SUPPLEMENTARY FILES (APPENDIX) Appendix Table 1. Operational definitions of Hepatitis C Virus Infection Specific Process Measures Quality Indicator Numerator Denominator Rate, % (N eligible) Pre-treatment Domain 1. Confirmation of HCV viremia Patients who received hepatitis C hepatitis C ribonucleic acid (RNA) test before or within 12 months after (+) antibody test Patients with (+) hepatitis C antibody test 90.2 (31,193) 2. Specialty referral Patients who saw a specialist# before or within 12 months after (+) RNA date Patients with (+) hepatitis RNA test 53.6 (34,212) 3. HCV genotype testing Patients who received HCV genotype test before or within 12 months after seeing a specialist. Patients with confirmed viremia who saw a specialist 75.9 (21,640) 4. Liver biopsy in genotype 1 patients Patients who received a liver biopsy before or within 12 months after seeing a specialist. Patients with genotype 1 HCV who saw a specialist 26.3 (13,268) 5. Autoimmune liver disease testing Patients who received testing to rule out autoimmune liver disease before or within 12 months after seeing a specialist. Patients with confirmed viremia who saw a specialist 53.8 (22,022) 6. Iron overload testing Patients who received testing to rule out iron overload before or within 12 months after seeing a specialist. Patients with confirmed viremia who saw a specialist 71.3 (22,022) 7. Hepatitis B testing Patients who received testing to rule out hepatitis B virus co-infection before or within 12 months after seeing a specialist. Patients with confirmed viremia who saw a specialist 91.2 (22,022) Preventive and Comorbid Care Domain 8. HIV testing Patients who received a HIV test within 12 months before or after (+) HCV test date Patients without a previous HIV diagnosis 27.7 (34,265) 9. Hepatitis A serology testing Patients who received a hepatitis A serology test within 12 months after (+) HCV test date Patients with no prior hepatitis A serology test or hepatitis A vaccination 66.5 (32,881) 10. Hepatitis B serology testing Patients who received a hepatitis B serology test within 12 months after (+) HCV test date Patients with no prior hepatitis B serology test or hepatitis B vaccination 81.6 (31,257) 11. Hepatitis A vaccination Patients who received at-least 1 hepatitis A vaccination‡ within 12 months after (+) HCV test Patients with no prior hepatitis A vaccination or documented immunity within 1 year after HCV test date 25.1 (26,171) 12. Hepatitis B vaccination Patients who received at-least 1 hepatitis B vaccination‡ within 12 months after (+) HCV test Patients with no prior hepatitis B vaccination or documented immunity within 1 year after HCV test date 30.1 (22,863) 13. Referral for depression management Patients who received >1 of the following treatments for depression: psychotherapy, Patients with HCV and a diagnosis of depression† 65.6 (13,326) antidepressant prescription, visit to mental health clinic within 28 days of depression diagnosis 14. Referral for substance abuse disorder (SUD) Patients who received > 1 of the following treatments for SUD: psychotherapy, aversion therapy, visit to mental health clinic within 28 days of SUD diagnosis Patients with HCV and a diagnosis of SUD† 48.7 (18,637) Patients who received at-least 1 prescription of interferon within 12 months of seeing a specialist Patients with genotype 1 or 4 HCV who saw a specialist Patients who received at-least 1 prescription of interferon within 12 months of seeing a specialist Patients with genotype 2 or 3 HCV who saw a specialist 17. Ribonucleic acid (RNA) testing prior to treatment Patients who received quantitative RNA test within 6 months prior to start of anti-viral therapy or 2 weeks after Patients who received first interferon prescription,§ and at-least 6 months of follow up before interferon start date 69.8 (5588) 18. RNA testing at treatment week 12 Patients who received RNA test between 10 – 14 weeks after start of anti-viral therapy Patients who received first interferon prescription before 9/24/2006,§ and atleast 12 weeks of ongoing treatment^ 62.3 (4696) 19. RNA testing at treatment week 24 Patients who received RNA test between 20 – 28 weeks after start of anti-viral therapy Patients who received first interferon prescription before 6/18/2006,§ and atleast 24 weeks of ongoing treatment^ 62.6 (3427) 20. RNA testing at treatment week 48 Patients who received RNA test between 44 – 56 weeks after start of anti-viral therapy Patients who received first interferon prescription before 12/4/2005,§ and atleast 48 weeks of ongoing treatment^ 80.3 (1024) 21. RNA testing at 24 weeks after end of treatment Patients who received RNA test anytime after post treatment week 22 Patients who received first interferon prescription§ before 1/1/2005 and had a negative RNA test at the end of treatment^ 90.5 22. Lowering ribavirin dose for anemia Patients who had a dose reduction or discontinuation of ribavirin within 35 days of hemoglobin test date Patients with hemoglobin < 10g/dl after first interferon start date and on ribavirin 22.2 (942) 23. No stimulating factors for low neutrophil count Patients who did not receive any prescription for colony stimulating growth factor after the low neutrophil count date Patients with neutrophil count of 500 700/mm3 after interferon start date 72.0 (579) Antiviral Treatment 15. Antiviral treatment in genotype 1/ 4 16. Antiviral treatment in genotype 2 or 3 22.9 (33,076) 26.7 (10,838) Treatment Monitoring Domain (2040) Appendix Table 1. Hepatitis C Specific Process Measures and their Operational Definitions For all laboratory tests (HCV antibody, HCV RNA, HCV genotype, hepatitis A and B serology, and HIV), we used LOINC codes in combination with laboratory test names to identify relevant tests. We then used laboratory test names and test results to limit to specific tests of interest. HCV medications were identified using medication name in the pharmacy data. #Anti-viral treatment is rendered by gastroenterologists (clinic stop code 307), infectious disease (310), and (in some VA facilities) by primary care providers (323). To ascertain which of these 3 clinics served as a specialty clinic for each VA facility, we used pharmacy data and selected the clinic responsible for writing majority of the first interferon prescriptions for HCV patients in a given facility. We classified a patient as having seen the specialists if s/he had a clinic visit to the specialty clinic which was accompanied with diagnostic codes for HCV, cirrhosis, or chronic liver disease not specified. §We included only those patients who received first course of interferon. All patients had > 3 months of follow up prior to first interferon prescription, ensuring that we did not include patients who might have entered the VA while on treatment, thus compromising the ascertainment of treatment initiation date. ^We defined treatment duration by calculating the cumulative days of supply of interferon prescriptions, as previously described by Backus et al. (1) We identified gaps in treatment as the difference between the last date covered by previous prescriptions and the fill date for the next prescription, and classified patients to have received sequential treatment if they had gaps greater than 45 days. &RNA testing at 24 weeks after end of treatment is used to assess sustained virologic response. In a sensitivity analysis, we restricted the time window for the test to include only those RNA tests that were performed between 20 and 28 week after end of treatment. We found that 57% of patients with a negative test at the end of treatment had at least 1 RNA test during this time frame. † Depression defined as 1 inpatient or 2 outpatient ICD-9 codes within 1 year. inpatient visit or outpatient ICD-9 code within 1 year ‡CPT 6 Substance use disorder (SUD) defined as 1 codes. hepatitis A vaccination: 90632, 90633, 90634,90636, 90730; hepatitis B vaccination: 90636, 90740, 90743, 90744, 90746, 90747, 90748, G0010. These codes have been reported to be highly predictive of presence of vaccination in patients’ medical records (positive and negative predictive values >90%) (2) Appendix Table 2. Sensitivity Analyses. Association of facility factors with overall care in patients with hepatitis C virus infection. The first column (Model 1) presents the results of the regression analysis limiting to patients without evidence of treatment contraindications. The second column (Model 2) presents the results in a subsample with cirrhosis. Variables Age (reference 66 yrs and older 56-65 yrs 46-55 yrs < 45 yrs Race (reference white) Black Other Number of visits/quarter Cirrhosis Depression Drug or alcohol use >1 medical comorbidity Weekly ½ day clinics1 No dedicated clinic 1-3 4-7 8-12 13 or more HCV quality improvement efforts <3 4 or more HCV patient load Lowest load (lowest quartile, <430 patients) Higher load Region West Mid-Atlantic Midwest 1 Odds ratio (95% confidence interval Model 1 Model 2 1.39 (1.09-1.79) 1.36 (1.09-1.70) 1.22 (0.92-1.62) 1.76 (1.24-2.49) 1.75 (1.26-2.44) 1.95 (1.30-2.9) 1.25 (1.03-1.51) 1.8 (0.99-3.28) 1.11 (1.08-1.14) 1.11 (0.78-1.59) NA NA NA 1.13 (0.92-1.39) 0.73 (0.42-1.26) 1.07 (1.05-1.09) NA 1.03 (0.87-1.21) 0.87 (0.75-1.01) 0.91 (0.76-1.09) -1.52 (0.70-3.27) 1.51 (0.77-2.97) 1.36 (0.66-2.77) 3.58 (1.81-7.05) -0.82 (0.52-1.29) 1.00 (0.68-1.48) 1.31 (0.87-1.96) 1.49 (1.00-2.23) -1.38 (0.84-2.28) -1.12 (0.82-1.53) -1.1 (0.64-1.9) -0.85 (0.60-1.21) Northeast -0.80 (0.46-1.37) 0.61 (0.35-1.07) 0.32 (0.15-0.69) South 0.68 (0.39-1.20) -1.22 (0.88-1.69) 0.99 (0.71-1.38) 1.11 (0.72-1.7) 1.33 (0.96-1.85) Standardized per 1000 HCV patients We removed patients with severe depression, drug and alcohol use, and severe medical comorbidity from Model 1. As a result, these variables are not included in the regression model. All patients in Model 2 had evidence of cirrhosis. As a result, Model 2 does not include a variable for cirrhosis. References 1. Backus LI, Boothroyd DB, Phillips BR, Mole LA. Predictors of response of US veterans to treatment for the hepatitis C virus. Hepatology. 2007;46:37-47. 2. Hachem CY, Kramer JR, Kanwal F, El-Serag HB. Hepatitis vaccination in patients with hepatitis C: practice and validation of codes at a large Veterans Administration Medical Centre. Aliment Pharmacol Ther. 2008;28:1078-87