araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Biomarkers in Tissue Samples From Patients With Ewing Sarcoma

Summary: RATIONALE: Studying samples of tissue in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help doctors understand how well patients respond to treatment.
  PURPOSE: This research study is studying biomarkers in tissue samples from patients with Ewing sarcoma.

Detailed description: OBJECTIVES:
  -  To describe the spectrum of GGAA-microsatellite polymorphisms at specific loci in genomic DNA prepared from Ewing sarcoma tumor specimens.
  -  To determine if there are differences in GGAA-microsatellite polymorphisms in genomic DNA prepared from Ewing sarcoma tumor specimens as compared to non-afflicted European and African normal genomic DNA.
  -  To determine if GGAA-microsatellite polymorphisms at specific loci in genomic DNA prepared from Ewing's sarcoma tumor specimens correlates with disease outcome in patients treated on COG protocol AEWS0031.
  -  To determine whether whole-genome amplification introduces alterations in GGAA-microsatellites as compared to non-amplified genomic DNA.
  OUTLINE: Genomic PCR is used to amplify the microsatellites in the NR0B1 and GSTM4 promoters. In addition to determining microsatellite size, each microsatellite is sequenced following cloning into the pCR4 vector (Invitrogen) using standard topoisomerase cloning protocols.

Eligibility: DISEASE CHARACTERISTICS:
  -  Specimens from patients with Ewing sarcoma used for protocol COG-AEWS08B1
  -  Obtained from patient samples taken from patients enrolled on COG-AEWS0031
  -  Whole genome-amplified DNA will be used
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Eltrombopag for the Prevention of Chemotherapy Induced Thrombocytopenia

Summary: The purpose of this study is to study the effect of eltrombopag on chemotherapy induced thrombocytopenia. Thrombocytopenia is when there is a low number of platelets in the blood. Sometimes, thrombocytopenia occurs as a side effect of chemotherapy treatments.

Detailed description: The combination chemotherapy regimen of gemcitabine and docetaxel has become an increasingly used treatment choice for subjects with advanced sarcomas. The regimen has shown activity in first and second line for subjects with metastatic uterine leiomyosarcoma, relapsed/refractory pediatric sarcomas, and improved progression-free survival and overall survival in persons with metastatic sarcoma when compared to gemcitabine alone. The regimen has additionally been recognized as a treatment option for subjects with advanced sarcoma.
  Chemotherapy-induced toxicity in the blood such as low platelet level is a common and often therapy-limiting side effect of treatment.
  There are two phases in this study. The purpose of the Phase I study is to determine the recommended dose of eltrombopag. The purpose of the Phase II study is to determine the safety, tolerability, and efficacy (how well the drug works) of eltrombopag in subjects who are receiving gemcitabine and docetaxel chemotherapy.
  Eltrombopag (Promacta) is an FDA approved drug for the treatment of chronic idiopathic thrombocytopenic purpura (ITP)- a condition of having an abnormally low platelet count. Eltrombopag is now being further investigated for other thrombocytopenic (low platelet)disorders.
  Participants will take the assigned dose of eltrombopag once a day starting five days before each cycle of chemotherapy and for 5 days after chemotherapy. Eltrombopag is not taken on the day of chemotherapy. Eltrombopag is taken orally.

Eligibility: Inclusion Criteria:
  -  Metastatic soft tissue or bone sarcoma
  -  18 years of age or older
  -  Adequate blood counts
  -  Adequate kidney and liver function
  -  At least 1 but no more than 3 prior systemic therapy regimens for this cancer
  -  Good performance status - able to carry out work of a light or sedentary nature
  Exclusion Criteria:
  -  Pre-existing hear disease such as congestive heart failure, or arrhythmia known to increase the risk of thromboembolic events (blood clots)
  -  Blood clot in the last 6 months, known clotting problem or platelet disorder
  -  History of brain cancer

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Mutation Analysis and Copy Number Changes of KRAS and BRAF Gene in Taiwanese Cases of Biliary Tact Adenocarcinoma

Summary: Cholangiocarcinoma is a fatal malignant neoplasm originating from biliary tracts and constitutes about 5-10% of primary liver cancers, characterized by a poor prognosis. High prevalence in southeast and eastern Asia has been observed. At present, the cellular and molecular mechanisms leading to oncogenesis of cholangiocarcinoma remain unclear.
  The RAS gene product has a key role in controlling cell growth and differentiation through its intrinsic GTPase activity. Point mutations that activate the RAS protein and its downstream cascade have been observed in human tumors. Both KRAS and BRAF are members of the RAS-RAF-MEK-ERK-MAP kinase pathway which mediates cellular response to growth signals. Somatic KRAS mutations are found at high rates in leukemia, colon cancer, pancreatic cancer and lung cancer. Studies from European and Japanese groups have recently described that activating KRAS/ BRAF mutations may play a role in the carcinogenesis of cholangiocarcinoma of the biliary tracts, but our preliminary data demonstrated low frequency of KRAS and BRAF mutation in the same tumor as well as the results from Thailand. In this study, the investigators hypothesize copy number changes rather than genetic mutation of either KRAS or BRAF genes may be the key findings of Taiwanese cases of the adenocarcinoma from the biliary tracts.


Eligibility: Inclusion Criteria:
  -  The patients diagnosed as biliary tact adenocarcinoma.

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: IPI-926 Extension Protocol for Continuation of Treatment With IPI-926

Summary: A treatment protocol that enables patients to have continued access to IPI-926.

Detailed description: The extension protocol is a continuation of treatment with IPI-926, as administered to each individual patient during participation in their original IPI-926 protocol.
  Patients who are completing their participation in the original IPI-926 protocol in which they enrolled, as defined in the original protocol, and, have stable disease or confirmed complete or partial response as defined by the original protocol may continue to receive treatment with IPI-926 in the extension protocol.

Eligibility: Inclusion Criteria:
  1. Voluntarily sign the informed consent form
  2. Currently receiving IPI-926 while participating in an Infinity-sponsored IPI-926 study. Note: For blinded studies, patient's treatment assignment must be unblinded according to the instructions in the original protocol to confirm they are receiving IPI-926.
  3. Eastern Cooperative Oncology Group (ECOG) performance status: 0 or 1.
  4. Documented response or stable disease, as defined in the original protocol, at the time of entry to the extension study.
  5. Willingness and ability to continue IPI-926 dispensation and follow-up procedures at the current investigational site.
  6. Willingness and ability to comply with scheduled visits, treatment plans, and laboratory tests and other study procedures.
  7. Women of child-bearing potential (WCBP), defined as a sexually mature woman who has not undergone a hysterectomy or tubal ligation or who has not been naturally postmenopausal for at least 24 consecutive months, must have a negative serum or urine pregnancy test prior to treatment. All WCBP, all sexually active male patients, and all partners of patients must agree to use adequate methods of birth control throughout the study.
  Exclusion Criteria:
  1. Discontinued IPI-926 or withdrew informed consent to participate in original Infinity-sponsored IPI-926 study.
  2. Require addition of or change to a new concomitant therapy to adequately treat the malignancy under study.

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Non Invasive IDentification of Gliomas With IDH1 Mutation

Summary: The recurrent mutation IDH1Arg132His leads to the cellular accumulation of D-2-hydroxyglutarate (2-HG), thus representing a diagnostic marker (this change is almost specific for gliomas) and prognostic (mutated gliomas have longer survival) of interest.
  The main objective is to identify the patients with IDH1 mutated glioma by three complementary approaches -genetic (identification of IDH1 mutation in plasmatic DNA), biochemical (2-HG dosage in the urine of patients) and radiological (2-HG

Detailed description: Our preliminary results indicate an extremely high amount of D-2HG in gliomas and CSF of the patients, and therefore the possibility to detect its presence by spectro-MRI, and to establish a non-invasive diagnosis of glioma with IDH1 mutation. Our goal is to identify and quantify by high-field MRI spectroscopy the presence of D-2HG to identify gliomas with IDH1 mutation. In parallel, we developed a technique for selective amplification of the mutated form of IDH1 (COLD PCR): by combining this technique with digital PCR, we already are able to detect IDH1 mutation from free plasma DNA with a sensitivity of 58% and a specificity of 100%. At the same time we have shown that D-2HG levels in urine of patients correlate with the status of the tumor IDH1.
  The main objective is to identify using this triple approach (detection of the mutation on plasma DNA detection, detection of urinary D-2HG, detection of tumor D-2HG by spectro-MRI) patients with IDH1arg132His mutation, the secondary objective is to evaluate the value of these markers for patients follow-up and for differentiating recurrence from treatment induced damage. 40 patients with grade II and grade III gliomas (20 mutated, 20 non mutated) will be included and followed up for one year (five measurements are planned).
  The first interest is diagnostic: the presence of the IDH1Arg132His mutation allows the diagnosis of glioma. This information is particularly valuable in patients not amenable to biopsy, because of the location of the tumor considered at risk, the general condition of the patient or the co-morbidities and medications. We hope also with these parameters to better monitor patient's follow-up, and to have a new method to differentiate tumor recurrence and radionecrosis or post-radiation leukoencephalopathy.

Eligibility: Inclusion Criteria:
  Inclusion Criteria
  -  Affiliated to Health Insurance regimen (sécurité sociale)
  -  Patient of 18 years or more
  -  written informed consent
  -  Glioma grade II or III histologically proven
  -  Frozen samples available
  -  Known status IDH1/IDH2
  -  Presence of a measurable residual tumor (> 2 cm in diameter FLAIR)
  -  Karnofsky Performance Status (KPS)> 60
  Exclusion Criteria:
  -  Contraindication to MRI *
  -  The rare patients with IDH2 mutation or with non Arg132His IDH1 mutation will be excluded
  -  Inability to provide informed consent
  -  Patient under guardianship or deprived of liberty by court

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: The Oncopanel Pilot (TOP) Study

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

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

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

Relevance to patient case: possibly relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Detection of Tumor DNA in Blood Samples From Cancer Patients

Summary: The aim of this study is to employ genomic detection methodologies to measure the relative amount of tumor nucleic acids in the blood of a cancer patient with diagnosed metastatic disease that is either commencing, currently undergoing or completed cytotoxic chemotherapy treatment. More generally, this approach will allow us to develop a quantitative measure of therapy efficacy via the counting of the relative changes in tumor molecules over the course of treatment.


Eligibility: Inclusion Criteria:
  -  Age 18 years or older
  -  Have metastatic disease with from a solid tumor (e.g. breast, lung, colon, pancreas, ovary, prostate...) or stage II or III solid tumors undergoing curative surgery or neoadjuvant therapy followed by surgery
  -  Starting treatment or a new line of treatment
  -  Able to understand and grant informed consent
  -  Able to have their blood drawn
  Exclusion Criteria:
  -  Unable to grant informed consent or comply with all study procedures.
  -  Has a hematological malignancy, i.e. myeloma, lymphoma, MDS, leukemia

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: Phase 2 Nab® -Paclitaxel (Abraxane®) Plus Gemcitabine in Subjects With Locally Advanced Pancreatic Cancer (LAPC)

Summary: This clinical study is in subjects who are 18 years old or older with locally advanced pancreatic cancer who have not received prior treatment for their pancreatic cancer. The study treats all subjects with nab-Paclitaxel plus gemcitabine for approximately 6 months of treatment. Subjects who complete the treatment will choose, with their treating physicians, what additional treatment should be given: more nab-Paclitaxel plus gemcitabine, Chemoradiation therapy, or surgery to treat the locally advanced pancreatic cancer.

Detailed description: This is an international, non-randomized, open-label, multi-center, Phase 2 study in subjects who are 18 years old or older with locally advanced pancreatic cancer who have not received prior treatment for their pancreatic cancer. All subjects will be treated with nab-paclitaxel plus gemcitabine for 6 cycles followed by an Investigator's Choice of continuation of treatment with nab-paclitaxel plus gemcitabine, chemoradiation therapy, or surgery.
  Safety assessments by laboratory testing and physical exams will be conducted through-out the study.
  Efficacy assessments by physical exam will be preformed through-out the study and tumor imaging will be conducted approximately every 2 months.
  Subjects will be considered active study participants from enrollment up to, but not including, survival follow-up period.

Eligibility: Inclusion Criteria:
  -  Non- metastasis, unresectable, adenocarcinoma pancreatic cancer patients
  -  No prior anticancer therapy for pancreatic cancer
  •≥ 18 years of age with a performance status of 0 or 1•Adequate complete blood counts, hepatic function, and renal function
  -  Signed informed Consent
  Exclusion Criteria:
  -  Active bacterial, viral, or fungal infection
  -  Infection with hepatitis B or C, or history of human immunodeficiency virus (HIV) infection, or receiving immunosuppressive or myelosuppressive
  -  Subjects with sensory neuropathy, ascites, or plastic biliary stent.
  -  Serious medical risk factors involving any of the major organ systems, or serious psychiatric disorders (including but not limited to connective tissue disorders, lung disease, and cardiac or seizure disorders)
  -  Women who are pregnant or breast feeding

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: A Study to Evaluate the Safety and Effectiveness of PCV Chemotherapy in Patients With Recurrent High-grade Glioma With IDH1/2 Mutation

Summary: This trial is aimed at evaluating the safety and effectiveness of PCV chemotherapy in patients with recurrent high-grade glioma with IDH1/2 mutation.

Detailed description: This trial is aimed at evaluating the safety and effectiveness of PCV chemotherapy in patients with recurrent high-grade glioma with IDH1/2 mutation. And, this trial is approved by medical ethics committee of hebei yanda hospital. Also, the trial has got a registry code "ChiCTR-OOC-15005759" in China clinical trial registry. Researchers will conduct thsi trial from 2015/02 to 2017/12, and 100 recurrent high-grade glioma with IDH1/2 mutation patients will be recruited. Patients who are recruited will get PCV chemotherapy in ether Hebei Yanda Hospital or Beijing Tiantan hospital, and get follow-ups from clinicians.

Eligibility: Inclusion Criteria:
  -  A diagnosis of high-grade glioma was established by pathological method,and the recurrency of the disease is ongoing.
  -  The report of the pathological diagnosis contained the status of IDH gene, and showed that IDH1/2 mutation existed.
  -  The age of the patient is between 18 years old and 70 years old.
  -  The condition of the patient permits the procedure of chemotherapy using PCV schema.
  -  The patient is informed consent, and willing to join in this research.
  Exclusion Criteria:
  -  The diagnosis is not recurrent high-grade glioma.
  -  The diagnosis of high-grade glioma was not established by pathological method.
  -  No molecular neuropathological report is available, or the report showed that IDH1/2 mutation did not exist.
  -  The age of the patient does not meet the requirement of this research.
  -  The condition of the patient does not permit the procedure of chemotherapy using PCV schema.
  -  There are other conditions that the clinicians believe that the PCV chemotherapy is not appropriate for the patient.
  -  The patient is not willing to join in this research.

Relevance to patient case: not relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: A Study of IDH305 in Patients With Advanced Malignancies That Harbor IDH1R132 Mutations

Summary: A Phase I study of IDH305 in patients with advanced malignancies that harbor IDH1R132 mutations.


Eligibility: Inclusion Criteria:
  -  Documented IDH1R132-mutant tumors
  -  ECOG performance status ≤ 2
  Exclusion Criteria:
  -  Patients who have received prior treatment with a mutant-specific IDH1 inhibitor (with the exception of glioma patients)
  -  Medical conditions that would prevent the patient's participation in the clinical study due to safety concerns or compliance with clinical study procedures such as the presence of other clinically significant cardiac, respiratory, gastrointestinal, renal, hepatic or neurological disease.
  -  Acute Promyelocytic Leukemia
  -  Women who are pregnant or lactating
  Other protocol-defined Inclusion/Exclusion may apply

Relevance to patient case: possibly relevant
Patient case: 26-year-old female with chondrosarcoma; genetic feature: IDH1

Clinical trial: A Trial of TAS-114 in Combination With S-1

Summary: A Phase I, Open-Label, International, Multicenter, Non-Randomized, Dose-Escalating Safety, Tolerance and Pharmacokinetic Study of Oral Administration of TAS-114 in Combination with S-1 in a Twice Daily Schedule for 14 Days in Patients with Advanced Solid Tumors.

Detailed description: This is an open-label, non-randomized, dose-escalation Phase I study of TAS-114 administered in combination with S-1, evaluating the safety, tolerability, pharmacokinetics and preliminary antitumor activity of the TAS-114/S-1 regimen in patients with advanced solid tumors.
  The study will be conducted in two parts: a Dose-Escalation Phase (Part 1) to determine the MTD; and an Expansion Phase (Part 2) to further evaluate the safety and preliminary efficacy with the MTD. Patients will receive the study medication according to the proposed treatment schedule until disease progression (PD), occurrence of intolerable side effects, removal by the Investigator or withdrawal of consent. A patient is considered discontinued from study treatment when TAS-114 is discontinued.
  Male or female patients age 18 years or older with confirmed advanced solid tumor(s) for which no standard therapy exists.
  TAS-114/S-1 will be administered BID for 14 days followed by a 7-day recovery period, every 21 days (1 cycle) in patients with advanced solid tumors.

Eligibility: Inclusion Criteria:
  1. Has provided written informed consent.
  2. Is ≥18 years of age
  3. Has histologically or cytologically confirmed advanced or metastatic solid tumor(s) for which no standard therapy exists.
  4. Expansion Phase only: Has at least one measurable lesion
  5. Is able to take medications orally (e.g., no feeding tube).
  6. Has adequate organ function
  7. Women of child-bearing potential must have a negative pregnancy test (urine or serum) within 7 days prior to starting the study drug.
  8. Is willing and able to comply with scheduled visits and study procedures.
  Exclusion Criteria:
  1. Has received treatment with any proscribed treatments within specified time frames prior to study drug administration.
  2. Has a serious illness or medical condition(s)
  3. Is receiving concomitant treatment with drugs that may interact with S-1

Relevance to patient case: not relevant