receptor (EGFR). OSI-774 is an investigational drug that has not yet been approved by the U.S. Food and Drug Administration (FDA).


Eligibility: -  Clinical diagnosis of stage IIIB or IV non-small cell lung cancer.
  -  Must have evidence of disease (clinical or radiological).
  -  Have failed 1 but no more than 2 prior chemotherapy regimens, have recovered from any side effects and have not had any chemotherapy for at least 21 days.
  -  If the patient has had surgery, the surgery was at least 2 weeks ago.
  -  Patients whose cancer has spread to their brain or central nervous system are eligible, providing that they have been on stable dose of steroids for at least 4 weeks and are free of symptoms.
  -  If the patient received radiation therapy, treatment was at least 4 weeks ago.

Relevance to patient case: not relevant
Patient case: 64-year-old male with gastric cancer; genetic feature: ERBB2 amplification

Clinical trial: Study of Cetuximab, Oxaliplatin, 5-FU/LV Versus Oxaliplatin, 5-FU/LV in Patients With Previously Treated Metastatic, EGFR-Positive Colorectal Cancer

Summary: The purpose of this study is to compare overall survival in patients with previously-treated metastatic, epidermal growth factor receptor (EGFR)-positive colorectal cancer treated with oxaliplatin, 5-fluorouracil and leucovorin (FOLFOX4) and cetuximab with FOLFOX4 alone.


Eligibility: Inclusion Criteria:
  -  Documented colorectal cancer which is EGFR-positive and is metastatic.
  -  Prior irinotecan, alone or in combination, as first-line treatment of metastatic disease.
  Exclusion Criteria:
  -  A serious uncontrolled medical disorder that, in the opinion of the Investigator, would impair the ability of the subject to receive protocol therapy.
  -  Known dihydropyrimidine dehydrogenase (DPD) deficiency.
  -  Known metastases in the central nervous system.
  -  Symptomatic sensory or peripheral neuropathy.
  -  More than one prior chemotherapy regimen for the treatment of metastatic colorectal cancer.
  -  Prior oxaliplatin therapy.
  -  Prior cetuximab or other therapy which targets the EGF pathway.
  -  Prior chimerized or murine monoclonal antibody therapy.

Relevance to patient case: not relevant
Patient case: 64-year-old male with gastric cancer; genetic feature: ERBB2 amplification

Clinical trial: GW572016 For Treatment Of Refractory Metastatic Breast Cancer

Summary: This study was designed to determine the efficacy of an oral dual kinase inhibitor for the treatment of metastatic breast cancer tumors that are known to overexpress ErbB2 in a refractory patient population.


Eligibility: Inclusion Criteria:
  -  Signed Informed Consent.
  -  Histologically confirmed Stage IIIb or IV breast cancer.
  -  Refractory breast cancer defined as progression in the metastatic setting after prior therapy with anthracyclines, taxanes and capecitibine.
  -  Subjects with documented ErbB2 tumor overexpression must have received at least 6 cycles of trastuzumab.
  -  Documented disease progression of the most recent treatment is required.
  -  Archived tumor tissue available for testing.
  -  Measurable lesions according to Response Evaluation Criteria In Solid Tumors (RECIST).
  -  At least 3 weeks since prior cancer therapies except for trastuzumab which must be discontinued at least 2 weeks prior to the beginning of study drug.
  -  Bisphosphonate therapy initiated prior to study entry is allowed, however, initiation of bisphosphonates following study entry is not allowed.
  -  Able to swallow and retain oral medication.
  -  Cardiac ejection fraction within the institutional normal range as measured by echocardiogram or MUGA (Multiple Gated Acquisition) scan.
  -  Adequate kidney and liver function.
  -  Adequate bone marrow function.
  Exclusion criteria:
  -  Pregnant or lactating.
  -  Copies of nadir scans and/or photographs of the tumor prior to disease progression as well as scans documenting disease progression are not available for review.
  -  Malabsorption syndrome, ulcerative colitis, disease significantly affecting gastrointestinal function or resection of the stomach or small bowel.
  -  History of other malignancy.
  -  Serious medical or psychiatric disorder that would interfere with the patient''s safety or informed consent.
  -  Active or uncontrolled infection.
  -  Known history of uncontrolled or symptomatic angina, arrhythmias or congestive heart failure.
  -  Known history of or clinical evidence of leptomeningeal carcinomatosis.
  -  Active infection.
  -  Concurrent cancer therapy or investigational therapy.
  -  Use of oral or IV steroids.
  -  Unresolved or unstable serious toxicity from prior therapy.
  -  Prior treatment with an ErbB1 and/or ERbB2 inhibitor other than trastuzumab.

Relevance to patient case: not relevant
Patient case: 64-year-old male with gastric cancer; genetic feature: ERBB2 amplification

Clinical trial: Study of Irinotecan and Cetuximab Versus Irinotecan as Second-Line Treatment in Patients With Metastatic, EGFR-Positive Colorectal Cancer

Summary: The purpose of this study is to determine whether overall survival is prolonged in subjects with metastatic, epidermal growth factor receptor (EGFR)-positive colorectal cancer treated with cetuximab in combination with irinotecan compared with irinotecan alone as second-line therapy following treatment with a fluoropyrimidine and oxaliplatin based, non-irinotecan-containing regimen.


Eligibility: Inclusion Criteria:
  -  Histologically documented colorectal cancer which is EGFR-positive by immunohistochemistry [IHC] (may be based on archival samples) and is metastatic.
  -  Prior oxaliplatin administered for the first-line treatment of metastatic colorectal cancer.
  -  Prior fluoropyrimidine-containing regimen (5-fluorouracil [5-FU], capecitabine, or uracil/tegafur [UFT]), for the first-line treatment of metastatic disease.
  Exclusion Criteria:
  -  A serious uncontrolled medical disorder that, in the opinion of the Investigator, would impair the ability of the subject to receive protocol therapy
  -  Unresolved diarrhea, bowel obstruction, or history of inflammatory bowel disease
  -  Known or documented brain metastases

Relevance to patient case: not relevant
Patient case: 64-year-old male with gastric cancer; genetic feature: ERBB2 amplification

Clinical trial: Paclitaxel With / Without GW572016 (Lapatinib) As First Line Therapy For Women With Advanced Or Metastatic Breast Cancer

Summary: The purpose of this study is to determine the efficacy and safety of an oral dual tyrosine kinase inhibitor (GW572016) in combination with paclitaxel compared to paclitaxel alone in first line advanced or metastatic breast cancer.


Eligibility: Inclusion criteria:
  -  Signed Informed Consent
  -  Able to swallow an oral medication
  -  Cardiac ejection fraction within the institutional range of normal as measured by echocardiogram
  -  Adequate kidney and liver function
  -  Adequate bone marrow function
  -  Tumor tissue available for testing
  -  Prior adjuvant or neoadjuvant therapy is permitted with an anthracycline or anthracenedione-containing regimen however, subjects must have had cumulative doses of less than 360 mg/m2 of doxorubicin, 720 mg/m2 of epirubicin, or 72 mg/m2 of mitoxantrone
  -  No Her2/neu overexpression in tumor tissue tested or status unknown if tissue has never been tested
  Exclusion criteria:
  -  Prior treatment regimens for advanced or metastatic breast cancer.
  -  Pregnant or lactating
  -  Conditions that would effect the absorption of an oral drug
  -  Active infection
  -  Brain metastases
  -  Treatment with EGFR (Endothelial Growth Factor Receptor) inhibitor.
  -  Known hypersensitivity to Taxol or excipients of Taxol
  -  Peripheral neuropathy of Grade 2 or greater is not permitted
  -  Severe Cardiovascular disease or cardiac disease requiring a device.
  -  Serious medical or psychiatric disorder that would interfere with the patient's safety or informed consent.

Relevance to patient case: not relevant
Patient case: 64-year-old male with gastric cancer; genetic feature: ERBB2 amplification

Clinical trial: Lapatinib In Chemotherapy-Naive Or Metastatic Breast Cancer

Summary: This phase II study will evaluate and compare the efficacy and tolerability of two dose schedules (1500 mg QD and 500 mg BID) of oral Lapatinib as treatment for patients with advanced or metastatic breast cancer.


Eligibility: Inclusion criteria:
  -  Histologically confirmed invasive breast cancer with incurable stage IIIB, IIIC with T4 lesion or stage IV disease at primary diagnosis or at relapse after curative intent surgery.
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0 or 1.
  -  Documented amplification of ErbB2 by Fluorescence in situ hybridization (FISH)
  -  Measurable disease by Response Evaluation Criteria In Solid Tumors (RECIST)
  -  Adequate renal, hepatic and cardiac function
  Exclusion criteria:
  -  Prior chemotherapy, immunotherapy, biologic therapy or anti-ErbB1/ErbB2 therapy other than adjuvant therapy. [Prior neo-adjuvant or adjuvant therapy (including trastuzumab) will be allowed provided it was stopped at least 12 months before study entry.
  -  Patients with active brain metastases
  -  Patients with bilateral breast cancer, bone metastases as the only disease site or metastases to more than 30% of the hepatic parenchyma.

Relevance to patient case: not relevant
Patient case: 64-year-old male with gastric cancer; genetic feature: ERBB2 amplification

Clinical trial: Study of AEE788 in Patients With Recurrent/Relapse Glioblastoma Multiforme (GBM)

Summary: AEE788 is an orally active, reversible, small-molecule, multi-targeted kinase inhibitor with potent inhibitory activity against the ErbB and VEGF receptor family of tyrosine kinases. It has an IC50 of less than 100 nM against p-EGFR, p-ErbB2, and p-KDR (VEGFR2). This study will assess the safety, pharmacokinetic/pharmacodynamic (PK/PD) profiles and clinical activity of AEE788 in a recurrent GBM population.


Eligibility: Inclusion Criteria:
  -  Histologically confirmed GBM in first or second recurrence or relapse
  -  Adequate hematologic, hepatic and renal function
  -  Age ≥ 18 years
  -  Karnofsky performance status score ≥ 70%
  -  Life expectancy ≥ 12 weeks
  Exclusion Criteria:
  -  Peripheral neuropathy > grade 1
  -  Diarrhea > grade 1
  -  Gastrointestinal dysfunction
  -  Compromised cardiac function
  -  Concurrent severe and/or uncontrolled medical conditions

Relevance to patient case: not relevant
Patient case: 64-year-old male with gastric cancer; genetic feature: ERBB2 amplification

Clinical trial: Her-2/Neu in Patients With Metastatic Breast Cancer (AdHERe)

Summary: The purpose of this study is to determine the maximum tolerated dose and/or maximum attainable dose of a vaccine consisting of human autologous dendritic cells transduced by an adenovector expressing rat Her-2/neu (AdHer-2/neu) in patients with metastatic breast cancer.


Eligibility: Inclusion Criteria:
  1. Metastatic or locally recurrent breast cancer
  2. 18 years of age or older
  3. Her-2/neu positive (3+ by immunohistochemistry or fluorescence in-situ hybridization [FISH] +)
  4. One of the following:
  1. currently receiving hormonal therapy or are candidates for such, or
  2. being considered for trastuzumab, or
  3. cancer has progressed on trastuzumab.
  Exclusion Criteria:
  1. Pregnant or lactating women.
  2. Prior or concurrent malignancies except for treated basal cell or squamous cell carcinoma of the skin or in situ cancer of the cervix or any other cancer treated and presumed cured for more than five years prior to study entry.
  3. Currently receiving chemotherapy, immunotherapy, adenoviral gene therapy or biological cancer therapy. [Note: concurrent hormonal therapy (tamoxifen, aromatase inhibitors, or megace) is permitted.]
  4. Treatment with trastuzumab within 4 weeks prior to first dose of vaccine therapy.
  5. Hemoglobin < 80 g/L or granulocytes < 1.5 × 10^9/L or lymphocytes < 1.0 × 10^9/L or platelets < 100 × 10^9/L.
  6. Baseline liver enzymes (AST or ALT) greater than 3 times the upper limit of normal or greater than 5 times the upper limit of normal if liver metastases are present and/or bilirubin is greater than 50 mmol.
  7. CD4 cells < 0.5 ×10^9/L
  8. Patients with documented brain metastases.
  9. Patients with any acute illness that would interfere with the collection of CD34+ cells or administration of vaccination cellular therapy (i.e. unstable angina, renal or liver failure, or severe chronic obstructive airway disease).
  10. Any patients requiring concurrent immunosuppressive therapy (e.g. corticosteroids).
  11. Eastern Cooperative Oncology Group (ECOG) performance status of > 2.
  12. Patients with a life expectancy of less than 6 months.
  13. Geographic inaccessibility which would preclude follow-up. Patients registered on the trial must be treated and followed at the Juravinski Cancer Center and the Henderson site of the Hamilton Health Sciences.
  14. Failure to give written informed consent.
  15. Baseline left ventricular ejection fraction (LVEF) < 55% by echocardiography or multigated acquisition (MUGA) scan.

Relevance to patient case: not relevant
Patient case: 64-year-old male with gastric cancer; genetic feature: ERBB2 amplification

Clinical trial: Study of the Efficacy and Safety of Letrozole Combined With Trastuzumab in Patients With Metastatic Breast Cancer

Summary: Phase IV trial to investigate the effect of the combination of Letrozole with trastuzumab in metastatic breast cancer patients


Eligibility: Inclusion Criteria:
  -  Postmenopausal
  -  Her-2 overexpression and ER and/or PgR positive
  -  Metastatic Breast Cancer
  Exclusion Criteria:
  -  Previous treatment with trastuzumab
  -  Significant Liver or renal impairment
  -  Erbb2 negative and/or ER and PgR negative
  Other protocol-defined inclusion / exclusion criteria may apply.

Relevance to patient case: not relevant
Patient case: 64-year-old male with gastric cancer; genetic feature: ERBB2 amplification

Clinical trial: Trial of Adjuvant Chemotherapy for Gastric Cancer

Summary: This study is designed to evaluate the efficacy of the intraperitoneal chemotherapy with early mitomycin administration and adding cisplatin to prolonged treatment with doxifluridine compared to mitomycin plus doxifluridine in resected advanced gastric cancer.

Detailed description: Stomach cancer is the most common cancer in Korea and one of the major health problems worldwide. The most effective treatment for gastric cancer is curative surgical resection of primary tumor. However, a substantial number of patients eventually die of recurrences after curative resection. A number of randomized trials investigating the role of adjuvant chemotherapy have been conducted. However, the efficacy of adjuvant chemotherapy is still controversial and varied between Western and Asian trials. Meta-analysis of Western trials didn't demonstrate the benefit of adjuvant chemotherapy after curative resection. Conversely, some Asian studies have demonstrated the efficacy of adjuvant chemotherapy after curative resection. In a previous study, mitomycin plus tegafur prolonged the survival in resected gastric cancer compared to no treatment.
  This study is designed to evaluate the efficacy of the intraperitoneal chemotherapy with early mitomycin administration and adding cisplatin to prolonged treatment with doxifluridine compared to mitomycin plus doxifluridine.

Eligibility: Inclusion Criteria:
  -  Pathologically proven gastric adenocarcinoma
  -  Grossly serosa invasion of primary tumor is suspicious
  -  Curative resection was done
  -  Stage II, IIIA, IIIB, IV (including T4, lesions or N3, but excluding M1 lymph node metastasis)
  -  Age: 18-69 years old
  -  Performance status: Eastern Cooperative Oncology Group (ECOG) 0-2
  -  Adequate bone marrow function (white blood cell counts ≥ 4,000/ul, platelet count ≥ 100,000/ul, hemoglobin ≥ 10 g/dl)
  -  Adequate renal function (serum creatinine≤ 1.5)
  -  Adequate liver function (serum bilirubin ≤1.5 mg/dl, aspartate aminotransferase (AST)/alanine aminotransferase (ALT) ≤ 3 x normal upper limit)
  -  Written informed consent was signed by the patient
  Exclusion Criteria:
  -  Previous chemotherapy or radiotherapy
  -  Active ongoing infection which antibiotic treatment is needed
  -  Pregnant or lactating women
  -  Psychosis or convulsion disorder
  -  Ascites in preoperative abdomen computed tomography (CT)
  -  Systemic disease which interfere the administration of chemotherapy
  -  Postoperative pathologic stage IA, IB
  -  Postoperative pathology indicates that resection margin is involved
  -  Previous history of other malignancy except cured non-malignant skin cancer and uterine cervical cancer in situ

Relevance to patient case: not relevant