araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: A Study of Onartuzumab (MetMAb) in Combination With mFOLFOX6 in Patients With Metastatic Human Epidermal Growth Factor Receptor 2 (HER2) Negative Gastroesophageal Cancer

Summary: This randomized, multicenter, double-blind, placebo-controlled study will evaluate the efficacy and safety of onartuzumab (MetMAb) in combination with mFOLFOX6 in patients with metastatic HER2-negative adenocarcinoma of the stomach or gastroesophageal junction. Patients will be randomized in a 1:1 ratio to receive either onartuzumab (MetMAb) or placebo in combination with mFOLFOX6. Patients may continue to receive onartuzumab (MetMAb) or placebo until disease progression, unacceptable toxicity, patient or physician decision to discontinue treatment.


Eligibility: Inclusion Criteria:
  -  Adult patients, 18 years of age and older
  -  Adenocarcinoma of the stomach or gastroesophageal junction with inoperable, metastatic disease, not amenable for curative therapy
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0 or 1
  -  Life expectancy >3 months
  -  Presence of tissue sample for immunohistochemistry assay of Met receptor and HER2 status (if unknown)
  -  Radiographic evidence of disease; measurable disease or non-measurable but evaluable disease, according to the Response Evaluation Criteria in Solid Tumors (RECIST v1.1); Patients with peritoneal disease would generally be regarded as having evaluable disease and allowed to enter the trial.
  -  For women who are not postmenopausal or surgically sterile; agreement to use an adequate method of contraception (e.g., hormonal implant) during the treatment period and for at least 90 days after the last dose of onartuzumab/placebo and 6 months after the last dose of oxaliplatin
  -  For men: agreement to use a barrier method of contraception during the treatment period and for 90 days after the last dose of onartuzumab/placebo and 6 months after the last dose of oxaliplatin
  -  Adequate laboratory values
  Exclusion Criteria:
  -  HER2-positive tumor (primary tumor or metastasis)
  -  Previous chemotherapy for locally advanced or metastatic gastric carcinoma (adjuvant or neoadjuvant chemotherapy must be completed at least 6 months prior to randomization)
  -  Prior treatment with investigational drugs that target the hepatocyte growth factor (HGF) or Met pathway
  -  History of other malignancy within the previous 5 years, except for appropriately treated and presumed cured carcinoma in situ of the cervix, non-melanoma skin carcinoma, Stage 1 uterine cancer, and localized prostate cancer
  -  Receipt of an investigational drug within 28 days prior to study start
  -  Clinically significant gastrointestinal abnormalities, except from gastric cancer (e.g., Crohn's disease)
  -  Significant history of cardiac disease
  -  Significant vascular disease
  -  Infection with human immunodeficiency virus, hepatitis B, or hepatitis C

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: A Study of MM-111 and Paclitaxel With Trastuzumab in Patients HER2 Positive Carcinomas of the Distal Esophagus, Gastroesophageal (GE) Junction and Stomach

Summary: To determine whether the combination of MM-111 plus paclitaxel and trastuzumab is more effective than paclitaxel and trastuzumab alone

Detailed description: This is a randomized, open Label, Phase 2 Study of MM-111 and Paclitaxel withTrastuzumab in Patients with HER2 Positive Carcinomas of the Distal Esophagus, Gastroesophageal (GE) Junction and Stomach Who Have Failed Front Line Metastatic or Locally Advanced Therapy. Approximately 120 patients will be randomized in a 1:1 ratio between the experimental and comparator arms.

Eligibility: Inclusion Criteria:
  -  Patients must have documentation of histologically or cytologically confirmed metastatic or locally advanced adenocarcinoma of the distal esophagus, GE junction or stomach
  -  Patients must have documentation of histologically or cytologically confirmed HER2 expression
  -  Patients must be ≥18 years of age
  -  Patients must have ECOG PS of 0, 1, or 2
  -  Patients must have adequate hematologic status, renal and hepatic function
  Exclusion Criteria:
  -  Patients with known hypersensitivity to any of the components of MM-111
  -  Patients with a known history of hypersensitivity to paclitaxel or other drugs formulated in Cremophor® EL
  -  Patients with a known history of hypersensitivity to trastuzumab or any of its components (group 1 patients only)
  -  Patients with an active infection or with an unexplained fever >38.5°C

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Trial of Intravenous Azithromycin to Eradicate Ureaplasma Respiratory Tract Infection in Preterm Infants

Summary: The purpose of this study is to determine whether intravenous azithromycin is effective in eradicating Ureaplasma respiratory tract infection in preterm infants born at 24 to 28 weeks gestation.

Detailed description: The study design will be a double-blind, placebo-controlled clinical trial to test the efficacy and safety of azithromycin 20 mg/kg x 3 days to eradicate Ureaplasma spp from the respiratory tract of preterm infants 24 weeks 0 days to 28 weeks 6 days gestation exposed to positive pressure ventilation. The primary outcome will be survival with microbiological eradication of Ureaplasma defined as survival to discharge or transfer with 3 negative cultures obtained post-therapy. Secondary outcomes will include physiologic BPD at 36 weeks post-menstrual age (PMA), overall mortality, incidence of co-morbidities of prematurity such as intraventricular hemorrhage, periventricular leukomalacia, necrotizing enterocolitis, bacterial and fungal nosocomial infection, pulmonary air leak, patent ductus arteriosus, retinopathy of prematurity, number of days of positive pressure ventilation, number of days of oxygen supplementation, use of postnatal steroids, and use of non-study antibiotics. At 6 and 18 months adjusted age, a pulmonary outcome questionnaire will be administered by phone or in person interview. At 18-22 months adjusted age, neurodevelopmental outcomes will be assessed by 1) Bayley Scale of Infant and Toddler Development, 3rd edition (BSID-III); 2) Amiel-Tison neurologic examination; 3) Gross Motor Function Classification System; and 4) medical record review for hearing impairment with or without amplification and vision impairment (vision <20/200).

Eligibility: Inclusion Criteria:
  -  Gestational age 24 weeks 0 days-28weeks 6 days by best obstetrical estimate
  -  <72 h age
  -  Positive pressure ventilation for at least 1 hour duration during the first 72 hours of life
  -  Presence of indwelling intravenous line for drug administration
  Exclusion Criteria:
  -  Any patient judged to be non-viable or for whom withdrawal of life support is planned
  -  Patients with major lethal congenital anomalies
  -  Triplets or higher order multiples
  -  Patients delivered for maternal indications (low risk of Ureaplasma colonization)
  -  Patients with EKG QT interval corrected for heart rate (Qtc) ≥ 450 ms
  -  Patients with significant hepatic impairment (direct bilirubin >1.5 mg/dL)
  -  Patients exposed to other systemic macrolide
  -  Patients with clinically suspected Ureaplasma central nervous system (CNS) infection or other confirmed bacterial/viral infection
  -  Patients participating in other clinical trials involving investigational products.

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Clinical Value of 89Zr-trastuzumab PET

Summary: Information about the presence of human epidermal growth factor receptor 2 (HER2) in tumor lesions in breast cancer patients is essential for diagnostic and therapeutic management of metastatic breast cancer. In daily practice however, obtaining a metastasis biopsy can be difficult or impracticable. Therefore, clinicians can be faced with a persistent clinical dilemma in some breast cancer patients, leading to suboptimal therapy decisions due to lack of HER2 receptor information. Circulating tumor cells (CTCs), which may provide additional information, have so far not been able to replace the biopsy. To solve this problem, non-invasive whole body visualization and quantification of HER2 expression by means of the HER2-PET may be a valuable tool.
  In this prospective multicenter imaging study, eligible patients will receive one HER2-PET and CTC analysis in addition to standard work up for metastatic disease. Subsequent administration of anti-HER2 therapy will be evaluated. Referring physicians fill in three questionnaires, one before HER2-PET and two after HER2-PET.


Eligibility: Inclusion Criteria:
  1. Patients with a history of histological and/or cytological proven HER2-positive primary breast cancer. In the Netherlands HER2-positivity is defined as:
  -  HER2 immunohistochemical score of 3+, or
  -  HER2 immunohistochemical score of 2+ and positive FISH for HER2/c-erbB2 amplification.
  In Belgium HER2-positivity is defined as positive FISH for HER2/c-erbB2 amplification.
  2. Patients with suspected metastatic disease or local recurrence of HER2-positive breast cancer and a clinical dilemma:
  -  in whom standard work up with imaging has failed to solve the clinical dilemma (diagnostic/therapeutic), leaving issues with regard to HER2 status of lesions and
  -  in whom a biopsy is desirable but cannot (easily) be performed due to technical or patient factors or otherwise.
  3. Standard work-up with imaging is defined as CT chest and abdomen, bone scintigraphy, as well as FDG-PET.
  4. Age >18 years of age.
  5. WHO performance status 0-2.
  6. Signed written informed consent.
  7. Able to comply with the protocol.
  Exclusion Criteria:
  1. Pregnant or lactating women.
  2. Prior allergic reaction to immunoglobulins or immunoglobulin allergy.
  3. Inability to comply with study procedures

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Neratinib HER Mutation Basket Study (SUMMIT)

Summary: This is an open-label, non-randomized, multicenter, multinational, Phase 2 study exploring the efficacy and safety of neratinib as monotherapy or in combination with other therapies in patients with ERBB mutation-positive or EGFR gene-amplified solid tumors.

Detailed description: This is an open-label, multicenter, multinational, Phase 2 study exploring the efficacy and safety of neratinib therapy in patients with solid tumors with activating HER2, HER3 or EGFR mutations or with EGFR gene amplification.
  The trial will consist of a screening period, a treatment period, and an end of treatment visit occurring when neratinib is discontinued for any reason, a safety follow-up visit occurring 28 to 42 days after the last dose of neratinib and a survival follow-up period lasting for a maximum of 12 months for each patient after their last dose of neratinib or until initiation of additional anti-cancer therapy.

Eligibility: Inclusion Criteria:
  -  Histologically confirmed cancers for which no curative therapy exists.
  -  Documented HER2 mutation.
  -  Pediatric patients (at least 12 but less than 18 years of age at signing of informed consent) may be recruited in the Fibrolamellar Carcinoma cohort.
  Exclusion Criteria:
  -  Prior treatment with any pan-HER tyrosine kinase inhibitor (eg, lapatinib, afatinib, dacomitinib, neratinib).
  -  Patients who are receiving any other anticancer agents.
  -  Symptomatic or unstable brain metastases.
  -  Women who are pregnant or breast-feeding.
  Note: There are additional inclusion and exclusion criteria. The study center will determine if you meet all of the criteria.

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Maintenance Bevacizumab or Observation After Taxane Based First Line Chemotherapy In Metastatic Breast Cancer

Summary: Investigators propose to assess,the safety and tolerability profile (number of participants with adverse events)of bevacizumab (Avastin) when combined with standard chemotherapy as first line treatment of patients with metastatic Breast Cancer.

Detailed description: Nowadays in clinical practice patients with previously untreated metastatic breast cancer often receive taxane-based chemotherapy (paclitaxel or docetaxel) in combination with bevacizumab as it has been shown to increase progression-free survival. There is currently minimal information whether bevacizumab should be given as maintenance therapy after discontinuation of chemotherapy.

Eligibility: Inclusion Criteria:
  -  Written informed consent
  -  Age ≥18 years
  -  Patients with histologically or cytologically confirmed, HER2-negative, metastatic Breast Cancer
  -  No prior first line treatment for metastatic Breast Cancer
  -  Previous hormonotherapy for metastatic Breast Cancer is allowed
  -  One or more measurable lesions (≥1cm in diameter with spiral CT scan or ≥2cm with conventional techniques) according to RECIST criteria
  -  ECOG performance status ≤2
  -  Adequate haematological, renal and hepatic function
  -  Urine protein <2+ (dipstick)
  -  Life expectancy of ≥12 weeks
  Exclusion Criteria:
  -  Previous first line treatment for metastatic colorectal cancer(progression >12 months after the end of adjuvant treatment)
  -  Previous radiotherapy to target lesions
  -  Patients with brain metastases and/or cancerous meningitis
  -  Presence or history of other neoplasm except properly treated basal cell skin cancer or in situ cervical carcinoma
  -  Patients participating in interventional clinical trial

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: OctavaColon Cancer Blood Tests OctavaGold and OctavaSilver - Blood Tests for the Help in Diagnosis of Colon Cancer Clinical Study Protocol

Summary: The OctavaColon tests are qualitative plasma tests that are indicated to people above 18 years of age suspected with colon abnormality. The blood tests will provide additional information to the doctor in the course of colon cancer diagnosis for both normal population and high risk population

Detailed description: The clinical objective of this study is to develop two antibody-based blood tests for additional information during colon cancer diagnosis -
  1. Highly specific (OctavaGold) - provides additional information to doctors during evaluation of normal population.
  2. Highly sensitive (OctavaSilver) - provides additional information to doctors during evaluation of high risk population.
  The study will be considered successful it can achieve at least one of the following sets of performances -
  1. For the OctavaGold - 95% specificity with at least 50% sensitivity.
  2. For the OctavaSilver - 95% sensitivity with at least 50% specificity. The biological objective of this study is to find the best set of antigens, that when combined with the appropriate algorithm will support each of the above clinical objectives

Eligibility: Inclusion Criteria:
  Subjects 18 years or over. Subjects scheduled for colonoscopy or surgery
  Exclusion Criteria:
  -  Subjects less than 18 years of age
  -  Previous or concurrent synchronous cancers other than previous malignancies of the colon and recovered melanoma
  -  Autoimmune disorders diagnosed subjects
  -  Hematological malignancies
  -  Subjects under active chemotherapy treatment or chemotherapy in the past 6 months
  -  Steroid treatment in the past 3 months
  -  Subject undergoing immunosuppressive treatments
  -  Subject with verified melanoma colon cancer
  -  Subject with verified sarcoma colon cancer

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Simultaneaous Detection of Quantitative Somatic Alterations Using the Qantitative Multiplex Pcr of Short Fluorescent Fragments Method (QMPSF) in Stage II-III Colon Cancer: a Prospective Study

Summary: Lymph node involvement remains the main criteria for postoperative chemotherapy in patients with colon cancer (CC) without distant metastasis. To date, the prognostic value of the somatic quantitative molecular alterations such as loss or gain of genomic region is not established in CC.
  AIMS & METHODS: Using the one-step screening method based on the Quantitative Multiplex PCR of Short fluorescent Fragments (QMPSF), we aimed to assess the prognostic role of the simultaneous detection of main quantitative somatic alterations in stage II-III CC.
  Patients and Methods. We enrolled and collected all baseline characteristics of patients operated for a stage II-III CC with storage frozen tissues. The QMPSF was based on a simultaneous amplification of 9 selected target genomic sequences from literature: DCC (18q21); EGFR (7p12); P53 (17p13.1); BLK (8p23-p22); c-myc (8q24.12); APC (5q22.2); ERBB2 (17q12); STK6 (20q13.31); NR21 (14p11.1) and two control: DCOHM (5q31.1); HMBS (11q23.3). Comparison of each amplicon electropherograms obtained from tumour vs normal peritumoral tissue allowed us to identified gain or loss genomic region. The primary end-point was the local and/or distant recurrence and relation between clinical and single or combined molecular alterations and recurrence were evaluated.


Eligibility: Inclusion Criteria:
  -  age over 18
  -  localized colon cancer
  -  proven adenocarcinoma
  -  surgery R0
  -  no metastatic disease
  -  stage II or III
  -  WHO performance status 0, 1 or 2
  -  availaible frozen tissue
  -  written consent
  -  no major co-morbidities
  Exclusion Criteria:
  -  metastatic disease
  -  hereditary colorectal cancer
  -  rectal cancer

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Metabiomics Colon Cancer Clinical Research Study

Summary: The specific aim of the study is to determine the false negative rate of the Metabiomics Colon Polyp and Colorectal Cancer Assay for Cancer.

Detailed description: The purpose of this study is to conduct clinical research to investigate the association of the gut microbiome with colonic neoplasia. In this case several types of gut microbiome samples will be collected from patients undergoing colectomy for colonic adenocarcinoma; those samples will be tested by Metabiomics Colon Polyp and Colorectal Cancer Assay and the percentage of false negative (test returns a negative for cancer) results determined.

Eligibility: Inclusion Criteria:
  -  Recently diagnosed with colorectal cancer (CRC) and scheduled for colectomy
  -  Male or female,
  -  Age: 18-95 years,
  -  Able to comprehend, sign, and date the written informed consent form (ICF),
  -  Able to give informed consent in English
  -  Women and minorities will be included.
  Exclusion Criteria:
  -  History of Inflammatory Bowel Disease
  -  Antibiotics within 2 weeks of sample collection.
  -  Colonoscopy, colon prep or bowel contrast agent within 7 days prior to sample collection
  -  Any radiation therapy

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: One Step Nucleic Acid Amplification in Endobronchial Ultrasound-guided Needle Aspiration Samples

Summary: The aim of our study is to investigate if CK19 mRNA-detection via OSNA can accurately detect lymph node metastases in lung cancer patients using EBUS-TBNA samples.

Detailed description: Regional lymph nodes are assessed before tumor resection and before initiation of chemo- or radiotherapy. Endobronchial ultrasound-guided needle aspiration (EBUS-TBNA) is a well-established method for mediastinal and hilar lymph node staging [2, 3]. Samples obtained via this route are much smaller than surgical lymph node biopsies, yet they are able to provide complete and thorough evaluation, this includes current molecular testing.
  One Step Nucleic Acid Amplification (OSNA), a molecular test that utilizes CK 19 mRNA-concentration as a target marker is becoming a rapidly dynamic method in quick detection of sentinel lymph node (SLN) metastases in breast cancer, colon cancer and other cancers.
  In lung cancer, the role of SLN is not well established. However, recent publications suggest an accurate and rapid detection of lymph node metastases in NSCLC. However this requires complete lymph node dissection either with mediastinoscopy or by other surgical means such as thoracotomy.
  The aim of our study is to investigate if CK19 mRNA-detection via OSNA can accurately detect lymph node metastases in lung cancer patients using EBUS-TBNA samples.

Eligibility: Inclusion Criteria:
  -  CT-scan suspicious for lung cancer,
  -  enlarged mediastinal lymph nodes (>10 mm),
  -  EBUS-TBNA to be performed,
  -  age: 18-99 years
  Exclusion Criteria:
  -  age: <18 years

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Study of WNT974 in Combination With LGX818 and Cetuximab in Patients With BRAF-mutant Metastatic Colorectal Cancer (mCRC) and Wnt Pathway Mutations

Summary: The purpose of this study is to assess the safety and anti-tumor activity of the triple combination of WNT974, LGX818 and cetuximab in BRAFV600-mutant mCRC with RNF43 mutations or RSPO fusions.
  The design of this study is based upon the translational and pre-clinical data that suggest that Wnt pathway signals, increased due to RNF43 mutations or RSPO fusions, cooperate with the EGFR and BRAF signals to maintain the growth of BRAFV600 CRCs. Inhibition of these signals with the triple combination of WNT974, LGX818 and cetuximab may result in anti-tumor activity.


Eligibility: Inclusion Criteria:
  -  Male or female aged ≥ 18 years
  -  Histological or cytological confirmed metastatic colorectal cancer
  -  Written documentation of KRAS wild-type status and BRAFV600-mutation with RNF43 mutation and/or RSPO fusion
  -  Progression of disease after at least one prior standard of care regimen or intolerant to irinotecan based regimens
  -  Availability of a representative tumor specimen (primary or metastatic, archival or newly obtained)
  -  Measurable disease as per RECIST v1.1
  -  Eastern cooperative oncology group (ECOG) performance status ≤ 2
  Exclusion Criteria:
  -  Phase II only: Prior treatment with RAF inhibitors, Wnt pathway inhibitors, cetuximab, panitumumab, and/or other EGFR inhibitors
  -  Symptomatic brain metastasis. Patients previously treated or untreated for these conditions that are asymptomatic in the absence of corticosteroid and anti-epileptic therapy are allowed to enroll
  -  Current treatment with medications or consuming foods that are strong inhibitors or inducers of CYP3A4/5 or herbal medications and that cannot be discontinued at least one week prior to the start of treatment.
  -  Symptomatic or untreated leptomeningeal disease
  -  Acute or chronic pancreatitis
  -  Clinically significant cardiac disease
  -  Patients with any of the following laboratory values at Screening/baseline
  -  Absolute neutrophil count (ANC) <1,500/mm3
  -  Platelets < 100,000/mm3
  -  Hemoglobin < 9.0 g/dL
  -  Serum creatinine >1.5 x ULN or calculated or directly measured CrCl < 50% lower limit of normal
  -  Serum total bilirubin >1.5 x ULN
  -  AST/SGOT and/or ALT/SGPT > 2.5 x ULN, (> 5 x ULN if liver metastases present)
  -  Patients with impaired hepatic function as defined by Childs-Pugh class B or C
  -  Impairment of gastrointestinal (GI) function or GI disease that may significantly alter the absorption of oral WNT974/LGX818
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: not relevant