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

Clinical trial: Image-guided De-escalation of Neo-adjuvant Chemotherapy in HER2-positive Breast Cancer: the TRAIN-3 Study

Summary: This is a multicenter, single arm, phase II study evaluating the efficacy of image-guided de-escalating neoadjuvant treatment with paclitaxel, Herceptin® (trastuzumab), carboplatin, and pertuzumab (PTC-Ptz) in stage II-Ill HER2-positive breast cancer.

Detailed description: High pathological complete response (pCR)-rates are seen using different neoadjuvant chemotherapy schedules with trastuzumab and pertuzumab in HER2-positive stage II - III breast cancer patients. Total pCR rates in breast and axilla have been described as high as 64%, and with an even higher rate of >80% in patients with HER2-positive and hormone receptor (HR) negative tumors. PCR is associated with better long-term outcomes in patients with HER2-positive breast cancer. Three year progression-free survival ranges between 85-90%. Neoadjuvant treatment of HER2-positive breast cancer typically consists of six to nine cycles of treatment. Longer duration of treatment is associated with higher pCR-rates but gives more toxicity. Pathological complete responses are sometimes seen after only 10-12 days of neoadjuvant treatment. It is therefore important to investigate which patients can safely be treated with less than six cycles of chemotherapy and who requires more than six cycles for maximum activity.
  The radiologic response of a breast tumor after neoadjuvant therapy is predictive of the pathologic response, although the accuracy differs between breast cancer subtypes. It is hypothesized that patients with an early complete radiologic response may not benefit from additional chemotherapy and can be referred for early surgery. Patients who have not achieved pCR after early surgery despite radiologic complete response (rCR) are candidates for further adjuvant chemotherapy to complete the initially planned number of treatment cycles and maintain maximum treatment activity. Imaged guided de-escalation in which the number of treatment cycles is determined by the radiologic response could thus reduce toxicity in neoadjuvant treatment while maintaining activity.
  This study will evaluate the efficacy of image-guided de-escalation of neoadjuvant chemotherapy in patients with HER2-positive breast cancer.

Eligibility: Inclusion Criteria:
  1. Histologically confirmed infiltrating breast cancer.
  2. Stage II or Ill disease.
  3. Overexpression and/or amplification of HER2 in an invasive component of the core biopsy.
  4. Age <:18
  5. ECOG Group performance status
  6. LVEF >50% measured by echocardiography, MRI or MUGA
  7. Known HR-status ( in percentages)
  Exclusion Criteria:
  1. Previous radiation therapy of chemotherapy
  2. Pregnancy or breastfeeding
  3. Evidence of distant metastases
  4. Evidence of bilateral infiltrating breast cancer
  5. Concurrent anti-cancer treatment or another investigational drug

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

Clinical trial: Evaluation of Accuracy of One-Step Nucleic Acid Amplification (OSNA) in Diagnosis of Lymph Node Metastases of Papillary Thyroid Carcinoma

Summary: The incidence of node metastases in papillary thyroid carcinoma (PTC) is high, ranging from 20% to 90%. Prophylactic central lymph node compartment dissection (CLND), suggested from the latest guidelines for high-risk tumors, meets resistance due to the high incidence of postoperative complications. Recently, new molecular biologic techniques, such as One Step Nucleic Acid Amplification (OSNA), have spread widely, allowing to quickly isolate, amplify and quantify mRNA encoding for proteins selectively present in neoplastic cells, as Cytokeratine-19. The aim of this study is to evaluate the application of OSNA to intraoperative diagnosis of node metastases of PTC.

Detailed description: Papillary thyroid carcinoma (PTC) is the most common malignant thyroid neoplasm; it originates from follicular cells of thyroid gland, and represents over 80% of thyroid tumors. The incidence of PTC has progressively been increasing in the last decades, doubling since the 1970s, due to the diffusion of screening ultrasound. Although PTCs are considered slow-growing tumors, the incidence of node metastases is high, ranging from 20% to 90%. The real impact of node metastases on prognosis is still a matter of debate: reports in literature demonstrate a reduction of disease-free survival but are divergent on overall survival. Diagnostic tools have poor accuracy for central lymph node compartment, which is the most frequent site of metastases.
  The last guidelines suggest a prophylactic central lymph node compartment dissection (CLND) in patients with high-risk PTC; nevertheless, this indication meets resistance due to the higher incidence of postoperative complications, especially hypoparathyroidism and recurrent laryngeal nerve (RLN) palsy.
  Recently, new molecular biologic techniques have spread widely, mainly in diagnosis of node metastases in breast carcinoma; these assays allow to quickly isolate, amplify and quantify mRNA encoding for proteins selectively present in neoplastic cells, as Cytokeratine-19 (CK-19). One Step Nucleic Acid Amplification (OSNA) is routinely used in diagnosis of node metastasis in sentinel lymph node (SNL) of patients affected from breast cancer. The aim of this study is to evaluate if application of OSNA to intraoperative diagnosis of node metastases of PTC is possible.

Eligibility: Inclusion Criteria:
  Preoperative diagnosis of thyroid carcinoma
  Exclusion Criteria:
  -

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

Clinical trial: KN026 in Patients With HER2 Expressing Gastric/Gastroesophageal Junction Cancer

Summary: This is an open-label, phase 2 study of KN026 in subjects with HER2 expressing gastric/gastroesophageal junction cancer to evaluate efficacy and safety. The subjects will receive KN026 10 mg/kg QW or 20 mg/kg Q2W until progressive disease, unacceptable toxicity or death.


Eligibility: Inclusion Criteria:
  -  Signed inform consent form(ICF)
  -  Age ≥ 18 years and ≤ 75 years, male or female
  -  Histologically or cytologically documented advanced gastric/gastroesophageal junction cancer HER2 overexpressing: IHC 3+ or IHC 2+ & ISH+ HER2 expressing: IHC2+ & ISH- or IHC 1+ & ISH+
  -  Received at least one prior standard therapy
  -  At least one measurable lesion according to Response Evaluation Criteria In Solid Tumors（RECISIT） v 1.1
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1
  -  Adequate organ function
  -  LVEF≥ 50% (ECHO)
  -  Female patients and males with partners of childbearing potential should be using highly effective contraceptive measures (failure rate of less than 1% per year). Contraception should be continued for a period of 24 weeks after dosing has been completed.
  -  Ability to comply with treatment, procedures and pharmacokinetics (PK) sample collection and the required study follow-up procedures
  Exclusion Criteria:
  -  Accepted any other anti-tumor drug therapies within 4 weeks before fist dose
  -  Accepted radiotherapy within 4 weeks before enrollment
  -  An anthracyclines antibiotic treatment was received exceeding 320 mg/m² or other equivalent dose antharcyclines
  -  Subjects are eligible with clinically controlled and stable neurologic function >= 4 weeks, which is no evidence of CNS disease progression; Subjects with spinal cord compression and cancerous meningitis are not eligible
  -  Pregnant or nursing females；or intend pregnancy within this study period or within 6 monthes after the end of this study
  -  History of immunodeficiency, including HIV positive or other acquired, congenital immunodeficiency disease, or a history of organ transplantation
  -  Severe chronic and active infection, need to system antibiosis/antiviral treatment
  -  Cavity effusion (pleural effusion, ascites, pericardial effusion, etc.) are not well controlled, and need locally treatment or repeated drainage

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

Clinical trial: A Safety and Efficacy Study of ZW25 Plus Combination Chemotherapy in HER2-expressing Gastroesophageal Adenocarcinoma

Summary: This is a multicenter, global, Phase 2, open-label, 2-part, first-line study to investigate the safety, tolerability, and anti-tumor activity of ZW25 plus physician's choice of combination chemotherapy in HER2-expressing gastroesophageal adenocarcinoma (GEA). Eligible patients include those with unresectable, locally advanced, recurrent or metastatic HER2-expressing GEA.

Detailed description: Part 1 of the study will first evaluate the safety and tolerability of ZW25 plus physician's choice of first-line combination chemotherapy (XP, FP, or mFOLFOX6) and will confirm the recommended dosage (RD) of ZW25 when administered in combination with each of these multi-agent chemotherapy regimens. Then, Part 2 of the study will evaluate the anti-tumor activity of ZW25 plus physician's choice of combination chemotherapy in HER2-high GEA.

Eligibility: Inclusion:
  -  Disease diagnosis:
  -  Part 1: Unresectable, locally advanced, recurrent or metastatic HER2-expressing GEA (IHC 3+ or 2+ with or without gene amplification based upon local assessment)
  -  Part 2: Unresectable, locally advanced, recurrent or metastatic HER2-high GEA (IHC 3+, or IHC 2+ and FISH+ by central review)
  -  Tumor measurements as per Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1:
  -  Part 1: Measurable or non-measurable disease
  -  Part 2: Measurable disease
  -  ECOG performance status score of 0 or 1
  -  Adequate organ function
  -  Adequate cardiac left ventricular function, as defined by a LVEF >/= institutional standard of normal
  Exclusion:
  -  Prior treatment with a HER2-targeted agent
  -  Treatment with prior anti-cancer therapy, except prior adjuvant/neoadjuvant therapy, which must be completed at least 6 months prior to study treatment dosing
  -  Untreated known brain metastases (patients with treated brain metastases who are off steroids and are stable for at least 1 month at the time of screening are eligible)
  -  Having clinically significant cardiac disease or known myocardial infarction or unstable angina (within 6 months before first study treatment dosing)
  -  QTc Fridericia (QTcF) > 450 ms
  -  Peripheral neuropathy > Grade 1 per NCI-CTCAE v5.0
  -  Clinically significant interstitial lung disease
  -  Known active hepatitis B or C (per the Centers for Disease Control guidelines) or known infection with human immunodeficiency virus (HIV)

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

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: 50-year-old male with pancreatic cancer; genetic feature: BRCA2

Clinical trial: MRI for Detecting Cancer in Women Who Are at High Risk of Developing Breast Cancer

Summary: RATIONALE: Screening tests may help doctors detect cancer cells early and plan more effective treatment for breast cancer. Diagnostic procedures such as MRI may improve the ability to detect breast cancer.
  PURPOSE: Screening and diagnostic trial to study the effectiveness of MRI scans in women who are at high risk for developing breast cancer.

Detailed description: OBJECTIVES:
  -  Estimate the diagnostic yield and positive predictive value of breast magnetic resonance imaging (MRI) for the detection of cancer in women who are at greater than 25% lifetime risk for developing breast cancer.
  -  Compare the diagnostic yield and positive predictive value of MRI with conventional breast cancer screening (mammography and physical examination) for the detection of breast cancer in women with a greater than 25% lifetime risk of developing breast cancer.
  OUTLINE: All patients receive a physical exam within 90 days of initial MRI scan. Patients undergo a two view screening mammogram within 3 months prior to study entry. Patients undergo an MRI with gadolinium contrast at entry. All lesions identified as suspicious on physical examination, mammography, or MRI undergo a core needle or excisional biopsy.
  PROJECTED ACCRUAL: A total of 200 patients will be accrued for this study within 2 years.

Eligibility: DISEASE CHARACTERISTICS:
  -  Patients at greater than 25% lifetime risk for breast cancer on the basis of family history or a genetic test
  -  Prior breast cancer allowed if patient meets the greater than 25% lifetime risk
  -  Patients with greater than 5 years since diagnosis must have at least 50% probability for developing breast cancer by the Couch model or be positive for BRCA1 or BRCA2 mutation
  -  Hormone receptor status:
  -  Not specified
  PATIENT CHARACTERISTICS:
  Age:
  -  25 and over
  Sex:
  -  Female
  Menopausal status:
  -  Not specified
  Performance status:
  -  Not specified
  Life expectancy:
  -  Not specified
  Hematopoietic:
  -  Not specified
  Hepatic:
  -  Not specified
  Renal:
  -  Not specified
  Other:
  -  No contraindications to MRI scan including patients with pacemakers, magnetic aneurysm clips or other implanted magnetic devices, or severe claustrophobia
  -  Not pregnant
  PRIOR CONCURRENT THERAPY:
  Biologic therapy
  -  Not specified
  Chemotherapy
  -  Not specified
  Endocrine therapy
  -  Not specified
  Radiotherapy
  -  Not specified
  Surgery
  -  Not specified

Relevance to patient case: not relevant
Patient case: 50-year-old male with pancreatic cancer; genetic feature: BRCA2

Clinical trial: Cancer Detection in Pancreatic Cysts

Summary: The purpose of this study is to assist with early and accurate diagnosis of cancer in pancreatic cysts based on the analysis of DNA obtained by endoscopic ultrasound guided fine needle aspiration

Detailed description: The study of pancreatic diseases is hindered by the organ's deep seated location and especially lack of symptoms during the early stages of disease development and progression e.g. pancreatic cancer. This is particularly true of pancreatic cysts, the variety and the malignant potential of which encompass a broad spectrum. The radiological features distinguishing a benign from a pre-malignant to a frankly malignant cyst in the pancreas are frequently underwhelming and have lead to the clinical practice of sampling all but the most obvious. The yield of the aspirate in turn is frequently not of a quality upon which a clinical decision can be based.
  Most would agree that the best approach for management of pancreatic cystic neoplasm lies in early diagnosis, ideally at a precancerous stage. The effectiveness and applicability of this study is the based on the ability of the cyst DNA analysis to stratify the patients at risk of developing pancreatic cancer based on the extent of accumulated mutational damage.

Eligibility: Inclusion Criteria:
  -  Previously scheduled for Endoscopic ULtrasound for evaluation of pancreatic cyst
  Exclusion Criteria:
  -  Any condition that would preclude safe performance of EUS/FNA

Relevance to patient case: not relevant
Patient case: 50-year-old male with pancreatic cancer; genetic feature: BRCA2

Clinical trial: Monitoring of Biopsy-Proven Interstitial Polyomavirus Nephritis in Kidney and Kidney Pancreas Transplant Recipients

Summary: Evaluate techniques for monitoring the course of interstitial therapy for polyomavirus nephritis in kidney and kidney pancreas transplant recipients by monitoring blood, urine, and renal transplant biopsies of patients affected by polyomavirus.

Detailed description: Evaluate techniques for monitoring the course of interstitial therapy for polyomavirus nephritis in kidney and kidney pancreas transplant recipients by monitoring blood, urine, and renal transplant biopsies of patients affected by polyomavirus.

Eligibility: Inclusion Criteria:
  -  Recipients of a kidney or kidney pancreas transplant diagnosed with biopsy proven interstitial nephritis due to polyomavirus.
  -  Age 18 to 70 years.
  -  Capable of providing written informed consent.
  Exclusion Criteria:
  -  Age less than 18 years or greater than 70 years.
  -  Patient is on chronic warfarin or heparin therapy or has a disease that puts them at risk of bleeding.

Relevance to patient case: not relevant
Patient case: 50-year-old male with pancreatic cancer; genetic feature: BRCA2

Clinical trial: National Screening in Denmark With MR Versus Mammography and Ultrasound of Women With BRCA1 or BRCA2 Mutations

Summary: The purpose of the study is to determine whether MR of the breast is a better screening tool than mammography combined with ultrasound of the breast in women with BRCA1 or BRCA2 gene mutations.

Detailed description: Study type : Interventional Study design: Diagnostic,Prospective,Non Randomised,Blinded,Efficacy study
  Further study details as provided by DBCG ( Danish Breast Cancer Cooperative Group):
  Primary outcome measures:
  Diagnostic outcome of a yearly screening with MR versus combined mammography and ultrasound of the breast measured by accuracy, sensitivity, specificity, positive and negative predictive values.
  Secondary outcome measures:
  Comparison of diagnostic outcome of MR versus combined mammography and ultrasound, in women with dense breast tissue compared with women with fatty breast tissue.
  Comparison of the cancers found in women with BRCA gene mutations compared with the cancers found in the background population in respect of morphology, size, histological type, axillary lymph node status and grade.
  Study start : January 2007. Expected completion 2010.
  Women with BRCA gene mutations are more likely than others to develop the disease at a young age when breast density is higher than at older age.The tumours often are more rapidly developing with a short presymptomatic phase. These factors are known to reduce the effectiveness of screening with mammography and mammography seems to have a low sensitivity in women with BRCA gene mutations. Other studies have shown that more than 50% of the cancers appears as interval cancers between two mammography screening examinations and many have positive axillary nodes at the time of diagnosis.
  Around 610 women are tested BRCA gene positive in Denmark in year 2006. These women are offered a yearly screening with mammography combined with ultrasound and a clinical examination. The trial will test whether this screening offer should be combined with or replaced by MR mammography.

Eligibility: Inclusion Criteria:
  -  women tested positive of BRCA1 or BRCA2 gene mutations
  -  referred for screening
  -  aged 25 - 70 years
  Exclusion Criteria:
  -  general contraindications for MR
  -  pregnant or lactating
  -  men
  -  bilateral mastectomy
  -  ongoing treatment with chemotherapy
  -  metastatic breast cancer
  -  previous breast surgery less than 6 months before MR
  -  previous radiation therapy of the breast less than 1 year before
  -  incapable of managing her own affairs

Relevance to patient case: not relevant