1. Engineering a Program to Digitally Analyze Genetic Tests for HPV Stephen Trusheim and Daniel Mokhtari, 2007-2008

2. Human Papillomavirus Human Papillomavirus (HPV) is the most common cause of cervical cancer. Cervical cancer is the second most common type of cancer in women (Khan et al., 2005). HPV has multiple types, ranging from low-risk to high-risk for cervical cancer (Muñoz et al., 2003). http://upload.wikimedia.org/wikipedia/en/a/ad/EM_of_pap_virus%2C_basal_tissue_grafted_to_mouse.jpg

3. Diagnosing HPV Diagnosing HPV requires determining the type of HPV contained in a patient sample. Polyacrylamide gel electrophoresis is used for this purpose.

4. Gel Electrophoresis

10. Diagnosing HPV Currently, a double-blind human review process is used to diagnose HPV types in completed gel-electrophoresis tests Human review is often qualitative, slow, and expensive Computers have the potential to automate interpretation for gel- electrophoresis tests

11. Goals 1.To engineer a Java-based program to quantitatively interpret gel electrophoresis tests for HPV 2.To diagnose more than 95% of genetic tests for HPV correctly 3.To reduce the time, cost, and effort required in each gel test

12. Test Interpretation Program Original Gel Image Image-Analysis Algorithms Test-Interpretation Algorithm Test Result HPV Type 16 – High Risk

13. Test Interpretation Program Original Gel Image Image-Analysis Algorithms Test-Interpretation Algorithm Test Result HPV Type 16 – High Risk

15. Test Interpretation Program Original Gel Image Image-Analysis Algorithms Test-Interpretation Algorithm Test Result HPV Type 16 – High Risk

16. Image Analysis Algorithms 1.Orientation 2.Lane Detection 3.Noise Reduction 4.Band Detection

17. Image Analysis Algorithms 1.Orientation 2.Lane Detection 3.Noise Reduction 4.Band Detection

25. Image Analysis Algorithms 1.Orientation 2.Lane Detection 3.Noise Reduction 4.Band Detection

31. Image Analysis Algorithms 1.Orientation 2.Lane Detection 3.Noise Reduction 4.Band Detection

36. Image Analysis Algorithms 1.Orientation 2.Lane Detection 3.Noise Reduction 4.Band Detection

46. Test Interpretation Program Original Gel Image Image-Analysis Algorithms Test-Interpretation Algorithm

48. Accepted Ranges for HPV Type 16

49. Band Detected (Base-Pairs) Expected Band Location (Base-Pairs) Percent Correlation 845N/AUncorrelated 842N/AUncorrelated 45745081.3% 32231060.7% 242200-250N/A 737294.6%

50. Band Detected (Base-Pairs) Expected Band Location (Base-Pairs) Percent Correlation 845N/AUncorrelated 842N/AUncorrelated 45745081.33 32231060.65 242200-250N/A 737294.62 Average Correlation of HPV Type 16:78.9%

53. This patient is diagnosed with: HPV Type 16.

54. Test Interpretation Program Original Gel Image Image-Analysis Algorithms Test-Interpretation Algorithm Test Result HPV Type 16 – High Risk

55. Results

56. Future Studies Improve band detection Expand test interpretation capabilities for Chlamydia, Gonorrhea, Cystic Fibrosis, and Inherited Thrombophilia Improve program success rate with the goal of receiving FDA approval for HPV tests

57. Acknowledgements Mrs. Lois Fruen Dr. Ronald McGlennen MD Mr. Robert Schuldt Mr. Jeremy Raadt Ms. Bonita Bryant MT(ASCP), CLSpMB(NCA) Access Genetics Breck Team Research

58. Engineering a Program to Digitally Analyze Genetic Tests for HPV Stephen Trusheim and Daniel Mokhtari, 2007-2008