araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 64-year-old male with head and neck squamous cell carcinoma; genetic feature: CDKN2A

Clinical trial: Biomarkers to Detect Anal Intraepithelial Neoplasia in Thai Men Who Have Sex With Men

Summary: The goals of this application are to assess the usefulness of biomarkers, including p16 proteins, minichromosome maintenance (MCM) proteins, high-risk human papillomavirus (HPV) types, and E6 and E7 mRNA/oncoproteins, as adjunct tools to anal Pap smear in identifying HGAIN and to study the impact of HIV infection on the characteristics of anal cytology (by anal Pap smear) and biomarkers. To fulfill these goals, in addition to routine practice, it will be necessary to follow 450 MSM (315 HIV-positives and 135 HIV-negatives) over 60 months, and perform HRA and biomarkers on all clients at baseline and every 12 months. Information from this study would inform AIN screening and follow up approaches in HIV-positive and HIV-negative MSM in both resource-limited and resource-rich settings.

Detailed description: The goals of this application are to assess the usefulness of biomarkers, including p16 proteins, MCM proteins, high-risk HPV types, and E6 and E7 mRNA/oncoproteins, as adjunct tools to anal Pap smear in identifying HGAIN and to study the impact of HIV infection on the characteristics of anal cytology (by anal Pap smear) and biomarkers. To fulfill these goals, in addition to routine practice, it will be necessary to follow 450 MSM (315 HIV-positives and 135 HIV-negatives) over 60 months, and perform HRA and biomarkers on all clients at baseline and every 12 months. Information from this study would inform AIN screening and follow up approaches in HIV-positive and HIV-negative MSM in both resource-limited and resource-rich settings.

Eligibility: Inclusion Criteria:
  -  MSM with HIV negative
  -  MSM with HIV positive

Relevance to patient case: not relevant
Patient case: 64-year-old male with head and neck squamous cell carcinoma; genetic feature: CDKN2A

Clinical trial: Finding Predictors of Side Effects to Chemoradiation Treatment in Elderly Patients With Head and Neck Cancer

Summary: To look at what types of measures can be used to predict how an older person will tolerate chemoradiation treatment for head and neck cancer. This study uses surveys and a blood draw to look at the different measures.

Detailed description: Purpose: To identify baseline predictors of change in function over the course of treatment with chemoradiotherapy in patients with head and neck cancer.
  Participants: Patients 65 or older who have an appointment at the North Carolina Cancer Hospital (NCCH) or other participating sites, have planned chemoradiotherapy for head and neck cancer
  Procedures (methods): Consenting subjects will complete a Geriatric Assessment, Functional Assessment of Cancer Therapy - Head and Neck and give a blood sample for CBC and p16INK4a at the start of their chemoradiotherapy, at week four, at the end and 90 days post therapy. They will also complete a health behavior questionnaire at baseline.

Eligibility: Inclusion Criteria
  -  Patients will be eligible for this protocol provided they have an appointment at the North Carolina Cancer Hospital (NCCH), have planned chemoradiotherapy for head and neck cancer (any histology) and consent to complete the Geriatric Assessment. No exclusions will be made based on gender, ethnicity, performance status or race. Patient must be able to read and speak English.
  -  Signed, IRB approved written informed consent.
  -  Age of at least 65 years.
  -  Enrollment in other studies, both therapeutic and observational, will not result in exclusion.
  Exclusion Criteria
  -  Inability to read and speak English.
  -  Inability to comply with study for any other reason than language

Relevance to patient case: not relevant
Patient case: 64-year-old male with head and neck squamous cell carcinoma; genetic feature: CDKN2A

Clinical trial: Early Diagnosis of Oral Cancer by Detecting p16 Methylation

Summary: The purpose of this study is to verify the function of p16 methylation diagnostic reagents in early diagnosis of oral cancer.

Detailed description: Background:Oral epithelial dysplasia (OED) is one of the common precancerous lesions among Chinese adults. To investigate the clinical predictive value of p16 methylation diagnostic reagents in the early diagnosis of oral cancer, the investigators carried out the prospective multi-center double-blind cohort study.
  Methods:180 patients with histologically confirmed mild or moderate OED were included in the present study. The investigators using p16 methylation diagnostic reagents to analysis of the p16 methylation status in these patients. Building two follow-up queue by p16-methylated and p16-unmethylated. The Statistical analysis used SAS6.12 software. All P-values were two-sided. P<0.05 was considered to test for statistical significance difference.

Eligibility: Inclusion Criteria:
  -  Histopathological diagnosis of oral lesions meet the epithelial diagnostic criteria for mild to moderate grade OED
  -  No local area stimulate by residual root and crown, sharp cusp, poor restoration and biting cheek or lips
  -  Without the OCE treatment history by laser , radiation or chemical
  -  Be able to Sign the informed consent
  Exclusion Criteria:
  -  Histopathological diagnosis of oral lesions do not meet the epithelium of mild to moderate dysplasia diagnostic criteria; histological diagnosis of severe grade OED or malignant disease
  -  Pregnancy or breast-feeding women
  -  Serious heart, lung, liver , kidney and other systemic diseases
  -  local area stimulate by residual root and crown, sharp cusp, poor restoration and biting cheek or lips
  -  OED treatment history by LASER, radiotherapy, or chemotherapy
  -  Tumor and psychiatric patients
  -  Patients are unable to cooperate

Relevance to patient case: not relevant
Patient case: 64-year-old male with head and neck squamous cell carcinoma; genetic feature: CDKN2A

Clinical trial: Valproic Acid and Platinum-based Chemoradiation in Locally Advanced Head and Neck Squamous Cell Carcinoma

Summary: The purpose of this study is to evaluate if the addition of valproic acid to standard platinum-based chemoradiation as definitive treatment of locally advanced Head and Neck squamous cell carcinoma can improve treatment outcomes, such as response rate.

Detailed description: Valproic acid is a known histone deacetylase inhibitor. In addition to activating apoptosis pathways, cell differentiation and downregulating expression of growth factors, it also promotes radiosensitization.
  Most patients with Head and Neck squamous cell carcinoma are diagnosed with locally advanced disease, in which long term disease control is still a challenge. The incorporation of epigenetic regulation into standard treatment could improve results of definitive platinum-based chemoradiation in such patients.

Eligibility: Inclusion Criteria:
  -  Unresectable Oropharyngeal or oral cavity squamous cell carcinoma
  -  Candidate for definitive chemoradiation
  -  No previous treatment
  -  Measurable disease according to RECIST v 1.1
  -  Previous neoplasia, other than Head and Neck, with more than five years without evidence of disease; basocellular carcinoma of the skin and in situ cervical dysplasia if resected
  -  Age under 60 years
  -  ECOG performance status 0-2
  -  Ability of understanding and giving informed consent
  -  Adequate renal and hepatic function
  -  Adequate bone marrow function
  -  Normal serum magnesium
  -  Absence of QTc prolongation
  -  Life expectancy of over 12 weeks
  Exclusion Criteria:
  -  Pregnancy
  -  Distant metastasis
  -  Hypersensibility to valproic acid or other antiepileptic drugs
  -  Valproic acid chronic use
  -  Severe neurologic impairment
  -  Uncontrolled comorbidity
  -  Hypoalbuminemia
  -  Known history of hepatitis B, C or HIV

Relevance to patient case: not relevant
Patient case: 64-year-old male with head and neck squamous cell carcinoma; genetic feature: CDKN2A

Clinical trial: DAHANCA 28A: Phase I/II Study on Accelerated, Hyperfractionated Radiotherapy With Concomitant Cisplatin and Nimorazole

Summary: P16 negative cancers continue to have a dismal prognosis despite advances in the treatment of head and neck cancer. Acceleration, dose-escalation, hyperfractionation, chemotherapy and nimorazole has been shown to improve local control. The purpose of the study i to investigate the level of co-morbidity and performance status (PS) that allows the combination of all of the above means of treatment intensification


Eligibility: Inclusion Criteria:
  -  Squamous Cell Carcinoma head and neck cancer of the pharynx, larynx and oral cavity
  -  P16 negative
  -  T1-4
  -  N1-3
  -  M0
  -  Organ function and performance status allowing radical chemo-radiotherapy
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 64-year-old male with head and neck squamous cell carcinoma; genetic feature: CDKN2A

Clinical trial: An Imaging Study in Patients With Thyroid Cancer or Head and Neck Cancer With Pertechnetate Made in a Cyclotron (C-PERT)

Summary: Doctors at the Cross Cancer Institute have developed a new method of producing 99mTc Pertechnetate in a cyclotron unit. A study done at the Cross Cancer Institute in 2011 with ten patients using this imaging agent showed that it was safe and produced images with the same pattern as generator produced Pertechnetate. This study is now being done in larger numbers of patients to again show that the imaging pattern of both agents is the same, and to again demonstrate its safety.

Detailed description: To demonstrate the efficacy of cyclotron-produced Tc-99m pertechnetate (C-PERT; manufactured by the Edmonton PET Centre/ERC) in comparison to generator-produced Tc-99m pertechnetate (G-PERT; from approved commercial source; using qualitative and quantitative clinical imaging biodistribution data.

Eligibility: Inclusion Criteria:
  -  thyroid cancer, or
  -  Head and Neck cancer for salivary gland transfer
  -  age 18-79
  -  biochemical parameters < 5x ULN
  -  WBC > 3.0/uL
  -  ANC > 1.5/uL
  -  platelets > 75,000/uL
  -  hemoglobin > 10 g/dL
  -  Karnofsky 50-100
  Exclusion Criteria:
  -  nursing or pregnant females
  -  < 18 or > 79 Years
  -  uncontrolled asthma
  -  acute iritis
  -  narrow angle glaucoma
  -  previous radiation to head/neck

Relevance to patient case: not relevant
Patient case: 64-year-old male with head and neck squamous cell carcinoma; genetic feature: CDKN2A

Clinical trial: Chromoendoscopy to Detect Early Synchronous Second Primary Esophageal Carcinoma

Summary: Patients with HNSCC represent a high-risk group for the development of SESCC. Thus, esophagogastrofibroscopy should be performed to detect possible synchronous esophageal carcinomas in these patients.
  Although only two patients with synchronous primary carcinomas were found among the patients with newly diagnosed HNSCC in this study, esophagoscopy and better some of advanced endoscopic methods should be recommended after detection of HNSCC to exclude secondary esophageal carcinoma or dysplasia. Staining of the esophagus with Lugol's solution is an easy and inexpensive option and can be done in most of gastroenterology offices.

Detailed description: ABSTRACT Objective: To evaluate the use of flexible esophagoscopy and chromoendoscopy with Lugol's solution in the detection of early esophageal carcinomas (second primary carcinomas) in patients with squamous cell carcinoma of the head and neck (HNSCC).
  Methods: All patients with newly diagnosed HNSCC underwent office-based Lugol chromoendoscopy. After flexible esophagoscopy with white light, 3.0% Lugol iodine solution was sprayed over the entire esophageal mucosa. Areas with less-intense staining (LVLs) were evaluated and biopsies taken.

Eligibility: Inclusion Criteria:
  -  Newly diagnosed patients with head and neck carcinoma
  -  Age 18-65
  Exclusion Criteria:
  -  Recurrent head and neck carcinomas
  -  Previously diagnosed oesophageal cancer

Relevance to patient case: not relevant
Patient case: 64-year-old male with head and neck squamous cell carcinoma; genetic feature: CDKN2A

Clinical trial: Study on the Interplay Between Twist1 and Other EMT Regulators Through microRNA-29 Family.

Summary: Investigation of the molecular mechanism and clinical significance of the interplay between Twist1 and other EMT regulators through microRNA-29 family.

Detailed description: Head and neck squamous cell carcinoma (HNSCC) is one of the leading causes of cancer deaths worldwide, and it ranks the fourth male cancer-related death in Taiwan. In HNSCC, invasiveness and metastasis of cancer cells contribute to the major cause of mortality; therefore, elucidation of the mechanism and development of new strategies against metastasis is the utmost importance in treating advanced HNSCC. Epithelial-mesenchymal transition (EMT) is a process by which epithelial cells lose their polarity and are converted to a mesenchymal phenotype, and recently is considered as the major mechanism for cancer metastasis. The initiation of EMT is hallmarked by suppression of the intercellular junctional protein E-cadherin by a variety of transcriptional factors, including Twist1, Snail, Slug, SIP1, Zeb1 and E47. However, during metastatic evolution, the interplay between different EMT inducers has been investigated limitedly. Previously study demonstrated that hypoxia induces EMT of HNSCC through induction of Twist1 expression. Additionally showed that Twist1 promotes EMT and tumor-initiating capability through upregulation of Bmi1, and co-expression Twist1 and Bmi1 predicts a worse prognosis of HNSCC cases. Accumulated evidence suggests that microRNAs play essential roles in cancer progression and metastasis. Therefore, we aim to investigate the role of microRNA in Twist1-mediated cancer metastasis, and the interplay between Twist1 and other EMT regulators. Our preliminary data showed that the expression of miR-29 family, including miR-29a, b, and c were increased in Twist1-overexpressing HNSCC cells. Furthermore, we discovered that SIN3A, a co-repressor of another EMT regulator Snail, is a target of miR-29s. We therefore speculate that Twist1 modifies the function of Snail through microRNA machinery. In this proposal, we will delineate the regulatory mechanism of the Twist1-miR29s-SIN3A axis. We will also investigate the molecular interplay between Twist1 and Snail through Twist1-miR29s-SIN3A signal pathway. Furthermore, we will elucidate the molecular basis and pathophysiologic significance of Twist1-Snail interaction under hypoxic environment. Finally, we will confirm the in vitro finding by in vivo animal study and HNSCC samples. These results will provide crucial information for understanding the molecular basis of HNSCC metastasis, and will be valuable for developing new therapeutic strategies against advanced HNSCC.

Eligibility: Inclusion Criteria:
  -  Head and neck cancer
  Exclusion Criteria:
  -  pregnant woman

Relevance to patient case: not relevant
Patient case: 64-year-old male with head and neck squamous cell carcinoma; genetic feature: CDKN2A

Clinical trial: International Cancer of the Head and Neck, Genetics and Environment (InterCHANGE) Study

Summary: Our overall objective is to understand the role of lifestyle factors, genetics and HPV infection in the development and prognosis of head and neck cancer particularly in Asia.


Eligibility: Inclusion Criteria:
  Age 18~80 Incident head and neck cancer patients
  -  Oral, oropharynx and hypopharynx (C00-C14)
  -  Laryngreal cancer (C32)
  -  *Esophageal cancer if possible (C15)
  Exclusion Criteria:
  -  Salivary gland (C07-C08)
  -  Nasopharynx (C11)
  -  Thyroid (C79.3)

Relevance to patient case: not relevant
Patient case: 64-year-old male with head and neck squamous cell carcinoma; genetic feature: CDKN2A

Clinical trial: Post-operative Radiation With Cetuximab for Locally Advanced Cutaneous Squamous Cell Carcinoma of the Head and Neck

Summary: The standard treatment of surgery followed by radiation therapy can stop tumors from growing in the head and neck region in most patients. However, the cancer can recur or can spread to other parts of the body. Cetuximab is a drug that may delay or prevent tumor growth by blocking certain cellular chemical pathways that lead to tumor development. It was approved by the United States Food and Drug Administration (FDA) in 2006 for the treatment of head and neck cancer.
  The purpose of this study is to determine how easily cetuximab can be added to treatment with radiation therapy in patients with cutaneous cancer of the head and neck. This study will also look at how well cetuximab added to radiation therapy works over time and how well this treatment is tolerated.

Detailed description: This is a Phase II trial to characterize the feasibility of treating patients with locally advanced cutaneous squamous cell carcinomas of the head and neck with post-operative radiotherapy and cetuximab. Cetuximab has previously been given safely in conjunction with head and neck radiotherapy for mucosal squamous cell carcinoma in multiple phase III trials, and so Phase I data is not necessary here.

Eligibility: Inclusion Criteria:
  -  Pathologically (histologically) proven diagnosis of cutaneous squamous cell carcinoma of the head and neck
  -  Clinical stage >/= T3 or >/= N1, M0 including no distant metastases
  -  Gross total resection of the primary tumor with curative intent must be completed within 7 weeks of registration
  -  Performance status of 0-1 within 2 weeks prior to registration
  -  Age >/= 18
  -  Adequate labs within 2 weeks prior to registration
  Exclusion Criteria:
  -  Prior invasive malignancy unless disease free for a minimum of 3 years; noninvasive cancers (For example, carcinoma in situ of the breast, oral cavity, or cervix are all permissible) are permitted even if diagnosed and treated < 3 years ago. Patients with a history of T1-2, N0, M0 resected differentiated thyroid carcinoma are considered eligible.
  -  Prior systemic chemotherapy or anti-epidermal growth factor therapy for the study cancer or for a different prior cancer
  -  Prior radiotherapy to the region of the study cancer that would result in overlap of radiation therapy fields

Relevance to patient case: not relevant
Patient case: 64-year-old male with head and neck squamous cell carcinoma; genetic feature: CDKN2A

Clinical trial: HPV Serum DNA Levels Predicting Outcome in p16+ Squamous Cell Head and Neck Cancer

Summary: To assess in an exploratory manner, the pronostic utility for locoregional control, progression-free and distant metastasis-free survival of a pre-therapy and post-therapy blood DNA test of HPV E6 and E7 DNA for subtypes 16 and 18 in p16+ and/or HPV+ oropharyngeal cancer patients. This will entail analysis of both initial pre-therapy HPV level as a continuous variable and initial post-therapy HPV level as a dichotomous variable.


Eligibility: Inclusion Criteria:
  -  Histoloically proven primary cancer of the oropharynx, p16(+) and/or HPV (+), who are planned for treatment with resection, radiation and/or chemotherapy.
  -  Subsites of oropharynx:include tonsil, base of tongue, vallecula, oropharyngeal wall, soft palate, glossotonsillar sulcus.
  -  No or minimal smoking history (</= 10 pack-year, no smoking in the past 12 months last 10 years based on documented history and/or subject report)
  -  Age 18 years or older
  -  Subjects are capable of giving informed consent or have an acceptabl;e surrogate capable of giving consent on the subjects behalf.
  -  Enrollment on any other study, regardless of therapy is allowed.
  -  Enrollment on any other tumor or tissue banking study is allowed.
  -  Patients who have had blood drawn as part of another study, including the IRB-approved ENT Tumor Bank Study, may be included in this study even if the patient has already had surgery.
  Exclusion Criteria:
  -  Previous chemotherapy or radiation therapy to the head and neck unrelated to current disease.
  -  Previous surgery for head and neck cancer unrelated to current disease.
  -  Widespread , biopsy-proven metastatic disease (stage IVC disease) at time of presentation (small indeterminate lung or mediastinal nodules are allowed)
  -  Patients who have started induction chemotherapy prior to consideration for study eligibility.
  -  Another active cancer except nonmelanomatous skin cancer.
  -  History of cervical penile or anal cancer.
  -  Patient treated with surgery, adjuvant radiation therapy or chemotherapy outside of the University of Pennsylvania.
  -  History of smoking in the past last 12 months 10 years
  -  History of 10 pack-years of cigarette smoking based on documented history and/or subject report
  -  Presence of sidespread leukoplakia or erythroplakia.

Relevance to patient case: definitely relevant
Patient case: 64-year-old male with head and neck squamous cell carcinoma; genetic feature: CDKN2A

Clinical trial: Soy Isoflavones in Preventing Head and Neck Cancer Recurrence in Patients With Stage I-IV Head and Neck Cancer Undergoing Surgery

Summary: This phase II clinical trial studies how well soy isoflavones work in preventing head and neck cancer in patients with stage I-IV head and neck cancer undergoing surgery. Chemoprevention is the use of certain drugs to keep cancer from forming. The use of soy isoflavones may prevent head and neck cancer recurrence.

Detailed description: PRIMARY OBJECTIVES:
  I. To determine if short term, preoperative (300 mg/day x 14 treatment days) soy isoflavone supplementation modulates p16 methylation (% CpG sites methylated) and expression of p16, cyclooxygenase 2 [COX-2], vascular endothelial growth factor receptor [VEGF], epidermal growth factor receptor [EGFR], interleukin-6 [IL6], p53 and B-cell lymphoma-extra large [Bcl-xL] in tumor and non-tumor adjacent mucosa of patients with head and neck squamous carcinoma undergoing curative tumor resection.
  II. To estimate correlations of tumor p16 methylation (% CpG sites methylated) with expression of p16 and levels of, IL6, VEGF, and 15-F2t-isoprostane in serum and saliva.
  SECONDARY OBJECTIVES:
  I. Describe the toxicity of short-term, preoperative treatment with soy isoflavone.
  II. To determine overall and relapse-free survival.
  OUTLINE:
  Patients receive soy isoflavones orally (PO) for approximately 14 days before undergoing surgery.
  After completion of treatment, patients are followed up, within the routine cancer management schedule, at 3, 6, 12, and 24 months.

Eligibility: Inclusion Criteria:
  -  Patients must have pathologically-confirmed, resectable, squamous cell carcinoma of the oral cavity, oropharynx, larynx or hypopharynx
  -  Disease must be Stage I, II, III or IVa
  -  Tumor must be potentially surgically resectable and curable with conventional surgery and radiation therapy
  -  Eastern Cooperative Oncology Group (ECOG) Performance status 0-2
  -  Patients must give documented informed consent to participate in this study
  Exclusion Criteria:
  -  Documented evidence of distant metastases
  -  Ongoing acute medical condition such as uncontrolled coronary artery disease, emphysema, or diabetes mellitus that would preclude surgical resection
  -  Pregnancy or lactation; patients of child bearing age must agree to use adequate contraception (hormonal or barrier method of birth control) prior to study entry and for the duration of soy administration
  -  A medical or psychiatric illness which would compromise the patient's ability to tolerate this treatment or comply with administration of study drug
  -  Patients residing in prison
  -  Any patient with a history of breast or ovarian cancer
  -  Allergy to soy products

Relevance to patient case: not relevant