Trial of Electronic Medical Record Integrated Next-Generation Sequencing Ordering in Veterans Affairs Cancer Care

PURPOSE

Previous studies document underuse of next-generation sequencing (NGS). We examined the impact to oncology care for veterans of incorporating NGS ordering into the Veterans Affairs (VA) electronic medical record (EMR) at two New York City VA Medical Centers.

METHODS

We identified patients with non-small cell lung cancer and prostate cancer with oncology clinic visits and NGS testing indications between January and December 2021. Patients were divided into external ordering (EO) with visits before we implemented an EMR ordering system for NGS in July 2021, and internal ordering (IO) with visits after this date. The primary outcome was proportion of NGS testing performed in EO versus IO groups. Secondary outcomes were time between metastatic disease diagnosis to receipt of test by vendor, time of metastatic diagnosis to result, and proportion of testing by race.

RESULTS

A total of 168 patients were identified, 116 EO and 52 IO patients. Between IO and EO periods, testing significantly increased from 52% to 87% (P ≤ .01); it was conducted more quickly, with time from metastatic diagnosis to sample receipt by the NGS vendor improving to median 37 days from 299 days (P = .03); and the time from documented metastatic disease to a test result improved to median 56 days from 309 days (P = .03). The proportion of tissue received by the vendor was not significantly different between the two groups. There were no significant differences in testing according to self-reported race.

CONCLUSION

Integration of NGS ordering in the EMR led to increased proportion and speed of testing for a vulnerable patient population served by the country's largest health system.

Effect of incorporating NGS ordering into computerized patient records system (CPRS) on VA precision oncology care

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Background: Precision oncology, targeting therapy to the molecular specifics of one patient’s cancer, improves outcomes and decreases toxicity. Previous studies have documented underuse of next generation sequencing (NGS) in both the Veterans Health Administration (VHA) and private sector cancer care. Our group’s work has found that requiring providers to order and review tests in multiple electronic medical record systems for a single patient is a significant barrier to precision oncology. Following the incorporation of electronic medical record (EMR) NGS ordering into the VA EMR (CPRS) at a New York VA Medical Center, we examined the effect of the ordering change on precision oncology care for veterans. Methods: We identified patients eligible for NGS testing who had medical oncology clinic visits at the Manhattan VA in 2021, and divided patients into those whose NGS required external ordering (EO) (i.e. direct to Foundation Medicine (FM)) and those whose NGS used internal ordering (IO) (i.e. integrated CPRS ordering). We collected demographic and clinical information, including intention to order NGS, date of NGS order, specimen receipt, and testing results, on all patients from CPRS and FM web-based portal. Descriptive statistics were calculated and variables were compared with chi-square, T-tests, and Mood’s median test. Results: A total of 138 patients were identified, 99 in the EO group and 38 in the IO group. The groups were vastly male, (100% EO vs 95% IO), had similar ages (average age 69 and 75, respectively, p = 0.24), approximately half were self-reported Black race (48% EO vs 46% IO; p = 0.89), and the preponderance of prostate cancer was higher in the EO group vs the IO group (81% EO vs 62% IO, p = 0.02). For the 99 EO patients, 74 (75%) had a documented intention to order, and 47 (64%) of those had a specimen received by FM. Of the 38 patients in the IO group, 38 (100%) had intention to order and 25 had results received by FM (66% vs 64% IO vs EO p = 0.91). Compared to the EO group, the IO group had shorter time from intention to order to sample received (among those with positive values): mean 172 days (d) vs 18 d and median 40 d vs 6 d (p = 0.04). Among those with metastatic disease and documented intention to order NGS (EO n = 72, IO n = 32), the time from diagnosis of metastatic disease to intention to order NGS was significantly shorter after implementation of internal ordering: mean 764 d vs 698 d, median 226 d vs 15 d, (p = 0.004). The time from diagnosis of metastatic disease to NGS result in FM was also significantly shorter for IO patients (mean 980 d vs 251 d; median 46 d vs 428 d, p = 0.0003). Conclusions: We found that incorporating NGS testing into CPRS decreased delay from diagnosis of metastatic disease to intention to order NGS testing, and from intention to order NGS testing to results received, ultimately enabling faster precision oncology care for patients.

Germline alterations in patients with biliary tract cancers: A spectrum of significant and previously underappreciated findings

BACKGROUND

With limited information on germline mutations in biliary tract cancers, this study performed somatic and germline testing for patients at Memorial Sloan Kettering Cancer Center with known biliary tract carcinoma with the aim of determining the frequency and range of pathogenic germline alterations (PGAs).

METHODS

Patients with biliary tract carcinoma were consented for somatic tumor and matched blood testing of up to 468 genes via the Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actionable Cancer Targets next-generation sequencing platform. A germline variant analysis was performed on a panel of up to 88 genes associated with an increased predisposition for cancer. Demographic and diagnostic details were collected.

RESULTS

Germline mutations were tested in 131 patients. Intrahepatic cholangiocarcinoma was the most common cancer (63.4%), and it was followed by gallbladder adenocarcinoma (16.8%), extrahepatic cholangiocarcinoma (16%), and otherwise unspecified biliary tract cancer (3.8%). Known and likely PGAs were present in 21 patients (16.0%), with 9.9% harboring a PGA in a high/moderate-penetrance cancer predisposition gene. Among high-penetrance cancer susceptibility genes, PGAs were most commonly observed in BRCA1 and BRCA2 (33.3%), which made up 5.3% of the entire cohort, and they were followed by PALB2, BAP1, and PMS2. Mutations in ATM, MITF, and NBN, moderate-penetrance cancer susceptibility genes, were identified in 1 patient each. There was no observed difference in the types of mutations among the subtypes of biliary tract cancer.

CONCLUSIONS

The frequency of PGAs found was comparable to existing data on the prevalence of germline mutations in other solid tumor types with matched tumor analysis. This provides support for the role of the BRCA1/2, ATM, and BAP1 genes in biliary tract cancer susceptibility.

Prospective Evaluation of Germline Alterations in Patients With Exocrine Pancreatic Neoplasms

Background

Identification of pathogenic germline alterations (PGAs) has important clinical and therapeutic implications in pancreas cancer. We performed comprehensive germline testing (GT) in an unselected prospective cohort of patients with exocrine pancreatic neoplasms with genotype and phenotype association to facilitate identification of prognostic and/or predictive biomarkers and examine potential therapeutic implications.

Methods

Six hundred fifteen unselected patients with exocrine pancreatic neoplasms were prospectively consented for somatic tumor and matched sample profiling for 410-468 genes. GT for PGAs in 76 genes associated with cancer susceptibility was performed in an "identified" manner in 356 (57.9%) patients and in an "anonymized" manner in 259 (42.1%) patients, using an institutional review board-approved protocol. Detailed clinical and pathological features, response to platinum, and overall survival (OS) were collected for the identified cohort. OS was analyzed with Kaplan-Meier curves.

Results

PGAs were present in 122 (19.8%) of 615 patients involving 24 different genes, including BRCA1/2, ATM, PALB2, and multiple additional genes associated with the DNA damage response pathway. Of 122 patients with germline alterations, 41.8% did not meet current guidelines for GT. The difference in median OS was not statistically significant between patients with and without PGA (50.8 months, 95% confidence interval = 34.5 to not reached, two-sided P = .94). Loss of heterozygosity was found in 60.0% of BRCA1/2.

Conclusions

PGAs frequently occur in pancreas exocrine neoplasms and involve multiple genes beyond those previously associated with hereditary pancreatic cancer. These PGAs are therapeutically actionable in about 5% to 10% of patients. These data support routinely offering GT in all pancreatic ductal adenocarcimona patients with a broad panel of known hereditary cancer predisposition genes.

Phase 1 trial evaluating cisplatin, gemcitabine, and veliparib in 2 patient cohorts: Germline BRCA mutation carriers and wild-type BRCA pancreatic ductal adenocarcinoma

BACKGROUND

A phase 1 trial was used to evaluate a combination of cisplatin, gemcitabine, and escalating doses of veliparib in patients with untreated advanced pancreatic ductal adenocarcinoma (PDAC) in 2 cohorts: a germline BRCA1/2-mutated (BRCA+) cohort and a wild-type BRCA (BRCA-) cohort. The aims were to determine the safety, dose-limiting toxicities (DLTs), maximum tolerated dose, and recommended phase 2 dose (RP2D) of veliparib combined with cisplatin and gemcitabine and to assess the antitumor efficacy (Response Evaluation Criteria in Solid Tumors, version 1.1) and overall survival.

METHODS

Gemcitabine and cisplatin were dosed at 600 and 25 mg/m2 , respectively, over 30 minutes on days 3 and 10 of a 21-day cycle. Four dose levels of veliparib were evaluated: 20 (dose level 0), 40 (dose level 1), and 80 mg (dose level 2) given orally twice daily on days 1 to 12 and 80 mg given twice daily on days 1 to 21 (dose level 2A [DL2A]).

RESULTS

Seventeen patients were enrolled: 9 BRCA+ patients, 7 BRCA- patients, and 1 patient with an unknown status. DLTs were reached at DL2A (80 mg twice daily on days 1 to 21). Two of the 5 patients in this cohort (40%) experienced grade 4 neutropenia and thrombocytopenia. Two grade 5 events occurred on protocol. The objective response rate in the BRCA+ cohort was 7 of 9 (77.8%). The median overall survival for BRCA+ patients was 23.3 months (95% confidence interval [CI], 3.8-30.2 months). The median overall survival for BRCA- patients was 11 months (95% CI, 1.5-12.1 months).

CONCLUSIONS

The RP2D of veliparib was 80 mg by mouth twice daily on days 1 to 12 in combination with cisplatin and gemcitabine; the DLT was myelosuppression. Substantial antitumor activity was seen in BRCA+ PDAC. A randomized phase 2 trial is currently evaluating cisplatin and gemcitabine with and without veliparib for BRCA+ PDAC (NCT01585805). Cancer 2018;124:1374-82. © 2018 American Cancer Society.

Phase II trial of veliparib in patients with previously treated BRCA-mutated pancreas ductal adenocarcinoma

PURPOSE

BRCA-associated cancers have increased sensitivity to poly(ADP-ribose) polymerase inhibitors (PARPis). This single arm, non-randomised, multicentre phase II trial evaluated the response rate of veliparib in patients with previously treated BRCA1/2- or PALB2-mutant pancreatic adenocarcinoma (PDAC).

METHODS

Patients with stage III/IV PDAC and known germline BRCA1/2 or PALB2 mutation, 1-2 lines of treatment, Eastern Cooperative Oncology Group 0-2, were enrolled. Veliparib was dosed at a volume of 300 mg twice-daily (N = 3), then 400 mg twice-daily (N = 15) days 1-28. The primary end-point was to determine the response rate of veliparib; secondary end-points included progression-free survival (PFS), duration of response, overall survival (OS) and safety.

RESULTS

Sixteen patients were enrolled; male N = 8 (50%). Median age was 52 years (range 43-77). Five (31%) had a BRCA1 and 11 (69%) had a BRCA2 mutation. Fourteen (88%) patients had received prior platinum-based therapy. No confirmed partial responses (PRs) were seen: one (6%) unconfirmed PR was observed at 4 months with disease progression (PD) at 6 months; four (25%) had stable disease (SD), whereas 11 (69%) had PD as best response including one with clinical PD. Median PFS was 1.7 months (95% confidence interval [CI] 1.57-1.83) and median OS was 3.1 months (95% CI 1.9-4.1). Six (38%) patients had grade III toxicity, including fatigue (N = 3), haematology (N = 2) and nausea (N = 1).

CONCLUSIONS

Veliparib was well tolerated, but no confirmed response was observed although four (25%) patients remained on study with SD for ≥ 4 months. Additional strategies in this population are needed, and ongoing trials are evaluating PARPis combined with chemotherapy (NCT01585805) and as a maintenance strategy (NCT02184195).

Real-Time Genomic Profiling of Pancreatic Ductal Adenocarcinoma: Potential Actionability and Correlation with Clinical Phenotype

Purpose: Molecular profiling in cancer has identified potential actionable drug targets that have prompted attempts to discover clinically validated biomarkers to guide therapeutic decision-making and enrollment to clinical trials. We evaluated whether comprehensive genetic analysis of patients with pancreatic adenocarcinoma is feasible within a clinically relevant timeframe and whether such analyses provide predictive and/or prognostic information along with identification of potential targets for therapy.Experimental Design: Archival or prospectively acquired FFPE samples and matched normal DNA from N = 336 patients with pancreatic cancer were analyzed using a hybridization capture-based, next-generation sequencing assay designed to perform targeted deep sequencing of all exons and selected introns of 410 key cancer-associated genes. Demographic and treatment data were prospectively collected with the goal of correlating treatment outcomes and drug response with molecular profiles.Results: The median time from protocol consent to reporting of the genomic results was 45 days with a median time from tissue delivery of 20 days. All genetic alterations identified were stratified based upon prior evidence that the mutation is a predictive biomarker of drug response using the MSKCC OncoKB classification. Three of 225 patients (1%) received a matched therapy based upon the sequencing results.Conclusions: The practical application of molecular results to guide individual patient treatment is currently limited in patients with pancreatic adenocarcinoma. Future prospective molecular profiling efforts should seek to incorporate routine germline genetic analysis and the identification of DNA profiles that predict for clinical benefit from agents that target DNA damage repair and or immunotherapy. Clin Cancer Res; 23(20); 6094-100. ©2017 AACR.

Overall survival and clinical characteristics of BRCA mutation carriers with stage I/II pancreatic cancer

BACKGROUND

BRCA1/BRCA2 germ line (GL) mutation carriers with pancreatic adenocarcinoma (PDAC) may have distinct outcomes. We recently described an apparent more favourable prognosis of surgically resected BRCA-associated PDAC patients in a single-arm, uncontrolled, retrospective study. However, the prognostic impact of GL BRCA1/2 mutations in surgically resected PDAC has not been compared with a matched control population.

METHODS

A larger multi-centre, case-control retrospective analysis was performed. Cases were patients with surgically resected, BRCA1/2-associated PDAC from 2004 to 2013. Controls included surgically resected PDAC cases treated during the same time period that were either BRCA non-carriers, or had no family history of breast, ovarian or pancreatic cancers. Cases and controls were matched by: age at diagnosis (within ±5-year period) and institution. Demographics, clinical history, overall survival (OS) and disease-free survival (DFS) were abstracted from patient records. Statistical comparisons were assessed using χ²- and Fisher's exact test, and median DFS/OS using Kaplan-Meier method and log-rank testing.

RESULTS

Twenty-five patients with BRCA1-(n=4) or BRCA2 (N=21)-associated resectable PDAC were identified. Mean age was 55.7 years (range, 34-78 years), 48% (n=12) were females and 76% (n=19) were Jewish. Cases were compared (1 : 2) with 49 resectable PDAC controls, and were balanced for age, ethnicity and other relevant clinical and pathological features. BRCA-associated PDAC patients received neoadjuvant, or adjuvant platinum-based treatment more frequently than controls (7 out of 8 vs 6 out of 14) and (7 out of 21 vs 3 out of 44), respectively. No significant difference in median OS (37.06 vs 38.77 months, P=0.838) and in DFS (14.3 vs 12.0 months, P=0.303) could be demonstrated between cases and controls. A trend to increased DFS was observed among BRCA-positive cases treated with neoadjuvant/adjuvant platinum-containing regimens (n=10) compared with similarly treated controls (n=7) (39.1 vs 12.4 months, P=0.255).

CONCLUSIONS

In this retrospective analysis, the prognosis of surgically resectable BRCA-associated PDAC is no different than that of sporadic PDAC from the same institution. The role of platinum-based adjuvant therapy in this setting requires prospective investigation.

Phase II trial of veliparib (V) in patients (pts) with previously treated BRCA or PALB2-mutated (mut) pancreas adenocarcinoma (PC)

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Background: BRCA1, BRCA2, and PALB2 germline mutations are associated with an increased risk of PC. Other BRCA-associated cancers have demonstrated increased sensitivity to PARP inhibitors (PARPi) and early trials have shown activity of PARPi in untreated BRCAmut PC. We evaluated theactivity of V in patients with previously treated BRCA/PALB2mutPC. Methods: Eligibility: BRCA1/2, or PALB2mutPC, at least 1 and up to 2 prior treatment regimens, measurable stage III/IVPC; ECOG 0-1. Treatment Plan: V 300mg BID (N= 3 pts), then V 400mg BID day1- 28. Primary endpoint: RECIST 1.1 response rate (RR). Statistical plan: Single-arm, non-randomized, open-label, phase II, two-stage design, unacceptable RR 10%, promising 28%, type I, II error rates 10%. Secondary endpoints: progression-free survival (PFS), duration of response, overall survival, safety, tolerability and archival tumor analyses. Results: Between 05/12 and 12/13, N= 16 enrolled. Male= 8, Female= 8. Median age= 52 years (range 43- 77). BRCA1 mut=5. BRCA2 mut=11. N= 1AJCC stage III PC, N= 15 AJCC stage IV PC. N= 8 and N= 8 (50%) had 1 and 2 prior lines of therapy respectively. N= 13 (81%) received prior platinum therapy. Response: N= 1 unconfirmed PR (PR at 4 months (mo), POD at 6 mo), N= 4 stable disease (SD), N= 10 progressive disease (PD); N= 1 inevaluable (12 days of V only due to disease-related complications). Median PFS was 52 days (range 12 to 423). Three pts treated at 400mg V were dose-reduced for toxicity. Six pts had V related grade 3 toxicity including fatigue (N=3), hematologic (N=2) and nausea (N=1). No therapy-related grade 4-5 toxicities were observed. Conclusions: V was well tolerated. While no confirmed partial responses were observed, single-agent activity of V in previously treated PC was noted, and N= 4 (25%) remained on study with SD for ≥ 4mo (4, 6, 6, 9 mo). A randomized phase II trial evaluating cisplatin,gemcitabine +/- V is underway in untreated BRCA/PALB2mutPC (NCT01585805). Results of correlative studies will be presented. Acknowledgements: Lustgarten Foundation. NCI.AbbVie. Clinical trial information: NCT01585805.

Evidence of case management effect on traumatic-brain-injured adults in rehabilitation

The purpose of this study was to evaluate the evidence for effectiveness of case management during recovery from traumatic brain injury (TBI) in adults. After an overview of TBI incidence, prevalence, and problems, and a brief explanation of case management, the study methods are described, the findings are discussed and recommendations are made for future research. Medline, HealthSTAR, CINAHL, PsychINFO, and the Cochrane Library databases were searched and 83 articles met the criteria for review. The strongest studies (n = 3) were critically appraised and their design features and data were placed in two evidence tables. Due to methodological limitations, there was neither clear evidence of effectiveness nor of ineffectiveness. For future research, we recommend controlled research designs, standardization of measures, adequate statistical analysis and specification of health outcomes of importance to persons with TBI and their families.

Effect of cognitive rehabilitation on outcomes for persons with traumatic brain injury: A systematic review

We evaluated evidence for the effectiveness of cognitive rehabilitation methods to improve outcomes for persons with traumatic brain injury (TBI). A search of MEDLINE, HealthSTAR, CINAHL, PsycINFO, and the Cochrane Library produced 600 potential references. Thirty-two studies met predetermined inclusion criteria and were abstracted; data from 24 were placed into evidence tables. Two randomized controlled trials and one observational study provided evidence that specific forms of cognitive rehabilitation reduce memory failures and anxiety, and improve self-concept and interpersonal relationships for persons with TBI. The durability and clinical relevance of these findings is not established. Future research utilizing control groups and multivariate analysis must incorporate subject variability and must include standard definitions of the intervention and relevant outcome measures that reflect health and function.

Summary report: evidence for the effectiveness of rehabilitation for persons with traumatic brain injury

We evaluated the evidence for effectiveness of rehabilitation methods throughout the phases of recovery from traumatic brain injury (TBI) in adults. MEDLINE, HealthSTAR, CINAHL, PsycINFO, and the Cochrane Library were searched, and a total of 3,098 abstracts were reviewed. The strongest studies were critically appraised and their data placed in evidence tables. Results showed that to determine the effectiveness of rehabilitation interventions for persons with TBI, a commitment must be made to population-based studies, strong controlled research design, standardization of measures, adequate statistical analysis, and specification of health outcomes of importance to persons with TBI and their families.

Visualization of proteoglycans and link protein in embryonic chick limb cartilage via cryofixation, freeze-substitution and immunochemical techniques

Chick embryo limb bud cartilage contains a family of proteoglycans, a few of which have been identified ultrastructurally by antibody labelling. Limb bud cartilage from stage 30-34 chick embryos was high-pressure frozen, freeze-substituted and embedded in Lowicryl resin. Sections were treated with polyclonal antibodies for core protein and monoclonal antibodies for chondroitin-6-sulphate and link protein. Label for core protein was demonstrated on both structural matrix and free within the compartmental space. Quantitative analysis indicates that core protein is preferentially localized on electron-dense structural matrix, and that this distribution is uniform between stages 30 and 34. The association of protein epitopes on electron-dense lattice is strongly influenced, rather than a chance observation. Significant quantities of core protein are also located in the free compartments of the cartilaginous lattice. Chondroitin-6-sulphate and link protein were localized predominantly within the compartments of the embryonic lattice. Our data provide convincing evidence that the proteoglycans were immobilized within a microcrystalline matrix of the embryonic compartments. A role for core protein as a stabilizer within the lattice and in the free space where it serves to aggregate polymeric proteoglycans is suggested from our results.