araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 56-year-old female with basal cell carcinoma; genetic feature: PTCH1

Clinical trial: DNA Analysis of Tumor Tissue Samples From Patients With Human Papilloma Virus-Associated Cancer of the Oropharynx

Summary: RATIONALE: Studying samples of tumor tissue in the laboratory from patients with cancer may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This laboratory study is looking at the DNA in tumor tissue samples from patients with human papilloma virus-associated cancer of the oropharynx.

Detailed description: OBJECTIVES:
  -  Analyze PIK3CA expression and mutation and p110α amplification and expression in tumor tissue samples from patients with human papilloma virus positive (HPV+) and human papilloma virus negative (HPV-) squamous cell carcinoma (SCC) of the oropharynx.
  -  Determine proliferation and survival after PI3K inhibition in HPV(+) and HPV(-) oropharyngeal SCC cell lines and in HPV E6 and E7 expressing cells.
  -  Determine proliferation and survival after PI3K inhibition in short-term cultures of tumor tissue samples from patients with HPV(+) and HPV(-) primary SCC of the oropharynx.
  OUTLINE: Previously collected tumor tissue samples are analyzed for HPV DNA by PCR amplification and direct sequencing of PCR products; expression of E6 protein and relative expression of PIK3CA by qRT-PCR; amplification of PIK3CA by Southern blotting; mutation of PIK3CA; expression of p110α, phospho-AKT, total AKT, and FOXO1 by polyacrylamide gel electrophoresis (PAGE) and immunoblotting; and the effect of PI3K inhibition on cell cycle and apoptosis by flow cytometry. Pharmacological studies are performed on oropharyngeal squamous cell carcinoma cell lines and short-term cultures and HPV E6 and E7 expressing cells using LY 294002 in vitro to analyze response to PI3K inhibition. Results of response to PI3K inhibition will be correlated with HPV status, PIK3CA expression, amplification, and mutation, and p110α expression.
  PROJECTED ACCRUAL: A total of 20 HPV(+) and 20 HPV(-) tumor tissue specimens from patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Undergoing operative procedures for biopsy and/or resection of squamous cell carcinoma (SCC) of the oropharynx
  -  Tumor tissue sample available from the Head and Neck Tissue Repository and Clinical Database of Vanderbilt University
  -  No tumors with human papilloma virus (HPV) DNA sequences but no expression of E6
  PATIENT CHARACTERISTICS:
  -  See Disease Characteristics
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 56-year-old female with basal cell carcinoma; genetic feature: PTCH1

Clinical trial: Collecting and Storing Tissue Samples From Patients With Head and Neck Cancer

Summary: RATIONALE: Collecting and storing samples of tissue, blood, and saliva from patients with cancer to study in the laboratory may help the study of cancer in the future.
  PURPOSE: This laboratory study is collecting and storing tissue samples from patients with head and neck cancer.

Detailed description: OBJECTIVES:
  -  Establish a tissue/specimen bank of biologic specimens collected from patients with proven or suspected head and neck cancer.
  -  Establish a database to link materials acquisition and pathologic and clinical information on these patients.
  -  Correlate clinical-pathological findings on these patients with future scientific studies using the patient database.
  -  Test new hypotheses as they emerge.
  OUTLINE: This is a prospective, multicenter study.
  Patients enrolled on active Radiation Therapy Oncology Group clinical trials undergo biopsy or surgical resection of head and neck tumors or premalignant lesions at participating institutions. Tissue and other specimens collected at the time of biopsy or surgery are submitted to the Head and Neck Cancer Tissue/Specimen Bank which acts as a central repository for processing, storing, and preserving patient specimens for translational research. Tissue samples include paraffin-embedded blocks or fresh or frozen samples of normal squamous mucosa, tumors, or premalignant lesions of the upper aerodigestive tract. Other specimens for tissue banking include serum, plasma, and lymphocytes isolated from peripheral blood, as well as samples of patient saliva. Cells obtained from tissue bank specimens may also be used to establish cell lines for future research.
  PROJECTED ACCRUAL: An unlimited number of specimens will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Confirmed or suspected head and neck cancer
  -  Primary site recurrence allowed
  -  Potentially eligible for or participating in an active Radiation Therapy Oncology Group treatment clinical trial
  PATIENT CHARACTERISTICS:
  -  Zubrod performance status 0-1
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics
  -  Concurrent radiotherapy, drug therapy, biopsy, or surgery allowed

Relevance to patient case: not relevant
Patient case: 56-year-old female with basal cell carcinoma; genetic feature: PTCH1

Clinical trial: Utilization of Genomic Signature as Decision-making for Adjuvant Treatment of Breast Cancer

Summary: Method: This multicentric prospective cohort is composed of patients with no metastatic breast cancer selected by tumor's genomic analysis and treated by chemotherapy with Anthracycline without Taxanes (6 cycles of FEC 100).
  The patient can be included before or after the surgery and a written consent must be signed for the proteomic and genomic analysis of the tumor.
  Patients who have a "good signature" for the genomic analysis will receive the standard chemotherapy.
  Primary objective:
  -  To compare metastasis free survival at 5 years in a cohort of patients with no metastatic breast cancer, who are selected by their genomic profile of the tumor and received a standard chemotherapy containing Anthracycline, with result of retrospectives studies.
  Secondary Objectives:
  -  Overall survival.
  -  Creation of a circuit (transport-extraction-genomic analysis-result) which allows the beginning of the chemotherapy within 6 weeks following the primary surgery.
  -  Histological and seric proteomic exploratory studies.


Eligibility: Inclusion Criteria:
  -  Women aged between 18 and 70
  -  Patient with life condition < 2 (WHO scale)
  -  One-sided breast adenocarcinoma with a histological evidence (all type)
  -  Clinical presentation which allowed a complete surgery with healthy limits
  -  Absence of metastasis detectable at clinical examination or radiology
  -  Histological evidence for homolateral axillary ganglionic invasion, whatever is the number of node invaded (N > 1)
  -  The beginning of the chemotherapy within 6 weeks following the primary surgery
  Exclusion Criteria:
  -  All metastatic affect
  -  Tumor classed >= T4a: cutaneous invasion, deep adherence, inflammatory breast
  -  All chemotherapy, hormonotherapy or radiotherapy before surgery
  -  Tumoral residue not removed
  -  Any suspect clinic or radiologic lesion, in the contralateral breast, which is not controlled
  -  History of invasive neoplasm, mammary or other (except in situ carcinoma of cervix uteri and epithelioma)

Relevance to patient case: not relevant
Patient case: 56-year-old female with basal cell carcinoma; genetic feature: PTCH1

Clinical trial: A Trial to Evaluate the Safety, Local Tolerability, Pharmacokinetics and Pharmacodynamics of LDE225 on Skin Basal Cell Carcinomas in Gorlin Syndrome Patients

Summary: Part I was a double-blind, randomized, vehicle-controlled Proof of Concept (PoC) study to evaluate the safety, local tolerability, pharmacokinetics and pharmacodynamics of multiple topical administrations of LDE225 (a specific Smoothened inhibitor) on skin basal cell carcinomas in Gorlin's syndrome patients.
  Following a 21-day screening period, patients were exposed to multiple doses of topically applied LDE225 twice daily for 4 weeks in a double-blind manner. The patients returned weekly for visits where each BCC was clinically evaluated and digital photographs taken. Local safety and tolerability was also assessed. After the last application of treatment, biopsies were taken from treated (both vehicle and LDE225) BCCs (three per patient) for histology, biomarker evaluation and for pharmacokinetics (skin exposure). In addition, a biopsy from LDE225-treated uninvolved perilesional skin was taken for pharmacokinetic evaluation. In total, 4 biopsies were taken: 2 for histology and biomarker and 2 for PK.
  Part II of this study consisted of a 21-day screening period, a baseline period (directly before commencing the treatment period) and a treatment period of 6 or 9 weeks, depending on randomization. A clinical assessment was performed on site on the last treatment day and if a full clinical response had been observed, approximately 3 weeks after the last treatment an excision of the BCC(s) would have been performed. The study completion visit occurred either 1 week after the excision (when this visit was planned) or 1 week after the last treatment. For a subset of patients, skin biopsies were collected on the last treatment day and an excision of a BCC was also performed at that same visit.


Eligibility: Inclusion Criteria:
  - Patients with multiple basal cell carcinomas and Gorlin syndrome, or patients with multiple basal cell carcinomas and a mutation in the PTCH1 gene at chromosome 9q22.3
  Exclusion Criteria:
  -  Previous treatment of the BCC's that are selected for treatment.
  -  Any systemic treatment which is known to affect BCCs esp. cytostatic treatments, retinoids and photodynamic treatments.
  Other protocol defined Incl./Excl. criteria may apply.

Relevance to patient case: definitely relevant
Patient case: 56-year-old female with basal cell carcinoma; genetic feature: PTCH1

Clinical trial: Evaluation of Efficacy of Photodynamic Therapy in Basal Cell Carcinoma

Summary: The purpose of this study is to evaluate the efficacy of pdt in treatment of bcc and factors that affect response rate.

Detailed description: Background and Aim: Basal cell carcinoma (BCC) is the most common skin cancer .Photodynamic therapy _as a novel , non-invasive therapeutic approach _may be considered a valuable strategy. This study was designed with the aim of the evaluation of efficacy of PDT in treatment of BCC and factors that may affect response rate.
  Materials and Methods: This was a clinical trial which was done on 28 BCCs. Patients were treated with ALA-PDT monthly for 1-6 sessions and evaluated for clinical response,cosmetic results and probable side effects.

Eligibility: Inclusion Criteria:
  -  Histologically proven BCCs
  Exclusion Criteria:
  -  rodent ulcer
  -  morphea type
  -  ANA +
  -  history of photosensitivity or photodermatosis or ingestion of phototoxic drugs during last month
  -  pregnancy
  -  breast feeding
  -  age< 18
  -  history of another therapeutic intervention for bcc during last 6 months

Relevance to patient case: not relevant
Patient case: 56-year-old female with basal cell carcinoma; genetic feature: PTCH1

Clinical trial: Evaluation of Efficacy of Photodynamic Therapy in Basal Cell Carcinoma With 6 Months Follow-up

Summary: The purpose of this study is to evaluate the efficacy of photodynamic therapy (PDT)in treatment of Basal cell carcinoma (BCC) and recurrence rate after 6 months.

Detailed description: Background and Aim:
  Basal cell carcinoma (BCC) is the most common skin cancer .Photodynamic therapy _as a novel , non-invasive therapeutic approach _may be considered a valuable strategy. This study was designed with the aim of the evaluation of efficacy of PDT in treatment of BCC and recurrence rate after 6 months .
  Materials and Methods:
  This was a clinical trial which was done on 28 BCCs. Patients were treated with ALA-PDT monthly for 1-6 sessions and evaluated for clinical response,cosmetic results,recurrence rate and probable side effects.

Eligibility: Inclusion Criteria:
  -  Histologically proven BCCs
  Exclusion Criteria:
  -  Rodent ulcer
  -  Morphea type
  -  ANA +
  -  History of photosensitivity or photodermatosis or ingestion of phototoxic drugs during last month
  -  Pregnancy
  -  Breast feeding
  -  Age< 18
  -  History of another therapeutic intervention for bcc during last 6 months

Relevance to patient case: not relevant
Patient case: 56-year-old female with basal cell carcinoma; genetic feature: PTCH1

Clinical trial: Short Term Effects of Photodynamic Therapy in Basal Cell Carcinoma

Summary: The purpose of this study is to evaluate the efficacy of photodynamic therapy in treatment of Basal cell carcinoma (BCC) and factors that affect response rate.

Detailed description: Background and Aim: Basal cell carcinoma (BCC) is the most common skin cancer .Photodynamic therapy _as a novel , non-invasive therapeutic approach _may be considered a valuable strategy. This study was designed with the aim of the evaluation of efficacy of PDT in treatment of BCC and factors that may affect response rate.
  Materials and Methods: This was a clinical trial which was done on 28 BCCs. Patients were treated with ALA-PDT monthly for 1-6 sessions and evaluated for clinical response,cosmetic results and probable side effects.

Eligibility: Inclusion Criteria:
  -  Histologically proven BCCs
  Exclusion Criteria:
  -  Rodent ulcer
  -  Morphea type
  -  ANA +
  -  History of photosensitivity or photodermatosis or ingestion of phototoxic
  -  Drugs during last month
  -  Pregnancy
  -  Breast feeding
  -  Age< 18
  -  History of another therapeutic intervention for bcc during last 6 months

Relevance to patient case: not relevant
Patient case: 56-year-old female with basal cell carcinoma; genetic feature: PTCH1

Clinical trial: Golimumab Plus UVB-311nm in Psoriasis

Summary: Golimumab, a TNF-alpha antibody, has been approved in the EC and USA for the treatment of psoriatic arthritis. The aim of this study is to determine in a randomized half-side comparison whether additional narrowband UVB-311nm phototherapy accelerates and improves the clearance of psoriatic skin lesions in golimumab-treated patients.

Detailed description: Psoriatic skin lesions of patients with psoriatic arthritis who receive standard treatment with golimumab (50 mg or 100 mg s.c. once a month depending on total body weight whether below or above 100 kg, respectively) are exposed to UVB-311nm phototherapy on a randomized body half (left or right; head exempt) 3 x per week for six weeks and/or until complete response (defined as reduction in PASI to < 3). A patient qualifies if A) golimumab was started within a week or B) after 3 months of golimumab treatment the PASI reduction is smaller than 90%. PASI score, patient visual analogue score (VAS) for therapeutic response, and patient VAS for severity of skin lesions is assessed weekly; and at follow-up visits at month 3, 6, and 12. The primary hypothesis is that phototherapy increases the PASI reduction on the exposed body site by more than 20%. Paired Wilcoxon testing for differences in PASI and patient VAS scores is done; Fisher exact test is applied to determine differences in complete remission, PASI reduction > 90%, > 75% and/or 50% between body sites.

Eligibility: Inclusion Criteria:
  -  Age > 18 years
  -  Patients with psoriatic arthritis who receive treatment with golimumab
  -  Patient wish for treatment of psoriatic skin lesions
  Exclusion Criteria:
  -  Pregnancy or lactation
  -  Presence and/or history of malignant melanoma
  -  Presence and/or history of invasive squamous cell carcinoma of the skin
  -  Presence and/or history of more than 3 basal cell carcinomas
  -  Dysplastic nevus syndrome
  -  Antinuclear antibodies (ds-DNA, Ro/SSA, La/SSB)
  -  Autoimmune disorders such as lupus erythematosus or dermatomyositis
  -  Abnormal photosensitivity and photosensitive diseases such as porphyria, chronic actinic dermatitis, Xeroderma pigmentosum, basal cell nevus syndrome, and others
  -  General poor health status

Relevance to patient case: not relevant
Patient case: 56-year-old female with basal cell carcinoma; genetic feature: PTCH1

Clinical trial: L-lysine in Treating Oral Mucositis in Patients Undergoing Radiation Therapy With or Without Chemotherapy For Head and Neck Cancer

Summary: This pilot clinical trial studies L-lysine in treating oral mucositis in patients undergoing radiation therapy with or without chemotherapy for head and neck cancer. L-lysine may lessen the severity of oral mucositis, or mouth sores in patients receiving radiation therapy with or without chemotherapy for head and neck cancer

Detailed description: PRIMARY OBJECTIVES:
  I. To determine the complete response rate, decrease in severity, and time to complete response of oral mucositis related to head and neck cancer irradiation and chemotherapy after using L-lysine supplementation daily.
  SECONDARY OBJECTIVES:
  I. To determine the functional impact of use of L-lysine for oral mucositis on daily life as measured by the Functional Life Index-Cancer (FLIC) Questionnaire total score.
  OUTLINE:
  Patients receive L-lysine orally (PO) once daily (QD) until completion of radiotherapy and resolution of mucositis in the absence of disease progression or unacceptable toxicity.
  After completion of study treatment, patients are followed up weekly until mucositis resolves.

Eligibility: Inclusion Criteria:
  -  Cytologically or pathologically proven cancer of the oropharynx, lip, oral cavity, larynx, hypopharynx, nasopharynx, and salivary glands
  -  Predicted life expectancy greater than 12 weeks
  -  Eastern Cooperative Oncology Group (ECOG) Performance Status 0-2
  -  Renal function with a calculated creatinine clearance of 55 ml/min or greater, per Cockcroft-Gault formula
  -  Patients undergoing radiation therapy with or without concurrent chemotherapy
  -  Ability to understand and the willingness to sign a written informed consent document
  Exclusion Criteria
  -  Use of illicit drugs, alcohol abuse, or tobacco abuse during treatment
  -  Subjects may not be receiving other investigational agents
  -  Inability or unwillingness to comply with radiation therapy and chemotherapy regimens
  -  Inability or unwillingness to take daily L-Lysine supplementation as prescribed
  -  Use of arginine supplementation
  -  History of renal failure or compromise

Relevance to patient case: not relevant
Patient case: 56-year-old female with basal cell carcinoma; genetic feature: PTCH1

Clinical trial: Safety and Tolerability of ToleroMune Grass in Grass Allergic Subjects With Rhinoconjunctivitis

Summary: Grass pollen allergens are universally recognised as a major cause of allergic diseases in humans and animals, including asthma, allergic rhinitis, conjunctivitis and dermatitis. Worldwide, at least 40% of allergic patients are sensitized to grass pollen allergens and between 50-90% of hayfever or seasonal allergy sufferers are allergic to grass pollen.
  ToleroMune Grass is a novel, synthetic, allergen-derived peptide desensitising vaccine, currently being developed for the treatment of grass allergy.
  The purpose of the present study is to evaluate the safety and tolerability of multiple ascending doses of ToleroMune Grass in subjects allergic to grass.

Detailed description: This study is designed as a randomised, double-blind, placebo-controlled study to evaluate the safety and tolerability of escalating multiple doses of ToleroMune Grass in subjects with a documented history of allergic rhinoconjunctivitis on exposure to grass. The efficacy of ToleroMune HDM will also be explored LPSR, EPSR, CPT and levels of grass specific IgE.
  The study will consist of 3 study periods. In Period 1, Screening will be performed up to a maximum of 6 weeks before randomisation.
  Period 2 (Treatment Period) will consist of 4 visits (Visits 3A-3D) four weeks apart. The first cohort will receive the lowest dose and successive dose groups will increasing doses of ToleroMune Grass, provided the first administration of the previous dose was safe and well tolerated.
  In Period 3, 2 Post-treatment Challenge visits will take place, the first will be 2 weeks after the last administration in the Treatment Period and the second will be 17 weeks after the first administration. Follow-up will be conducted 3-10 days after the second PTC.

Eligibility: Inclusion Criteria:
  -  Male or female, aged 18-65 years
  -  Minimum 2 year history of rhinoconjunctivitis on exposure to grass
  -  Positive skin prick test to whole grass allergen
  -  LPSR to whole grass allergen 8-10 hours after intradermal injection of greater than 35mm diameter response
  -  Positive CPT to whole grass allergen with a score ≥4
  Exclusion Criteria:
  -  Subjects with a history of asthma
  -  Subjects with an FEV1 <80% of predicted
  -  Subjects with a rye grass specific IgE >100 kU/L
  -  Subjects with an acute phase skin response to whole grass allergen with a mean wheal diameter > 50 mm
  -  Subjects who score >1 for redness of conjunctiva or who have any watering or itchiness in the eye before administration of the CPT
  -  Treatment with beta-blockers, alpha-adrenoreceptor blockers, tranquillisers or psychoactive drugs
  -  History of any significant disease or disorder (e.g. cardiovascular, pulmonary, gastrointestinal, liver, renal, neurological, musculoskeletal, endocrine, metabolic, malignant, psychiatric, major physical impairment)

Relevance to patient case: not relevant