araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Trial of Vemurafenib and Cobimetinib in Patients With Advanced BRAFV600 Mutant Melanoma

Summary: This trial explores the immunologic effects of vemurafenib (BRAF inhibitor) and cobimetinib (MEK inhibitor), administered alone and in combination, to patients with advanced BRAF V600E/K mutant melanoma.


Eligibility: Inclusion Criteria:
  -  Signed informed consent
  -  Signed HIV testing consent
  -  Life expectancy ≥ 12 weeks
  -  Able to swallow pills
  -  ECOG performance status 2 or less
  -  Adequate bone marrow function
  -  Adequate renal function
  -  Adequate liver function
  -  Negative urine pregnancy test within 7 days prior to commencement of dosing in premenopausal women
  -  Histological diagnosis of unresectable AJCC stage III or stage IV, BRAFV600E/K mutant melanoma
  -  Measurable disease
  -  Accessible tumor that can be biopsied
  -  Naive to targeted therapy (Prior immune-based therapy in the adjuvant setting or for advanced disease will be allowed if >2 weeks from study entry)
  Exclusion Criteria:
  -  Active systemic infection
  -  Active autoimmune disease or history of known or suspected autoimmune disease
  -  Active brain metastases or leptomeningeal metastases
  -  Treatment with any immunomodulatory medication within 4 weeks of initiation of study therapy.
  -  Positive test for hepatitis B virus
  -  Positive test for hepatitis C virus
  -  Positive test for human immunodeficiency virus (HIV)
  -  Pregnant, lactating or breast feeding women
  -  Localized radiation therapy within the last 14 days
  -  History of malabsorption
  -  No consumption of the following within 7 days prior to start of treatment:
  -  St. John's wort or hyperforin (potent cytochrome P450 CYP3A4 enzyme inducer)
  -  Grapefruit juice (potent cytochrome P450 CYP3A4 enzyme inhibitor
  -  History or evidence of cardiovascular risk
  -  History or evidence of retinal pathology

Relevance to patient case: not relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: ESHAP-Imatinib for Refractory/Relapsed Non-Hodgkin's Lymphoma

Summary: Open-labeled, multicenter, phase I/II study of imatinib combined with ESHAP as salvage therapy in relapsed/refractory non-Hodgkin's lymphoma


Eligibility: Inclusion Criteria:
  1. Histologically diagnosed non-Hodgkin's lymphoma, refractory or relapsed after 1st line treatment.
  2. Paraffin block of the lesions available for immunohistochemical analysis
  3. Candidate for ESHAP salvage therapy
  4. Evidence of at least one lesion with a diameter of 1.5 cm
  5. Age of over 20 years
  6. Eastern cooperative oncology group performance status (ECOG) less than or equal to 2.
  7. Adequate kidney function with serum creatinine< 2.5 mg/dL, creatinine clearance ≥ 50 mL/min
  8. Adequate liver function with aspartate transaminase (AST)/alanine aminotransferase (ALT) lower than or equal to 3 times the normal upper limit; Total bilirubin lower than or equal to 1.5 times the upper limit ;alkaline phosphatase lower than or equal to 5 times the normal upper limit.
  9. Adequate bone marrow function with absolute neutrophil count ≥ 1,000/uL; platelets ≥ 75,000/uL; hemoglobin ≥ 9.0 g/dL
  10. Patients who gave voluntarily informed consent before performing any test test that is not part of routine care of patients
  Exclusion Criteria:
  1. Patients with history of exposure to imatinib or other Bcr-Abl tyrosine-kinase inhibitors
  2. Known or suspected hypersensitivity to imatinib
  3. Potential use or usage alteration of CYP3A4 inducers or inhibitors from prior to 21 days of to the test regimen until the initiation of round 2 ESHAP. Exceptions are itraconazole and fluconazole for treatment or prevention of fungal infection, hydrocortisone and dexamethasone for treatment of nausea/vomiting/fluid retention, and methylprednisolone as a part of the ESHAP regimen.
  4. Known involvement of the central nervous system (CNS) by lymphoma.
  5. Pregnant or breast-feeding. Females of childbearing potential who do not agree to undergo pregnancy tests or repeated use effective birth control while included in the clinical trial.
  6. Serious or uncontrolled medical condition, such as presence of abnormal or clinically significant cardiac disease, such as acute myocardial infarction or unstable angina within 6 months prior to initiation of treatment with ESHAP-imatinib, serious neurological or psychological conditions such as dementia or epilepsy, or uncontrolled active infection.
  7. Prior history of malignancy other than to non-Hodgkin's lymphoma (except basal or squamous cell skin and in situ carcinoma of the cervix) unless the patient free of disease beyond 5 years are.
  8. HIV positive and in treatment.

Relevance to patient case: not relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Melanoma Perception and Health Literacy in People of Color

Summary: This study will examine the effectiveness of a targeted, health literate educational intervention for people of color compared to a standard melanoma education pamphlet for increasing knowledge and promoting early melanoma detection. It is hypothesized that people of color are less aware of their risk for developing melanoma and that a targeted educational intervention will help increase knowledge and promote early melanoma detection especially in individuals with low health literacy.

Detailed description: This targeted educational intervention will compare a standard melanoma education pamphlet with one that has been modified to target people of color. Both pamphlets will include the ABCDEs of melanoma, risk factors, prevention and treatment. In addition, the targeted pamphlet will incorporate the recommendations made by people of color in previous studies. The pamphlets will be randomized to subjects at a study visit along with a health literacy test and a questionnaire aimed at determining subjects' baseline melanoma knowledge and current melanoma prevention practices. 2 months post-intervention, a follow-up phone call will be made to assess subject knowledge retention and behavior change.

Eligibility: Inclusion Criteria:
  -  English-speaking
  -  Self-identifies with one of the following races/ethnicities: African American, Asian/Pacific Islander, American Indian and Alaskan Native, or Hispanic
  Exclusion Criteria:
  -  Not proficient in English
  -  Unable to give informed consent
  -  Does not self-identify with the following races/ethnicities: African American, Asian/Pacific Islander, American Indian and Alaskan Native, or Hispanic

Relevance to patient case: not relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Patients With Refractory, Metastatic Cancer Harboring KIT Mutation or Amplification to Investigate the Clinical Efficacy and Safety of Imatinib Therapy

Summary: KIT is a receptor tyrosine kinase that binds to stem-cell factor (SCF), activating a series of downstream effector pathways. KIT is an established therapeutic target in cancer with activating mutations of KIT, such as gastrointestinal stromal tumors (GIST), and significant benefit is achieved with various small molecule inhibitors of KIT such as imatinib mesylate. Moreover, there is increasing evidence implicating KIT mutations as tractable therapeutic targets in melanoma. Additional information is required to characterize the functional role of low-frequency mutations in KIT and to determine whether amplification of wild type KIT is a real driver that can be targeted therapeutically. Except GIST and melanoma, other solid cancers were reported to have KIT mutation even in low frequency. A molecular profiling of the tumors of patients referred to the phase I clinic at the M.D. Anderson Cancer Center showed KIT mutation in 7 patients in total of 431 patients (2%).
  Hence, the investigators planned this study to apply the molecularly targeted agent, imatinib to various types of cancers harboring KIT mutation or amplification.


Eligibility: Inclusion Criteria:
  1. age ≥ 20
  2. advanced, refractory cancer patients who failed standard of care (SOC)
  3. KIT aberration: defined as mutation in exons 9, 11, 13, 17 or 18, or nanostring CNV by quantitative PCR (greater than 3 copies) or subject with specific sensitivity (Z-score<-1) to imatinib by Avatar scan whose disease has progressed following standard therapy or that has not responded to standard therapy or for which there is no standard therapy
  4. ECOG performance status of 0~2
  5. measurable or evaluable lesion per RECIST 1.1 criteria
  6. adequate marrow, hepatic, renal and cardiac functions
  -  Serum aspartate transaminase (AST) and serum alanine transaminase (ALT) ≤ 2.5 x upper limit of normal (ULN), or AST and ALT ≤ 5 x ULN if liver function abnormalities are due to underlying malignancy
  -  Total serum bilirubin ≤ 1.5 x ULN
  -  Absolute neutrophil count(ANC) ≥ 1,500/uL
  -  Platelets ≥ 100,0000/uL
  -  Hemoglobin ≥ 9.0 g/dL
  7. provision of a signed written informed consent
  Exclusion Criteria:
  1. severe co-morbid illness and/or active infections
  2. pregnant or lactating women
  3. history of major surgery or radiotherapy within 4 weeks
  4. active CNS metastases not controllable with radiotherapy or corticosteroids (however, CNS metastases (except for leptomeningeal seeding) are allowed if controlled by gamma knife surgery or surgery or radiotherapy or steroid)
  5. known history of hypersensitivity to study drugs

Relevance to patient case: possibly relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Measuring Core Body Temperature Using TempuRing

Summary: This study evaluates the safety and usability of a continuous temperature sensor for women. Data will compare the date of ovulation identified by the continuous temperature sensor to that of transvaginal ultrasound and serum progesterone levels. Subjects will also compare sensor results to once-daily oral temperatures and urine luteinizing hormone (LH) status.

Detailed description: Up to 25 healthy female volunteers or females currently trying to conceive will wear the continuous temperature sensor for 3 menstrual cycles. Subjects will record their daily oral temperature, and record their urine luteinizing hormone (LH) status via ovulation prediction kits. Subjects will return to the clinic after a positive urinary LH test to receive transvaginal ultrasound scans to confirm ovulation (ultrasounds will be repeated daily until evidence of ovulation is documented by follicular collapse). Ovulation will also be confirmed by serum progesterone. Subjects will complete an online questionnaire to assess the usability and comfort of the continuous temperature monitor.

Eligibility: Inclusion Criteria:
  1. Participant is willing and able to give informed consent for participation
  2. Females aged 21 to 43 years
  3. Have a body mass index (BMI) above 19 and below 29
  4. Regular menstrual cycles, i.e. no greater than 7 days difference between the shortest and longest cycle in the last 6 months
  5. Minimum menstrual cycle 24 days
  6. Maximum menstrual cycle 35 days
  7. Normal pap smear within the last year
  8. Willing to use the fertility device for at least 3 cycles
  9. Willing to fill in online questionnaires
  10. Willing to attend clinic up to 6 times per cycle for transvaginal ultrasound and blood tests
  11. Willing to perform LH urine tests at home twice a day from day 8 of cycle until it is positive
  12. Willing to document the last day of the previous menses and first day of the following menses.
  13. Willing to measure and record oral at the same time each morning.
  14. Normal pelvic ultrasound and blood results obtained during screening tests
  Exclusion Criteria:
  1. Any diagnosed systemic illnesses including thyroid disease, diabetes, yeast infection, Chlamydia, gonorrhea, trichomonas, bacterial vaginosis, inflammatory diseases, or are in an immuncompromised state
  2. Polycystic ovary disease
  3. Endometriosis or other chronic pelvic pain or pelvic pathology
  4. Taking steroid medication, including oral contraceptives or anti inflammatory drugs
  5. Pregnant

Relevance to patient case: not relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: fPAM for the in Vivo Depth Measurement of Pigmented Lesions and Melanoma Depth

Summary: The investigators propose the use of functional photoacoustic microscopy (fPAM) to evaluate both benign and malignant pigmented lesions for tumor depth. Through fPAM analysis followed by histological examination, the investigators anticipate that they will be able to non-invasively determine tumor depth of pigmented lesions (moles and melanoma). In melanoma, tumor depth (Breslow's depth) is not only an important prognostic indicator, but also directs surgical treatment. The ultimate goal is to develop a sensitive clinical tool that will allow non-surgical evaluation of pigmented lesions, which eventually, will aid in melanoma diagnosis and management - potentially an earlier and more definitive surgical management.
  In addition, the investigators propose to use the combination of fPAM and single-cell PAM to respectively image CTCs in trunk vessels and cuticle capillaries. Based on the investigators' murine models, the investigators anticipate that they will be able to differentiate CTCs from other blood cells and reliably calculate CTC concentration in a non-invasive manner. CTC concentration has been demonstrated to be a valuable indicator of a melanoma's metastatic potential and a potential tool in evaluating treatment efficacy. The ultimate goal is to develop a sensitive imaging device that will allow accurate evaluation of the risk of melanoma recurrence and metastases, that may facilitate treatment monitoring.


Eligibility: Inclusion Criteria:
  Outcome Measure #1 and #2
  -  Healthy individuals with pigmented lesions or a partially biopsied melanoma whose treatment plan includes excision
  -  Participants must be 18 years or older
  -  Participants must be able to understand and willing to sign a written informed consent document
  Outcome Measures #3 and #4
  -  Patients with either cutaneous, visceral or brain melanoma metastases.
  -  Participants must be 18 years or older.
  -  Participants must be Eastern Cooperative Oncology Group (ECOG) status 0-3.
  -  Participants must be able to understand and willing to sign a written informed consent document.
  Exclusion Criteria:
  -  Minors, pregnant patients, incarcerated individuals, and individuals unable to give informed consent will be excluded from this study
  -  ECOG status > 3

Relevance to patient case: not relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Study to Analyze Mutations in V600 BRAF Oncogen in Participants With Metastatic Melanoma

Summary: This is a national, multicenter, cross-sectional epidemiological study in adult Spanish participants diagnosed with advanced or metastatic melanoma.


Eligibility: Inclusion Criteria:
  -  Valid tumor samples from participants diagnosed with Stage IIIc or IV melanoma
  -  Written informed consent granted
  Exclusion Criteria:
  - Do not fulfill one or more inclusion criteria

Relevance to patient case: not relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Self-sampling for Non-participants in an Organised Cervical Cancer Screening Programme

Summary: The trial will evaluate the effect on participation in organised screening programme of a human papilloma virus (HPV) self-sampling kit directly mailed home or mailed on demand compared with the standard second reminder for regular screening.

Detailed description: The CHOice trial is a parallel randomised controlled, open label trial. Participants will be equally randomised into three arms: 1) Directly mailed a second reminder including a HPV self-sampling kit; 2) Mailed a second reminder offering a HPV self-sampling kit, to be ordered by e-mail, by text message, by phone, or by website; and 3) Mailed a second reminder for a conventional practitioner-collected sample (control group).

Eligibility: Inclusion Criteria:
  -  Women resident in the Central Denmark Region who have not participate in cervical cancer screening after an invitation and one reminder
  Exclusion Criteria:
  -  Women younger than 30 years are not included due to the lower specificity of HPV DNA tests in younger women

Relevance to patient case: not relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Gut Microbiome & Gastrointestinal Toxicities as Determinants of Response to Neoadjuvant Chemo for Advanced Breast Cancer

Summary: The purpose of this research is to test whether bacteria that normally live in the intestines play a role in fighting cancer. It is believed that the development and behavior of these immune cells may be influenced by bacteria and other microorganisms living in the gut. In turn, the activities of these immune cells could work with anti-cancer therapies to make them more, or less, effective.

Detailed description: Many chemotherapeutic agents compromise the integrity of the mucosal barrier in the gut, allowing translocation of gram-positive bacteria in secondary lymphoid organs. While this has, until recently, been considered an undesirable side-effect, it may also represent one mechanism by which chemotherapy stimulates an effective anti-cancer immune response. The purpose of this research is to test whether bacteria that normally live in the intestines play a role in fighting cancer. It is believed that the development and behavior of these immune cells may be influenced by bacteria and other microorganisms living in the gut. In turn, the activities of these immune cells could work with anti-cancer therapies to make them more, or less, effective. The hypothesis is that gut microbial composition can influence immune response to the tumor, resulting in inter-individual differences in the response to anti-cancer therapies.

Eligibility: Inclusion Criteria:
  -  Diagnosed with invasive breast cancer and prescribed a regimen that includes neo-adjuvant therapy prior to breast surgery.
  -  Able to provide informed consent.
  Exclusion Criteria:
  -  History of previous malignancy, other than non-melanoma skin cancers
  -  Inability to tolerate phlebotomy
  -  Immunosuppressive therapy for any other condition
  -  Fever or active uncontrolled infection in the last 4 weeks
  -  Inflammatory bowel disease
  -  Surgery of the stomach, small or large intestines, appendectomy, gastric bypass or gastric banding in the past 6 months.
  -  Active autoimmune disease, including, but not limited to, Systemic lupus erythematosus (SLE), Multiple sclerosis (MS), ankylosing spondylitis

Relevance to patient case: not relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Comparison of Picosecond and Q-switched Laser for Benign Pigmented Lesions Treatment

Summary: The objective of this study is to evaluate the efficacy and safety of picosecond 532 and 1,064 nanometers laser in the treatment of benign pigmented lesions compared with q-switched 532 and 1,064 nanometers laser.

Detailed description: Benign pigmented lesions can be divided into epidermal lesions such as freckles, lentigines, solar lentigines or cafe au lait macules and dermal lesions such as Nevus of Ota or Hori's nevus.
  Q-switched 532 and 1064 nm lasers were reported to be safe and effective in the treatment of these benign pigmented lesions. By using selective photothermolysis theory, both q-switched 532 and 1064 nm lasers target on melanin causes photomechanical destruction of the melanin. However, the occurrence of post inflammatory hyperpigmentation (PIH) were reported especially in patients with darker skin type.
  Recently, picosecond 532, 755, 1064 nm laser was reported to treat benign pigmented lesions effectively. With their ultra short pulse duration (picosecond domain), it is ideally believed to be pure photomechanical effects without thermal injury to surrounding tissue. As a result, the incident of PIH should be reduced.
  The investigators then aimed to compared the efficacy and efficacy of different pulse duration between nanosecond and picosecond laser in the treatment of benign pigmented lesions.

Eligibility: Inclusion Criteria:
  -  age >18
  -  having any benign pigmented lesions on both sides of the face or any tattoo on any part of body which would like to be removed
  -  Fitzpatrick skin phototype 3-5
  Exclusion Criteria:
  -  Previously treated with any laser within 3 months before enrollment into the study
  -  Patients with lesions with any clinical suspicion of being pre-cancerous or skin malignancies of any kind
  -  Patients who have photosensitive dermatoses
  -  Pregnancy and lactation woman
  -  Patients with wound infections (herpes, other) on the day of treatment
  -  Patients with moderate and severe inflammatory acne, Immunosuppressed patients, history of vitiligo
  -  Patients with unrealistic concerns/expectations and inability to do the appropriate post-operative care

Relevance to patient case: not relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Clinical and Histological Features of Head and Neck Melanoma

Summary: The worldwide incidence of cutaneous melanoma has been increasing for the last 30 years in western populations. Among all melanomas, those located on the head and neck are more frequent than expected regarding the surface of this anatomical area, occur in older subjects than melanomas at other sites and have a worse prognosis than melanomas at other sites. The question whether head and neck melanomas could be a distinct entity has been debated.

Detailed description: Aim of the study was to compare clinical and histological characteristics between head and neck melanomas and melanomas at other sites.

Eligibility: Inclusion Criteria:
  -  patients with melanoma
  -  melanoma diagnosed between January 2004 and December 2011
  -  patients living in Champagne-Ardenne

Relevance to patient case: not relevant