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

Clinical trial: Novel Detection System for Lung Cancer Curative Effect Monitoring

Summary: The purpose of this study is to investigate the sensitivity，specificity and concordance rate of EGFR testing results in plasma in comparison of results in matched tumor tissues tested by amplification refractory mutation system(ARMS). Moreover, the investigators correlate our findings in plasma with survival of advanced patients.

Detailed description: Non-small cell lung cancer (NSCLC), accounting for 80% of all lung cancers, is a leading cause of cancer deaths worldwide. Inhibition of epidermal growth factor receptor (EGFR) kinase activity by EGFR tyrosine kinase inhibitors, such as gefitinib and erlotinib, can result in improved response and prolonged progression-free survival (PFS) in selected non-small cell lung cancer (NSCLC) patients harboring sensitizing EGFR mutations, especially the exon 19del and exon 21（L858R） mutations. Unfortunately, about 50%-60% patients who accept EGFR tyrosine kinase inhibitors with sensitizing mutations will receive resistance mutations, the T790M resistance is a target of active pharmaceutical development. So EGFR mutation testing is a step in identifying the right patients for EGFR tyrosine kinase inhibitors treatment. Now tissue samples and tumor cytologic samples are accepted as appropriate sample types for EGFR mutation detection, but these samples are not always available on or after diagnosis, and, even when available, they may be of insufficient quality or quantity for mutation testing. Noninvasive techniques for tumor genotyping may be needed to fully realize, such as plasma sample. Cell-free DNA (cf-DNA) in plasma is a kind of fresh and realtime sample, and has been shown to be promising for the detection of sensitizing EGFR mutations even the resistance mutation（T790M). However, a challenge was also raised about how to detect the low abundance of mutant alleles in plasma. In our study Droplet Digital polymerase chain reaction and Realtime polymerase chain reaction will be used to assess the EGFR mutation in plasma DNA samples from patients with advanced NSCLC before and after EGFR tyrosine kinase inhibitors therapy.

Eligibility: Inclusion Criteria:
  1. Aged 18-85 years old;
  2. The diagnosis of lung cancer by pathological examination;
  3. At least one specific measurable lung cancer lesions (according to RECIST criteria, application of spiral CT, the lesion diameter 10 mm or higher);
  4. People understand and are willing to accept the study, and sign the informed consent
  Exclusion Criteria:
  1. With severe hemorrhagic disease;
  2. Compliance is poor, can't cooperate with the visitor.

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

Clinical trial: Imatinib as Pre-operative Anti-Colon Cancer Targeted Therapy

Summary: In this proof-of-concept trial the investigators will study the effects of imatinib treatment on the biology of mesenchymal-type colon cancers.

Detailed description: Tumor biopsies from patients with newly diagnosed colon cancer will be pre-screened with an RT-qPCR test to identify tumors of the mesenchymal subtype. Patients with mesenchymal-type tumors that meet the in- and exclusion criteria will be treated with imatinib during the "window period" that normally precedes surgery. Immediately following tumor resection, biopsies will be taken from the surgical specimen. Gene and protein expression of the pre- and post-treatments biopsies will be compared to assess the effects of imatinib therapy on PDGFR- and cKIT-signalling and on the mesenchymal gene expression profile.

Eligibility: Inclusion Criteria:
  1. Male or female aged ≥18 years
  2. Histologically proven adenocarcinoma of the colon;
  3. Completed cancer staging with CT-abdomen and CT-thorax/X-thorax according to hospital's standard of care;
  4. Confirmed eligibility for surgery with curative intent as deemed by the hospital's multidisciplinary board (MDB) review;
  5. An intratumoural gene expression profile of PDGFR-α, PDGFR-β, PDGF-C and KIT, indicative of the mesenchymal phenotype, according to our diagnostic RT-qPCR test (i.e. more than 50% chance of having the mesenchymal phenotype);
  6. Minimum of four properly stored pre-treatment biopsies for gene expression analysis/ELISA;
  7. WHO performance status 0 or 1;
  8. Adequate haematology status and organ function, defined as:
  -  Normal creatinine clearance (≥60 ml/min (MRDR))
  -  ALAT within 2.5x upper limit of normal (ULN)
  -  PT-INR < 1.5
  -  Leukocytes > 1,5*10^9/L; Hb > 6.0 mmol/L; platelets > 100*10^9/L
  9. Willingness and ability to comply with scheduled visits, treatment plans and laboratory tests;
  10. Written informed consent.
  Exclusion Criteria:
  1. The presence of synchronous distant metastases;
  2. Current hospital standard of care dictates that subject should undergo any neoadjuvant therapy;
  3. Concurrent participation in another clinical trial using any medicinal product, or participation in such a trial in the period of three months prior to the current trial;
  4. Women who are pregnant, plan to become pregnant or are lactating during the study or for up to 30 days after the last dose of imatinib;
  5. Known HIV or Hepatitis B/C infection;
  6. Known symptomatic congestive heart failure;
  7. Co-morbidity requiring concomitant treatment with drugs that act as strong inducers of CYP3A4 or with drugs with a narrow therapeutic range influenced by imatinib

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

Clinical trial: Abraxane in Patients With Visceral Metastases Dominant Metastatic Breast Cancer

Summary: Abraxane in patients with visceral metastases dominant metastatic breast cancer

Detailed description: A Prospective, Single-center, Open-Label, Phase II Study of Abraxane in patients with visceral metastases dominant metastatic breast cancer

Eligibility: Inclusion Criteria:
  1. Histologically confirmed metastatic breast cancer;
  2. Radiologically or histologically confirmed visceral dominant metastases;
  3. Patients who are expected to acquire benefit from chemotherapy: ER and/or PR positive patients who developed resistance after prior endocrine therapy; HER2+ patients who experienced disease progression on prior target therapy and are not suitable for subsequent target therapy; mTNBC patients who relapsed after platinum therapy;
  4. At least one measurable disease according to the response evaluation criteria in solid tumor (RECIST 1.1);
  5. Patients who received paclitaxol in metastatic setting should be proven effective to prior paclitaxol based regimen and disease progressed after at least 3 months from the last administration of paclitaxol; those who received paclitaxel as neoadjuvant/adjuvant therapy can be enrolled if disease relapsed after at least 6 months from the completion of neoadjuvant/adjuvant chemotherapy. Patients who received docetaxol have no limitation for enrollment;
  6. Eastern Cooperative Oncology Group performance (ECOG) status of 0-1;
  7. All patients enrolled are required to have adequate hematologic, hepatic, and renal function;
  8. Life expectancy longer than 12 weeks;
  9. No medical history of serious cardiovascular, hepatic, respiratory or renal diseases;
  10. Informed consent;
  11. Patients with good compliance.
  Exclusion Criteria:
  1. Pregnant, lactating women or women of child-bearing potential, unwilling to use adequate contraceptive protection during the process of the study;
  2. Patients who are expected to acquire benefit from endocrine or target therapy;
  3. Radiotherapy of axial bones within 4 weeks before enrollment or lack of recovery from prior radiotherapy;
  4. Treatment with other experimental drug within 4 weeks before enrollment;
  5. Patients with symptomatic central nervous system metastases are not permitted, except for those with stable and asymptomatic brain metastases who have completed cranial irradiation, and have at least one measurable lesion outside the brain. Radiotherapy should be completed within 4 weeks prior to enrollment;
  6. Other active malignancies (including other hematologic malignancies) or other malignancies within the last 5 years, except for cured nonmelanoma skin cancer or cervical intraepithelial neoplasia;
  7. Patients with a history of symptomatic cardiovascular, hepatic, respiratory, renal , hematological, endocrinal, neurological or psychiatric diseases;
  8. Uncontrolled serious infection.

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

Clinical trial: Afatinib Monotherapy in Patients With ERBB-deregulated Metastatic Urothelial Tract Carcinoma After Failure of Platinum Based Chemotherapy

Summary: The purpose of this trial is to assess the anti-tumour activity and safety of afatinib monotherapy in patients with urothelial tract carcinoma carrying ERBB2 or ERBB3 mutations or ERBB2 amplifications (Cohort A), and EGFR amplification positive tumours (Cohort B), progressing despite previous platinum based chemotherapy, and thereby to improve their prognosis.
  The antitumour activity of afatinib monotherapy in these patients will be assessed by progression free survival rate at 6 months (PFS6). This will be the primary endpoint of the trial. A key secondary endpoint will also be defined, the objective response rate (ORR).


Eligibility: Inclusion criteria:
  -  Recurrent or metastatic urothelial cancer
  -  Patients must have failed prior platinum based treatment (adjuvant or 1st line)
  -  Archival tissue sample available for biomarker testing at pre-screening and tissue banking.
  -  Patients should complete a pre-screening biomarker analysis and should fulfill the following: for Cohort A tumour should show a ERBB2 (epidermal growth factor family receptor 2) or ERBB3 mutation, or ERBB2 gene amplification; for Cohort B tumour should show EGFR (Epidermal Growth Factor Receptor) amplification.
  -  Further inclusion criteria apply
  Exclusion criteria:
  -  Prior use of EGFR, ERBB2 or ERBB3 targeted treatment
  -  Chemotherapy within 4 weeks prior to the start of study treatment. Biological therapy or investigational agents within 4 weeks prior to the start of study treatment or prior to passing 5 half-lives, i.e. systemic clearance, whatever comes first
  -  Known brain metastases or signs hereof, uncontrolled spinal cord compression or leptomeningeal carcinomatosis
  -  Further exclusion criteria apply

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

Clinical trial: A Study of LY3039478 in Participants With Advanced or Metastatic Solid Tumors

Summary: The main purpose of this study is to evaluate the safety of the study drug known as LY3039478 in combination with other anticancer agents in participants with advanced or metastatic solid tumors.


Eligibility: Inclusion Criteria:
  -  For all parts: The participant must be, in the judgment of the investigator, an appropriate candidate for experimental therapy after available standard therapies have failed to provide clinical benefit for their advanced or metastatic cancer.
  -  For dose escalation for all combinations: The participant must have histological or cytological evidence of cancer, either a solid tumor or a lymphoma, which is advanced or metastatic.
  -  For Part A dose confirmation: All participants must have histological evidence of advanced or metastatic soft tissue sarcoma or breast cancer. Breast cancer participants must have prescreened mutations, amplification, or gene/protein expression alterations related to Notch pathway.
  -  For Part B dose confirmation: All participants must have histological evidence of advanced or metastatic colon cancer or soft tissue sarcoma. Colon cancer participants must have prescreened mutations, amplification, or gene/protein expression alterations related to Notch pathway.
  -  For Part C dose confirmation: All participants must have histological evidence of advanced or metastatic breast cancer and prescreened mutations, amplification, or gene/protein expression alterations related to Notch pathway.
  -  For Part D dose confirmation: All participants must have histological evidence of cholangiocarcinoma and prescreened mutations, amplification, or gene/protein expression alterations related to Notch pathway. Participants must not have received >1 line of prior systemic therapy for metastatic or resectable disease (that is, participants may have received adjuvant gemcitabine and then later gemcitabine/cisplatin for recurrent metastatic disease).
  -  For Part E dose confirmation: All participants must have histological evidence of locally advanced or metastatic triple negative breast cancer (TNBC) and prescreened mutations, amplification, or gene/protein expression alterations related to Notch pathway. Participants must not have received >2 lines of systemic treatment for advanced or metastatic TNBC.
  -  Have adequate organ function.
  -  Have a performance status of ≤1 on the Eastern Cooperative Oncology Group (ECOG) scale.
  -  Have discontinued all previous therapies for cancer.
  Exclusion Criteria:
  -  Have current acute leukemia.
  -  Have current or recent (within 3 months of study drug administration) gastrointestinal disease with chronic or intermittent diarrhea, or disorders that increase the risk of diarrhea, such as inflammatory bowel disease.

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

Clinical trial: Laparoscopic Surgery for T4 Tumor of the Colon Cancer

Summary: The purpose of this study is to compare the short- and long-term survival of laparoscopic surgery and conventional open surgery for T4 colon cancer.

Detailed description: The investigators previous study indicated that laparoscopic surgery is feasible in T4 colon cancers with comparable clinical and oncologic outcomes. Laparoscopy can be considered as an alternative approach for T4 colon cancers with the advantage of faster recovery. However, the clinical value of laparoscopic surgery for T4 colon cancer was only validated in some retrospective study and some prospective study in single institute with small sample of patients. The aim of the present study is to compare the short-and long-term survival outcomes of laparoscopic surgery and conventional open surgery for T4 colon cancer as well as the mortality and the morbidity.
  The number of patients needed to get a 80% power is 1960. The average number of patients/surgical center is approximately 200 in each of 10 surgical centers.
  The preoperative, intraoperative and postoperative period will be in complete accordance with the usual care of the center.
  The baseline demographics and conditions as well as the perioperative items and the postoperative occurrences will be recorded through a prior designed e-questionnaire.
  Systematically analyze and compare the disease free survival rate, the mortality, the morbidity, and the proportion of completion of laparoscopic surgery of the two surgical strategies (laparoscopy VS conventional open surgery).

Eligibility: Inclusion Criteria:
  -  Able to provide written informed consent
  -  Histologically confirmed diagnosis of colon carcinoma
  -  CT or MRI verified as T4 colon cancer without involvement of other organs
  -  Without multiple lesion other than carcinoma in situ
  -  Tumor size < 8 cm
  -  No bowel obstruction
  -  Sufficient organ function
  -  No history of gastrointestinal surgery
  -  18 years of age or older
  -  Performance Status (ECOG) 0, 1 or 2 and life expectancy > 12 weeks
  -  Operable patients
  Exclusion Criteria:
  -  Women who are pregnant (confirmed by serum b-HCG in women of reproductive age) or breast feeding
  -  Unstable or uncompensated respiratory or cardiac disease
  -  Serious active infections
  -  Hypersensitivity to capecitabine/fluorouracil or oxaliplatin
  -  Stomatitis, ulceration in the mouth or gastrointestinal tract
  -  Severe diarrhea
  -  Peripheral sensory neuropathy with functional impairment

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

Clinical trial: Neoadjuvant Chemotherapy for the Treatment of Resectable Locally Advanced Colon Cancer

Summary: A randomized controlled clinical trial to compare the short and long outcomes of Neoadjuvant chemotherapy with postoperative chemotherapy in patients with resectable locally advanced colon cancer

Detailed description: For resectable locally advanced colon cancer, the preferred treatment is colectomy with en bloc removal of the regional lymph nodes followed by chemotherapy of about 6 months. However, surgery may postpone the administration of chemotherapy due to postoperative complications such as anastomosis leakage, abdominal infection, thus leads to a poor survival. Some scholars suggested that for patients with locally advanced colon cancer, chemotherapy given before surgery might shrink or downstage tumor, facilitate surgery and promote a better oncological outcome. Whether adjuvant chemotherapy benefits these patients with better outcome still remains controversial.
  In this study, eligible patients will be randomly allocated to receive either adjuvant chemotherapy or not. For patients receiving adjuvant chemotherapy, surgery will be performed 3-4 weeks later. Preoperative and postoperative chemotherapy will be given for a total of about 6 months. For patients receiving no preoperative chemotherapy, chemotherapy will be given for about 6 months postoperatively. The recommended chemotherapy regimes includes FOLFOX, CapeOX, FOLFIRI, Capecitabine monotherapy. Patients will be followed up every 3 months for 2 year, every 6 months for 3 years postoperatively.

Eligibility: Inclusion Criteria:
  -  Patients suitable for curative surgery between 18 to 80 years old;
  -  American Society of Anesthesiologists(ASA) grade I-III;
  -  Pathological diagnosis of adenocarcinoma;
  -  Tumor located between the cecum and sigmoid colon;
  -  Enhanced CT scan of chest, abdominal and pelvic cavity: preoperative assessment of tumor stage is T3-T4 N0 or T any N+ (according to the National Comprehensive Cancer Network(NCCN) clinical practice guidelines in oncology: colon cancer version 2.2015);there is no distant metastasis;
  -  Informed consent;
  -  No preoperative chemoradiotherapy;
  -  No history of familial adenomatous polyposis, ulcerative colitis or Crohn's disease.
  Exclusion Criteria:
  -  Pregnant patient;
  -  History of psychiatric disease;
  -  Use of systemic steroids;
  -  Simultaneous multiple primary colorectal cancer;
  -  Preoperative imaging examination results show:
  1. distant metastasis;
  2. unable to perform R0 resection;
  -  Postoperative pathology of T1-T2 N0;
  -  History of any other malignant tumor in recent 5 years;
  -  Patients need emergency operation: mechanic ileus, perforation.

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

Clinical trial: International Prospective Observational Cohort Study for Optimal Bowel Resection Extent and Central Radicality for Colon Cancer

Summary: The T-REX study aims to clarify the actual status of metastatic lymph node (LN) distribution in colon cancer and provide reliable evidence regarding the optimal length of bowel resection and the extent of central lymph node dissection in colon cancer surgery.

Detailed description: In colon canser, the incidence of metastasis in the pericolic lymph nodes (LNs) located along the bowel and marginal artery is high. The optimal extent of bowel resection is closely associated with how we define 'regional' pericolic LNs, which should be resected because of the risk of metastasis. However, there are no standardised criteria for 'regional' LNs in the pericolic area.
  To establish a consensus for the extent of bowel resection and appropriate central LN dissection, international prospective stdies focusing on the distribution of metastatic LNs along the bowel and the primary feeding artery are conducted.

Eligibility: Inclusion Criteria:
  -  Histologically proven colon adenocarcinoma
  -  Pathological stage Ⅰ, Ⅱ or Ⅲ
  -  Potentially curative surgery
  -  Informed consent for observational data collection
  Exclusion Criteria:
  -  Tis (mucosal cancer)
  -  Multiple colon cancers
  -  All patients with preoperative adjuvant therapy

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

Clinical trial: Impact of Proximal Colon Retroflexion in Colorectal Cancer Screening Programme

Summary: Colorectal cancer (CRC) is the most common tumor and the second leading cause of death in the Western world. The decrease in incidence and mortality by CRC in the population undergoing screening has been observed. Colonoscopy is the recommended method for detecting tumors in early stages, as well as identifying and resecting adenomatous polyps, which are the precursor lesions of most CRCs. Colonoscopy should be of high quality to decrease incidence and mortality by CRC and avoid interval cancer. The literature shows that colonoscopy does not prevent right colon lesions in the same way as the left colon lesions, with most of the interval cancers located in the right colon. Studies published so far show an increase in the adenomas detection rate (ADT) in the right colon in a second visualization of this segment and an increase between 2 and 10% if this second examination is performed with the proximal retroflexion maneuver .Retroflexion is a safe maneuver in expert endoscopists. The aim of our study is to evaluate the ADT in right colon by means of a second visualization by performing proximal retroflexion or second frontal visualization at random in the CCR screening population.


Eligibility: Inclusion Criteria:
  -  Subjects participating in the Colorectal cancer Screening program with faecal immunological test > 100ng / ml.
  -  Ages between 50-69 years.
  -  Adequate preparation according to the Boston scale: in right colon (score> 2 in this section)
  -  Informed consent.
  Exclusion Criteria:
  -  Refusal to give informed consent.
  -  Subjects with elevated colorectal cancer risk due to family history or inherited diseases of polyposis or inflammatory bowel disease
  -  Symptomatic subjects.
  -  Diverticulitis, inflammatory bowel disease or colonic stenosis during the exploration
  -  Inadequate preparation according to Boston cleanliness scale (score ≤ 2 in right colon)

Relevance to patient case: not relevant