Team Research Aims & Tools for Genomic Data Analysis

This project focuses on team research aims, tools, and workflows for genomic data analysis. It involves tasks such as developing tools for data extraction, redesigning workflows, and creating digital learning modules for the next generation of scientists. The project aims to advance skills in reproducible research, utilizing a variety of technology and tools to enhance disease risk and treatment models. By leveraging community-developed tools and frameworks like Python, Flask, and GNapi, the team aims to streamline data analysis processes and enhance collaboration in research.

• Genomic Data Analysis
• Team Research
• Digital Learning Modules
• Workflow Tools
• Reproducible Research

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1. British Association of Dermatologists National Clinical Audit Programme 2014: NMSC excision

2. BAD-BSDS national audit on non-melanoma skin cancer excision Audit contributors BAD and BSDS members, with some contributions from non-members Leads David de Berker, Adam Bray, Daniel Keith, M. Firouz Mohd Mustapa Amalgamation of BAD quantitative (auditable) standards for both BCC and SCC, derived from BAD clinical guidelines for the management of BCC and SCC Audit standards source Completion date May 2014 Number of contributors 277 responses from 135 identifiable centres Number of patients 2739 Data collection Breakdown of the number of participants by region 40 (n=277) (n=2739) 30 20 10 0 Eire and N Ireland North London South London Yorkshire and the Humber East of England Scotland South West Wales East Midlands West Midlands South East Coast Thames Valley and Wessex North East North West Prospective (58.4%) Missing data (0.4%) Retrospective (41.2%)

3. Excision sites Excision sites - all diagnoses 25 20 (n=2738) 15 % Excision sites - all diagnoses 25 10 20 % 15 5 10 5 0 0 Genitalia, perineum, or perianal Periocular/Temple/Forehead/Eyebrow Nose (or within 1 cm) or Lips Cheek or Chin Hand or Foot Periocular/Temple/Forehead/Eyebrow Ear (or within 2 cm) Genitalia, perineum, or perianal Nose (or within 1 cm) or Lips Ear (or within 2 cm) Other Limb Cheek or Chin Other Limb Hand or Foot Trunk Trunk Scalp or Neck Scalp or Neck

4. Histology Pre-op diagnosis (n=2739) (n=2739) BCC (79.1%) Other NMSC: add comments (2.6%) Missing data (0.04%) Missing data (0.04%) SCC (17.9%) Incorrect data (0.4%) Incorrect data (0.4%) BCC (77.7%) Benign other lesion (3.0%) Bowen's (1.5%) Benign pigmented lesion (0.4%) Missing data (0.1%) SCC (14.0%) Other NMSC (1.6%) AK (1.5%) MM (0.2%) BCC (77.7%) Benign other lesion (3.0%) Bowen's (1.5%) Benign pigmented lesion (0.4%) Missing data (0.1%) SCC (14.0%) Other NMSC (1.6%) AK (1.5%) MM (0.2%) BCC (79.1%) Other NMSC: add comments (2.6%) SCC (17.9%)

5. Clinical and histological correlation Type No. of cases % Correlation All 2384/2728 87.1 prospective 1377/1600 86.1 retrospective 999/1128 88.6 BCC 2045/2167 94.4 prospective 1149/1227 93.6 retrospective 889/932 95.4 SCC 328/491 66.8 prospective 220/336 65.5 retrospective 107/153 69.9 Other NMSCs 11/70 15.7 prospective 8/37 21.6 retrospective 3/33 9.1

6. Clinical and histological correlation Histological diagnoses of non-correlated SCCs 30 20 % Histological diagnoses of non-correlated SCCs Histological diagnoses of non-correlated SCCs Histological diagnoses of non-correlated SCCs Histological diagnoses of non-correlated BCCs Histological diagnoses of non-correlated BCCs Histological diagnoses of non-correlated BCCs 10 40 40 40 30 30 30 (n=122) (n=163) 30 30 30 0 Benign pigmented lesion Benign other lesion Melanoma Bowen's BCC SCC Actinic keratosis Other NMSC 20 20 20 % 20 % % 20 20 % % % 10 10 10 10 10 10 0 0 0 0 0 0 Benign pigmented lesion Benign pigmented lesion Benign pigmented lesion Benign pigmented lesion Benign pigmented lesion Benign pigmented lesion Benign other lesion Benign other lesion Benign other lesion Benign other lesion Benign other lesion Benign other lesion Melanoma Bowen's Melanoma Melanoma Melanoma Melanoma Melanoma BCC SCC Bowen's Bowen's Bowen's Bowen's Bowen's Actinic keratosis Other NMSC BCC SCC BCC BCC SCC SCC BCC BCC SCC SCC Actinic keratosis Actinic keratosis Actinic keratosis Actinic keratosis Actinic keratosis Other NMSC Other NMSC Other NMSC Other NMSC Other NMSC

7. Types of excision and relative risk of complications Excision by type Excision (first treatment) 95.2% Re-excision 3.25% Punch biopsy (first treatment) 1.53% Relative risk of complications for re-excisions vs. excision Complications Excision Re-excision Total No 2233 75 2308 Yes 75 5 80 Total 2308 80 2388 Risk ratio of complication for re-excision = 1.92 (95% CI 0.80-4.62, p=0.18) Relatively small numbers of complications and re-excisions, therefore not statistically significant Possible under-reporting of complications due to most patients not being followed up in secondary care

8. Types of excision and proportions by body site

9. Location of histologically correlated excisions within 10 mm of a previous scar BCC excision sites within 10 mm of a previous scar SCC excision sites within 10 mm of a previous scar 25 30 Location of BCC excision sites within 10 mm of a previous scar Location of BCC excision sites within 10 mm of a previous scar 20 25 25 20 20 (n=123) (n=21) 15 20 % % 15 15 10 10 % % 10 10 5 5 5 0 0 0 0 Genitalia, perineum, or perianal Genitalia, perineum, or perianal Periocular/Temple/Forehead/Eyebrow Periocular/Temple/Forehead/Eyebrow Cheek or Chin Hand or Foot Trunk Other Limb Cheek or Chin Hand or Foot Hand or Foot Nose (or within 1 cm) or Lips Ear (or within 2 cm) Nose (or within 1 cm) or Lips Other Limb Trunk Ear (or within 2 cm) Cheek or Chin Scalp or Neck Other Limb Trunk Ear (or within 2 cm) Scalp or Neck Trunk Scalp or Neck Other Limb Hand or Foot Nose (or within 1 cm) or Lips Periocular/Temple/Forehead/Eyebrow Genitalia, perineum, or perianal Cheek or Chin Ear (or within 2cm) Scalp or Neck Nose (or within 1cm) or Lips Periocular/Temple/Forehead/Eyebrow Genitalia, perineum, or perianal

10. Deep and lateral margins of histologically correlated cases Distribution of BCC deep margin categories Distribution of SCC deep margin categories 80 80 60 60 (n=1901) (n=305) % % 40 40 20 20 0 0 0 Involved < 1 mm 1-5 mm > 5 mm 0 Involved < 1 mm 1-5 mm > 5 mm Distribution of SCC lateral margin categories Distribution of BCC lateral margin categories 80 80 60 60 (n=305) (n=1938) % 40 % 40 20 20 0 0 0 Involved < 1 mm 1-5 mm > 5 mm 0 Involved < 1 mm 1-5 mm > 5mm

11. Deep margins of histologically correlated BCCs prospective vs. retrospective Distribution of BCC deep margin categories - prospective Distribution of BCC deep margin categories - retrospective 80 80 60 60 (n=1062) (n=832) % % 40 40 20 20 0 0 Involved < 1 mm 1-5 mm > 5 mm Involved < 1 mm 1-5 mm > 5 mm Distribution of BCC deep margin categories - prospective vs. retrospective 80 70 60 50 Prospective (n = 1062) 40 % Retrospective (n = 832) 30 20 10 0 Involved < 1 mm 1-5 mm > 5 mm

12. Lateral margins of histologically correlated BCCs prospective vs. retrospective Distribution of BCC lateral margin categories - prospective Distribution of BCC lateral margin categories - retrospective 80 80 60 60 (n=1082) (n=849) % 40 % 40 20 20 0 0 Involved < 1 mm 1-5 mm > 5 mm Involved <1mm 1-5mm >5mm Distribution of BCC lateral margin categories - prospective vs. retrospective 90 80 70 60 50 Prospective (n = 1082) % 40 Retrospective (n = 849) 30 20 10 0 Involved < 1 mm 1-5 mm > 5 mm

13. Deep margins of histologically correlated SCCs prospective vs. retrospective Distribution of SCC deep margin categories - prospective Distribution of SCC deep margin categories - retrospective 80 80 60 60 (n=200) (n=104) % % 40 40 20 20 0 0 Involved < 1 mm 1-5 mm > 5 mm Involved < 1 mm 1-5 mm > 5 mm Distribution of SCC deep margin categories - prospective vs. retrospective 80 70 60 50 Prospective (n = 200) 40 % Retrospective (n = 104) 30 20 10 0 Involved < 1 mm 1-5 mm > 5 mm

14. Lateral margins of histologically correlated SCCs prospective vs. retrospective Distribution of SCC lateral margin categories - retrospective Distribution of SCC lateral margin categories - prospective 80 80 60 60 (n=199) (n=105) % % 40 40 20 20 0 0 Involved < 1 mm 1-5 mm > 5 mm Involved < 1 mm 1-5 mm > 5 mm Distribution of SCC lateral margin categories - prospective vs. retrospective 80 70 60 50 Prospective (n = 199) 40 % Retrospective (n = 105) 30 20 10 0 Involved < 1 mm 1-5 mm > 5 mm

15. Bleeding risk of histologically correlated cases Type Bleeding risk (aspirin & warfarin only) Complications BCC 406 9 (2.2%) SCC 95 10 (10.5%) BCC deep margins BCC lateral margins SCC deep margins SCC lateral margins

16. Distribution of tumour diameter Number of tumours with recorded diameters = 2388 Mean diameter 10.61 mm, standard deviation 6.92, error 0.14 Skew +4.8 Largest tumour = 130 mm

17. Deep margins of histologically correlated BCCs tumour size Breakdown of distribution of BCC lateral margin categories by tumour size Breakdown of distribution of BCC deep margin categories by tumour size 90 90 80 80 Largest tumour diameter Largest tumour diameter 70 70 60 60 10 mm 10 mm 50 50 % % 11-19 mm 11-19 mm 40 40 20 mm 20 mm 30 30 20 20 10 10 0 0 Involved < 1 mm 1-5 mm > 5 mm Involved < 1 mm 1-5 mm > 5 mm Breakdown of distribution of SCC lateral margin categories by tumour size Breakdown of distribution of SCC deep margin categories by tumour size 90 90 80 80 Largest tumour diameter Largest tumour diameter 70 70 60 60 10 mm 50 10 mm 50 % % 11-19 mm 11-19 mm 40 40 20 mm 20 mm 30 30 20 20 10 10 0 0 Involved < 1 mm 1-5 mm > 5 mm Involved < 1 mm 1-5 mm > 5 mm