This Flynnetal_readme.txt file was generated on 2022-10-13 by Michael Seth Flynn


GENERAL INFORMATION

1. Title of Dataset: Data from: Clinicopathologic Characteristics of Melanoma in Parkinson's Disease Patients

2. Author Information
	A. Principal Investigator Contact Information
		Name: Michelle Pavlis
		Institution: Duke University
		ORCID: https://orcid.org/0000-0001-5491-6653
		Email: michelle.pavlis@duke.edu

	B. Associate or Co-investigator Contact Information
		Name: Seth Flynn
		Institution: Duke University
		ORCID: https://orcid.org/0000-0002-7941-1069
		Email: msf45@duke.edu


3. Date of data collection (single date, range, approximate date) <suggested format YYYY-MM-DD>: January 1, 2007 - January 1, 2020

4. Geographic location of data collection <latitude, longitude, or city/region, State, Country, as appropriate>: Durham, NC, United States

5. Information about funding sources that supported the collection of the data: We wish to acknowledge support from the Biostatistics, Epidemiology and Research Design (BERD) Methods Core funded through Grant Award Number UL1TR002553 from the National Center for Advancing Translational Sciences (NCATS), a component of the National Institutes of Health (NIH). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Grant Award Number UL1TR002553


SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: CC0 Waiver

2. Links to publications that cite or use the data: N/A

3. Links to other publicly accessible locations of the data: N/A

4. Links/relationships to ancillary data sets: N/A

5. Was data derived from another source? No
	A. If yes, list source(s): 

6. Recommended citation for this dataset: Flynn, M. S., Robinson, C., Patel, S., Liu, B., Green, C., Pavlis, M. (2022): Data from: Clinicopathologic characteristics of melanoma in Parkinson's disease patients. Duke Research Data Repository. https://doi.org/10.7924/r4f47t77k


DATA & FILE OVERVIEW

1. File List: 
melanoma parkinsons project final data0826.csv

2. Relationship between files, if important: N/A

3. Additional related data collected that was not included in the current data package: None

4. Are there multiple versions of the dataset? No
	A. If yes, name of file(s) that was updated: 
		i. Why was the file updated? 
		ii. When was the file updated? 


METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 
Following approval by the Duke Health Institutional Review Board, case group patients were identified by review of a prospectively maintained institutional database, Duke Enterprise Data Unified Content Explorer (DEDUCE), of all melanoma patients with a concurrent diagnosis of PD at Duke University Medical Center from January 1, 2007 to January 1, 2020. Patients were excluded from the review if a full pathology report for a primary melanoma was not in the electronic records at Duke University. We conducted a retrospective review of 70 total patients ≥ 18 years of age. For our control group, we first identified all patients with melanoma and without Parkinson’s disease in the DEDUCE database in our study’s date range, limiting this group based on patients who also had pathology reports available in the DEDUCE Text Reports system (n = 6405). We then performed a 2:1 match between the control group and the case group. Each patient was matched for age (maximum age difference: 2 years), sex, and race. Age was defined as the age at first diagnosis of melanoma corresponding to International Classification of Diseases codes documented in the DEDUCE database. We then performed chart reviews to collect clinicopathologic data regarding the primary melanomas of these control group patients. The pathology reports of some patients in our study date range were related to nodal metastasis or distant metastatic disease and did not include a full report regarding the primary melanoma, so these patients were excluded during chart review. Subsequent rounds of matching were performed until each patient in the case group had at least one matching control randomly selected from control patients meeting criteria. Our final control cohort comprised 102 patients. Pertinent information regarding lesion characteristics of the primary melanoma including the anatomic location, histologic subtype, AJCC 8th Edition stage, Clark level, Breslow depth, ulceration, mitotic rate, presence or absence of lymphovascular and perineural invasion, tumor-infiltrating lymphocytes, regression, nodal involvement, and metastasis was collected. Additionally, we examined patient characteristics including the dates of diagnosis for both PD and melanoma, personal or family history of melanoma, personal history of nonmelanoma skin cancers, personal history of dysplastic nevi, and the medications used for treating Parkinson's disease.

2. Methods for processing the data: 
Variables of interest were collected directly from electronic health records and stored in Microsoft Excel files in the Duke Health Protected Analytics Computing Environment (PACE), a highly protected virtual network space. 

3. Instrument- or software-specific information needed to interpret the data: 
All statistical analyses were performed using SAS version 9.4 (SAS Institute Inc., Cary, NC).

4. Standards and calibration information, if appropriate: N/A

5. Environmental/experimental conditions: N/A

6. Describe any quality-assurance procedures performed on the data: N/A




DATA-SPECIFIC INFORMATION FOR: melanoma parkinsons project final data0826.csv

1. Number of variables: 37

2. Number of cases/rows: 184

3. Variable List: 
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
	A. record_id, a variable used to deidentify records in place of a medical record number
	B. Matching Number, the number assigned to cases during the case-control matching process
	C. Group, assignment of patients to case or control group
	D. Age at first diagnosis (DEDUCE), the age (in years) at which patients received their first diagnosis of a primary melanoma per the date of ICD code from the Duke DEDUCE database
	E. Age at Biopsy, the age (in years) at which the patient's melanoma was biopsied per review of electronic health record data
	F. Follow up time since Biopsy, the span between diagnostic biopsy and the most recent clinical follow-up visit with dermatology (in years)
	G. Age at Parkinson's Diagnosis, the age (in years) from the electronic health record data at which patients received their first diagnosis of Parkinson's disease.
	H. Follow up time since Parkinson's Diagnosis, the span between first diagnosis of Parkinson's disease and the most recent clinical follow-up visit for Parkinson's disease (in years)
	I. Melanoma before Parkinson's, for patients in the case group this yes/no variable indicates if their biopsy-proven diagnosis of melanoma preceded their Parkinson's disease diagnosis. 
	J. Sex, patient sex (male/female)
	K. Race, patient race (Caucasian/Other)
	L. Dead/alive, patient survival status as of January 1, 2020
	M. History of NMSC (non melanoma skin cancer), a variable indicating if patients had no history of NMSC (none), squamous cell carcinoma (SCC), basal cell carcinoma (BCC), or both SCC and BCC (both)
	N. Number of previous SCCs, a continuous variable indicating the number of SCCs diagnosed in case and control patients as of January 1, 2020
	O. Number of previous BCCs, a continuous variable indicating the number of BCCs diagnosed in case and control patients as of January 1, 2020
	P. History of dysplastic nevi, a yes/no variable indicating a history of previously biopsied dysplastic nevi. Does not indicate mild/moderate/severe atypia.
	Q. Site of primary melanoma, a variable indicating the body site where the primary melanoma was biopsied (head/neck, trunk, lower extremity (LE), upper extremity (UE), choroidal)
	R. Head/neck, a variable indicating if the primary melanoma originated on the head or neck (head/neck yes, head/neck no)
	S. Melanoma subtype, a variable indicating the histopathologic subtype of melanoma obtained from pathology reports in electronic health record (Nodular, superficial spreading, invasive desmoplastic, lentigo maligna, malignant melanoma in situ (MMIS), invasive spindle cell, mucosal, malignant blue nevus, unspecified)
	T. MMIS/Invasive, a binary variable indicating if the melanoma was in situ (MMIS) or invasive
	U. AJCC, a variable indicating the American Joint Committee on Cancer 8th Edition staging of the primary melanoma (clinical stages: MMIS (stage 0), 1a, 1b, 2a, 2b, 2c, 3a, 3b, 3c, 3d, 4)
	V. AJCC combined, a variable grouping clinical melanoma stagings into the following categories: MMIS (in situ, stage 0 disease), 1 (stage 1a, 1b), 2 (stage 2a, 2b, 2c), and >=3 (stage 3a, 3b, 3c, 3d, 4)
	W. Clark level, a variable indicating the anatomic depth of invasion using the Clark level system, abstracted from pathology reports in the electronic health record when available (Clark level 1, 2, 3, 4, and 5). If blank, was not in pathology report. 
	X. Breslow depth (mm), a continuous variable indicating the depth of invasion for melanoma in millimeters (mm)
	Y. Breslow depth for invasive tumors (mm), a variable including only Breslow depths (mm) for invasive tumors and leaving blank entries for melanoma in situ. 
	Z. Breslow depth, a variable grouping Breslow depths (mm) into the following categories: 0 mm (in situ disease), 0-1 mm, 2-4 mm, >4 mm.
	AA. SLNB, a variable indicating if a sentinel lymph node biopsy was performed, and if so, the results (No SLNB, negative (was performed and was negative), and positive (was performed with positive nodal disease). 
	AB. WLE, a variable indicating if patients were treated with wide local excision (yes/no)
	AC. MOHS, a variable indicating if patients were treated with Mohs micrographic surgery (yes/no)
	AD. Metastasis, a variable indicating if patients ever experienced distant metastasis as of January 1, 2020 (yes/no)
	AE. Systemic Therapy for melanoma, a variable indicating if a systemic chemotherapeutic or immunotherapeutic agent was used for treatment of melanoma
	AF. Ulceration, a yes/no variable extracted from review of pathology reports in the electronic health record to determine if ulceration was present on the biopsy specimen. If blank, was not available in pathology report. 
	AG. Mitotic rate, a continuous variable extracted from review of pathology reports in the electronic health record to determine the mitotic rate (in mitoses/square millimeter). If blank, was not available in pathology report. 
	AH. Lymphovascular invasion, a yes/no variable extracted from review of pathology reports in the electronic health record to determine if lymphovascular invasion was present on the biopsy specimen. If blank, was not available in pathology report. 
	AI. Perineural invasion, a yes/no variable extracted from review of pathology reports in the electronic health record to determine if perineural invasion was present on the biopsy specimen. If blank, was not available in pathology report. 
	AJ. Tumor infiltrating lymphocytes, a yes/no variable extracted from review of pathology reports in the electronic health record to determine if tumor-infiltrating lymphocytes were present on the biopsy specimen. If blank, was not available in pathology report. 
	AK. Regression, a yes/no variable extracted from review of pathology reports in the electronic health record to determine if regression was present on the biopsy specimen. If blank, was not available in pathology report. 

4. Missing data codes: N/A

5. Specialized formats or other abbreviations used:
- PD: Parkinson's disease
- SCC: squamous cell carcinoma
- BCC: basal cell carcinoma
- MMIS: malignant melanoma in situ
- SLNB: sentinel lymph node biopsy
- AJCC: American Joint Committee on Cancer