HCV screening, linkage to care, and treatment patterns at different sites across one academic medical center.

BACKGROUND: It is unclear whether sites that screen large numbers of patients for Hepatitis C Virus but achieve limited follow-up are more or less effective at having patients succeed through linkage and treatment than lower volume sites that have higher linkage percentages. The objective was to compare the rates of HCV identification, linkage to care, and treatment success between different study sites including the Emergency Department, 3 outpatient clinics with unique patients, and the inpatient setting at one medical center. METHODS: This is a descriptive analysis of 2 years of data from a protocol that integrated HCV screening and treatment into clinical services throughout multiple departments in one medical center. The program used a best practice advisory to prompt testing at all sites, with different triggers for it to fire at each site, and one central navigation program that attempted to link all patients diagnosed with hepatitis C virus to outpatient care. Outcomes included volume of tests performed in each site, Antibody and RNA rates at each site, demographic data, navigation and linkage outcomes, and post-linkage treatment completion. RESULTS: 28,435 patients were screened across 5 clinical locations. RNA+ rates and absolute numbers linked to MD (linkage rates among all RNA+) were: ED 7.2% RNA+, 224 (22.6%) linked; Inpatient 14.8% RNA+, 27 (17.6%) linked, General Internal Medicine 3.9% RNA+, 269 (65.8%) linked, Infectious Diseases 4.0% RNA+, 34(70.8%) linked, Family Medicine 2.0% RNA+, 28 (75.7%) linked. Demographics, linkage barriers, and treatment initiation rates were different at all sites. CONCLUSION: Among sites there were differences in the sociodemographic characteristics of patients diagnosed with HCV, as well as differences in the success linking patients to outpatient care. At this medical center, the ED screened the most patients, the inpatient area had the highest RNA positivity rate, the FM clinic had the highest linkage rate, GIM linked the most patients by absolute number, and GIM also had the highest number of patients start treatment.

A computational solution to improve biomarker reproducibility during long-term projects.

Biomarkers are fundamental to basic and clinical research outcomes by reporting host responses and providing insight into disease pathophysiology. Measuring biomarkers with research-use ELISA kits is universal, yet lack of kit standardization and unexpected lot-to-lot variability presents analytic challenges for long-term projects. During an ongoing two-year project measuring plasma biomarkers in cancer patients, control concentrations for one biomarker (PF) decreased significantly after changes in ELISA kit lots. A comprehensive operations review pointed to standard curve shifts with the new kits, an analytic variable that jeopardized data already collected on hundreds of patient samples. After excluding other reasonable contributors to data variability, a computational solution was developed to provide a uniform platform for data analysis across multiple ELISA kit lots. The solution (ELISAtools) was developed within open-access R software in which variability between kits is treated as a batch effect. A defined best-fit Reference standard curve is modelled, a unique Shift factor "S" is calculated for every standard curve and data adjusted accordingly. The averaged S factors for PF ELISA kit lots #1-5 ranged from -0.086 to 0.735, and reduced control inter-assay variability from 62.4% to <9%, within quality control limits. S factors calculated for four other biomarkers provided a quantitative metric to monitor ELISAs over the 10 month study period for quality control purposes. Reproducible biomarker measurements are essential, particularly for long-term projects with valuable patient samples. Use of research-use ELISA kits is ubiquitous and judicious use of this computational solution maximizes biomarker reproducibility.

The Biospecimen Preanalytical Variables Program: A Multiassay Comparison of Effects of Delay to Fixation and Fixation Duration on Nucleic Acid Quality.

CONTEXT.­: Despite widespread use of formalin-fixed, paraffin-embedded (FFPE) tissue in clinical and research settings, potential effects of variable tissue processing remain largely unknown. OBJECTIVE.­: To elucidate molecular effects associated with clinically relevant preanalytical variability, the National Cancer Institute initiated the Biospecimen Preanalytical Variables (BPV) program. DESIGN.­: The BPV program, a well-controlled series of systematic, blind and randomized studies, investigated whether a delay to fixation (DTF) or time in fixative (TIF) affects the quantity and quality of DNA and RNA isolated from FFPE colon, kidney, and ovarian tumors in comparison to case-matched snap-frozen controls. RESULTS.­: DNA and RNA yields were comparable among FFPE biospecimens subjected to different DTF and TIF time points. DNA and RNA quality metrics revealed assay- and time point-specific effects of DTF and TIF. A quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was superior when assessing RNA quality, consistently detecting differences between FFPE and snap-frozen biospecimens and among DTF and TIF time points. RNA Integrity Number and DV200 (representing the percentage of RNA fragments longer than 200 nucleotides) displayed more limited sensitivity. Differences in DNA quality (Q-ratio) between FFPE and snap-frozen biospecimens and among DTF and TIF time points were detected with a qPCR-based assay. CONCLUSIONS.­: DNA and RNA quality may be adversely affected in some tumor types by a 12-hour DTF or a TIF of 72 hours. Results presented here as well as those of additional BPV molecular analyses underway will aid in the identification of acceptable delays and optimal fixation times, and quality assays that are suitable predictors of an FFPE biospecimen's fit-for-purpose.

Implementation and Preliminary Results of an Emergency Department Nontargeted, Opt-out Hepatitis C Virus Screening Program.

BACKGROUND: Emergency department (ED) visits provide an opportunity for hepatitis C virus (HCV) screening for patients who otherwise might not be tested. We report on a novel nontargeted, opt-out HCV screening and linkage-to-care (LTC) program implemented in an urban ED. METHODS: This is a descriptive analysis from 3 months (November 2016-January 2017) of a nontargeted, opt-out ED HCV screening and LTC program among patients at least 13 years old undergoing phlebotomy for clinical purposes. A multipurpose best practice advisory (BPA) alerted providers to the program and generated order labels. For patients who authorized testing, specimens were drawn in the ED for HCV antibody (Ab) and reflex confirmatory RNA tests. Public health navigators attempted to contact RNA-positive patients and arrange outpatient visits. RESULTS: HCV Ab tests were performed on 3,808 patients, a 6,950% increase from preprogram. The proportion of HCV Ab test positivity was 13.2% (504/3,808, 95% confidence interval [CI] = 12.2%-14.3%) and of those 97.8% (493/504) had a follow-up RNA test performed. A total of 292 were confirmed positive for active infection, for an overall RNA positivity rate of 7.7% (95% CI = 6.8%-8.5%). Of those with active infection, 155 (53%) were outside the Centers for Disease Control and Prevention birth cohort for increased risk for HCV including 46 (15.8%, 95% CI = 11.8%-20.4%) who also did not report injection drug use. Linkage attempts were documented on 223 (76.4%) patients and appointments were scheduled for 102 (38% of attempted). Sixty-six patients attended their LTC visit (22.5% of all RNA-positive patients, 30% of linkage-eligible patients). CONCLUSIONS: Nontargeted opt-out HCV testing can be successfully implemented in an ED setting. A number of patients diagnosed were outside traditional risk groups. Once diagnosed, an ED population may be difficult to engage in care, but a structured interdisciplinary program can successfully link patients to HCV care.

Biobanking-Budgets and the Role of Pathology Biobanks in Precision Medicine.

Biobanks have become an important component of the routine practice of pathology. At the 2016 meeting of the Association of Pathology Chairs, a series of presentations covered several important aspects of biobanking. An often overlooked aspect of biobanking is the fiscal considerations. A biobank budget must address the costs of consenting, procuring, processing, and preserving high-quality biospecimens. Multiple revenue streams will frequently be necessary to create a sustainable biobank; partnering with other key stakeholders has been shown to be successful at academic institutions which may serve as a model. Biobanking needs to be a deeply science-driven and innovating process so that specimens help transform patient-centered clinical and basic research (ie, fulfill the promise of precision medicine). Pathology's role must be at the center of the biobanking process. This ensures that optimal research samples are collected while guaranteeing that clinical diagnostics are never impaired. Biobanks will continue to grow as important components in the mission of pathology, especially in the era of precision medicine.

Transcription factor YY1 expression in human gastrointestinal cancer cells.

Over-expression of the multifunctional zinc-finger transcription factor Yin Yang 1 (YY1) has been associated with cellular proliferation and resistance to apoptotic stimuli. In this study, we report that YY1 was uniformly highly over-expressed in a wide range of human cancer cell lines and in human colon cancer tissue samples. The examination of YY1-specific mRNA expression demonstrated at least six mRNA isoforms ubiquitously expressed in normal human adult and fetal tissues. Substantial over-expression of two specific mRNA isoforms of 7.5 and 2.9 kb size, respectively, was detected in gastrointestinal and other cancer cells in vitro, whereby mRNA stability differed significantly between various cell lines. YY1 protein expression levels were similar in different colon cancer cell lines. Using FISH analysis of several colorectal cancer cell lines, the human YY1 locus was expectedly identified on chromosome 14q32 and no evidence of gene amplification and chromosomal translocation was observed. However, varying degree of aneuploidy was noted in vitro. YY1 immunoreactivity in human colon tumor samples was found more intense in poorly differentiated tumors than in moderately and well differentiated colon cancers and lower expression levels tended to be associated with shorter survival. In conclusion, YY1 was over-expressed in colon cancer in the absence of gene amplification and chromosomal translocation. YY1 mRNA and protein stability are important regulatory mechanisms of YY1 expression in colon cancer.