The positive impact of implementing an onsite guideline-based genetic testing procedure for prostate cancer in a multidisciplinary uro-oncology clinic

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Background: Prior to the guidelines set forth by the 2017 Philadelphia consensus conference, genetic testing for prostate cancer was conducted based on personal and family history of malignancies pursuant to NCCN recommendations. The 2017 guidelines expanded testing criteria to included age at diagnosis, metastatic disease, and tumor sequencing. In spite of these advancements, limited literature is available regarding successful implementation of a streamlined system for genetic testing in prostate cancer. This paper explores the benefits of implementing an on-site guideline-based genetic testing process for prostate cancer patients treated at a multi-disciplinary uro-oncology practice. Methods: Data was retrospectively reviewed for 561 prostate cancer patients seen in a multi-disciplinary uro-oncology clinic since January 2017. Prior to January, 1, 2019 genetic testing was recommended to patients based on NCCN guidelines, and swabs for testing were procured off-site less than 1 mile from the clinic (n=107). After January, 1, 2019 genetic testing was recommended based on the guidelines set forth by the Philadelphia consensus conference, and swabs for testing were procured at the clinic itself (n=454). Results: A statistically significant increase in compliance with genetic testing was observed after the implementation of an on-site, guideline-based testing process. Patient compliance with genetic testing increased from 33.6% to 96.5%. The time to receive the genetic test results (calculated as the time between referral for genetic testing and obtaining the test results) was also significantly improved from 38 days to 21 days. Conclusions: The implementation of an on-site, guideline-based genetic testing model for prostate cancer patients significantly improved compliance with genetic testing to 96.5% and decreased the time to receive genetic test results by 17 days. Overall, adopting a guide-line based model with on-site genetic testing has the potential to significantly improve the detection rate for pathogenic and actionable mutations, increase the utilization of targeted therapies, and increase cascade testing to include at-risk family members.

A community oncology practice financial experience in oncology care model pilot (OCM)

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Background: Oncology Division of Michigan Health Professionals (MHP) participates in OCM, which requires effort from all MHP OCM providers to coordinate care at same or lower cost to Medicare. Palliative Care, Care Management, and End of Life Care programs established by MHP, in collaboration with Premiere Hospice and Integra Connect, have shown cost and quality benefits in the OCM patients. Quality improvement initiatives included monthly OCM provider meetings to review OCM results, identify cost & quality opportunities, and to design training and education sessions. In order to assess the impact of such a concerted initiative, this study aims to evaluate MHP OCM provider impact in OCM total cost of care relative to historical period. Methods: Retrospective review of reconciliation results provided by Centers for Medicare and Medicaid Innovation (CMMI) for OCM performance periods 1-4 (pp1-4). Total cost of care (ACTUAL) and cost categories were the summarized and adjusted expenditures during 6-month OCM period as reported by CMMI. ACTUAL and cost category experience was compared by OCM performance period to the trended-mean of matched historical OCM-eligible patients (Baseline Episodes from CMMI). Patients were matched by cancer type, comorbidity count, age group, radiation, surgery, and low-intensity/-risk cancer sub-type for prostate, bladder and breast cancers. Results: The largest pp1-4 cost category reductions were acute inpatient ($2.2M), physician services excluding drug-cost, imaging and labs ($1.2M), skilled nursing facility ($0.5M), ancillary which consists of imaging and lab ($0.5M), inpatient rehab ($0.3M), home health agency ($0.3M), radiation oncology ($0.1M). The largest pp1-4 increase in OCM expense relative to historical was Part D Drugs ($1.7M). Conclusions: MHP decreased non-drug costs by $5.1M compared to historical cost for matched patients. OCM costs were lower in facility (hospital and SNF) and physician sites of care. Drug costs increased by $1.7M. Study was limited by OCM claims available as of December 2019. Results may be refreshed as more data becomes available. [Table: see text]

A community oncology palliative care program: Pain-related inpatient utilization in oncology care model (OCM) patients

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Background: Oncology Division of Michigan Health Professionals (MHP) participates in OCM. A comprehensive community oncology program for early and timely involvement of palliative care (PC) was launched in September 2017 to help achieve the OCM program goals of high-quality, cost-effective, coordinated care. PC provides a single point of care for all-cause pain management. PC program included pre-program training and continuous education for early and timely involvement of PC. This study aims to assess the educative effect of PC to reduce pain-related inpatient admissions (Pain IP) in all MHP OCM patients, irrespective of PC-referral. Methods: This initiative was led by palliative care physicians and included continuous education and reinforcement of the benefits, every 2-4 weeks, by sharing PC outcomes data with MHP physicians. Physician feedback was part of the program enhancements that were regularly reviewed during monthly MHP physician meetings. Retrospective claims review was performed with OCM episodes from Oct 2016 – Mar 2019. Monthly Pain IP utilization (based on diagnosis code) per 1000 OCM patients (UPK) was analyzed within pre- and post- PC Program start (Sep 2017). Cost per Pain IP included mean of 30-day follow-up skilled nursing facility (SNF) stay and 30-day outpatient facility expenses. Monthly historical Pain IP (pre-PC UPK) was compared to post-PC Pain IP UPK to calculate OCM savings from PC education at MHP. Results: Pain IP peaked at 7.12 UPK in September 2017 when PC program training and education started, then fell as low as 0.87 UPK in January 2019. Unit cost per Pain IP was $12,473. Post-PC (Sep 2017 – Mar 2019), there were 40 fewer Pain IP admissions compared to Pre-PC Pain IP for a total cost savings of $498,920. Conclusions: After PC Program, Pain IP decreased in MHP OCM population (PC-referred and PC not referred). This trend suggests PC training and continuous education for OCM providers is reducing IP utilization. This also translated to a significant cost saving for OCM/Medicare of $498,920. Study was limited by OCM claims available as of December 2019. Results may be refreshed as more data becomes available.

OCM community oncology palliative care program: Opioid analgesic utilization

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Background: Oncology Division of Michigan Health Professionals participates in Oncology Care Model (OCM ). A community oncology program for early and timely involvement of palliative care (PC) was launched in September 2017 to improve cancer pain management. Under-treatment of cancer pain leads to continued patient suffering and impaired quality of life. Appropriate dosing, rotation and frequent assessments are essential for better pain control. This study aims to see the effect of PC on opioid analgesic utilization. Methods: Retrospective claims review was performed with PC patients referred from September 2017 – December 2018 with an opioid class (as defined by CDC) Part D claim (within OCM data). Opioid utilization across agents was measured in morphine-milligram-equivalents (MME). MME per patient per opioid month (PPM) was compared between PC-referred and PC-not referred patients, pre- and post- PC start. Average MME PPM was compared between PC-Engaged and PC declined or unable to reach patients. Within these 2 cohorts, Long-Acting (LA) vs. Short-Acting (SA) opioid utilization was calculated. Results: PC-not referred patients appear to have little monthly variation in opioid dosing. PC-referred patients showed wide variation in opioid dosing before PC. After PC start, opioid dosing stabilized. PC-Engaged patients had more than double MME PPM vs PC declined or unable to reach (2481 MME PPM vs 1198 MME PPM respectively). PC-Engaged patients utilized a higher percentage of LA (43%) whereas PC declined or unable to reach used much less LA (8%). Conclusions: In patients with uncontrolled pain, PC-referral led to decreased variation in opioid dosing and better pain control. Better pain control may be the result of higher utilization of both SA & LA opioids. Patients who do not engage in PC may be at-risk for under-treatment. Study was limited by OCM claims available as of June 2019. Results may be refreshed as more data becomes available.

OCM community oncology palliative care program: Sites of patient care in last 180 days before hospice or death by cancer types

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Background: Michigan Health Professionals (MHP) participates in Oncology Care Model (OCM). A community oncology program for early and timely involvement of palliative care (PC) was launched in 2017 to achieve OCM goals of high quality, cost-effective, coordinated care. Previously, we showed that early enrollment in PC increased hospice utilization, decreased hospitalization and outpatient facility cost in last 30-days of death or end of OCM episode. PC improved quality of care in OCM patients. This study aims to see the effect of PC by patient care setting in the last 180-days before hospice or death. Methods: Retrospective claims review was performed with PC patients referred from September 2017 – December 2018. Last 180-days was defined by the entry into hospice, patient death, or OCM claim limit (12/31/2018), whichever was first to occur. OCM claims were analyzed by Integra Connect. Patient care setting utilization, in days (LOS), was identified for FACILITY: inpatient, skilled nursing, outpatient facility (ER, observation, etc.), physician office, and HOME HEALTH: home health agency visits. When no claim was found within the last 180-days, the patient was assumed to be at home or with no-care (HOME). Results: PC-Engaged patients had lower LOS in FACILITY + HOME HEALTH care settings and more days at HOME vs PC declined or unable to reach (average difference of 14 days). PC-Engaged patients had lower LOS in FACILITY + HOME HEALTH vs. matched PC-not referred patients who died or entered hospice (average difference of 26 days). In lung cancer, PC-Engaged patients had lower LOS in FACILITY + HOME HEALTH vs. PC declined or unable to reach (average difference of 27 days). In pancreatic cancer, PC-Engaged patients had lower LOS in FACILITY + HOME HEALTH vs. PC declined or unable to reach (average difference of 17 days). Conclusions: Patients who are PC-Engaged spent more time at home and less time in facilities over the last 6 months before end-of-life. Patients who were referred to PC with advanced lung and pancreatic cancer showed the most opportunity for impact with PC engagement. Study was limited by OCM claims available as of June 2019. Results may be refreshed as more data becomes available.

A community oncology palliative program: Early results for cost and quality measures within OCM program claims data

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Background: Oncology Care Model (OCM) is an initiative of the Centers for Medicare and Medicaid Innovation which aims to provide higher quality and more coordinated oncology care while lowering the cost. Oncology Division of Michigan Health Professionals (MHP) participates in OCM. Palliative and End of Life care was identified as one of the quality improvement areas. A community oncology Palliative care (PC) program was launched in October 2017. Methods: The multidisciplinary PC team was led by Board certified palliative care and hospice physicians. Patients appropriate for PC referral were identified by participating medical oncologists. Patients were contacted by the PC team. If the patients agreed a Nurse Practitioner (NP) would assess and follow the patients at home. Care was coordinated by the NP’s in communication with the palliative care team and the primary medical oncologists. Last 30-day (limited by the OCM episode or patient death) OCM program claims data was analyzed by IntegraConnect. Results: From October 2017 to October 2018 a total of 273 patients were referred to the PC program. Fifty-eight patients were identified as having OCM episodes, of these 36 patients had claims data through June 30, 2018. Twenty patients accepted and were engaged with PC,16 patients declined or were unable to reach for PC and formed the comparison group. Even when drug and office costs were excluded, PC engaged patients spent 17% less versus the comparison group (93k vs 112k) in last 30-day claims data. PC engaged patients had a lower acute care facility costs which accounted for 50% (46k) of reimbursement, compared with 95% (105k) for the comparison group. Fourteen OCM patients referred to Palliative program died within episode. 80% (8/10) of engaged patients met quality measure for OCM-3, at least 3 days in hospice vs. 0% (0/4) of patients who declined palliative care, before episode-death. Conclusions: Palliative engaged OCM patients experienced more care at their homes at a lower cost. Palliative program improved practice performance in OCM-3 quality measure. MHP Palliative program is reaching patients in OCM episodes but the numbers are still small.

A community oncology end-of-life care program: Results for hospice length of stay analysis

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Background: Michigan Health Professionals (MHP) is a large multispecialty physician group. MHP Oncology Division participates in quality improvement projects. Palliative and End of Life (EOL) care has been identified as one of the quality improvement areas. A comprehensive community oncology program for early and timely involvement of palliative and EOL care was launched in October 2017. Methods: MHP Palliative and End of life care committee was created of mostly oncologists who are board certified in Palliative care and Hospice. The program, which included pre-program training, user-friendly referral process, and live physician engagement for early involvement of palliative care (PC) and EOL care was developed and implemented. A partnership was created with Premier Hospice to integrate EOL care services with the oncology offices and to collect data. Historical data for average hospice length of stay (LOS) in hospice service for MHP oncology patients was analyzed by Integra Connect. Results: From 1/1/2018 to 12/31/2018 a total of 133 patients (MHP-T) were referred and admitted to Hospice service. Sixty-one patients were on PC service (PC group) and 72 patients (NonPC group) were referred directly to hospice. Total of 527 patients from 2012 to 2017 were analyzed for historical comparison group (HC) and 124 patients were analyzed for MHP-T group. Average LOS was 16.8 days in the HC group. Average LOS for the MHP-T, PC group and NonPC group improved to 34, 35 and 33 days respectively. HC group had 82.2% of patients with average LOS < 30 days. After program implementation average LOS < 30 days improved to 63.7% MHP-T group, 60.0% PC group and 66.7% NonPC group. In HC group, 92 out of 527 patients had average LOS of 2 days or less. Only 2 patients out of 124 patients had average LOS of 2 days or less since the launch of MHP community oncology program. Conclusions: Early and timely patient referral to the EOL care services resulted in average hospice LOS which is more than double as compared to historical comparison group. Fewer number of patients had average LOS of < 30 days and LOS of 2 days or less as compared to the historical comparison group. There was a trend towards higher LOS observed for patients who were under palliative care (PC) before hospice admission.

Positive and negative forms of replicability in gene network analysis

MOTIVATION

Gene networks have become a central tool in the analysis of genomic data but are widely regarded as hard to interpret. This has motivated a great deal of comparative evaluation and research into best practices. We explore the possibility that this may lead to overfitting in the field as a whole.

RESULTS

We construct a model of 'research communities' sampling from real gene network data and machine learning methods to characterize performance trends. Our analysis reveals an important principle limiting the value of replication, namely that targeting it directly causes 'easy' or uninformative replication to dominate analyses. We find that when sampling across network data and algorithms with similar variability, the relationship between replicability and accuracy is positive (Spearman's correlation, rs ∼0.33) but where no such constraint is imposed, the relationship becomes negative for a given gene function (rs ∼ -0.13). We predict factors driving replicability in some prior analyses of gene networks and show that they are unconnected with the correctness of the original result, instead reflecting replicable biases. Without these biases, the original results also vanish replicably. We show these effects can occur quite far upstream in network data and that there is a strong tendency within protein-protein interaction data for highly replicable interactions to be associated with poor quality control.

AVAILABILITY AND IMPLEMENTATION

Algorithms, network data and a guide to the code available at: https://github.com/wimverleyen/AggregateGeneFunctionPrediction

CONTACT

jgillis@cshl.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

MOTIVATION

RNA-seq co-expression analysis is in its infancy and reasonable practices remain poorly defined. We assessed a variety of RNA-seq expression data to determine factors affecting functional connectivity and topology in co-expression networks.

RESULTS

We examine RNA-seq co-expression data generated from 1970 RNA-seq samples using a Guilt-By-Association framework, in which genes are assessed for the tendency of co-expression to reflect shared function. Minimal experimental criteria to obtain performance on par with microarrays were >20 samples with read depth >10 M per sample. While the aggregate network constructed shows good performance (area under the receiver operator characteristic curve ∼0.71), the dependency on number of experiments used is nearly identical to that present in microarrays, suggesting thousands of samples are required to obtain 'gold-standard' co-expression. We find a major topological difference between RNA-seq and microarray co-expression in the form of low overlaps between hub-like genes from each network due to changes in the correlation of expression noise within each technology.

CONTACT

jgillis@cshl.edu or sballouz@cshl.edu

SUPPLEMENTARY INFORMATION

Networks are available at: http://gillislab.labsites.cshl.edu/supplements/rna-seq-networks/ and supplementary data are available at Bioinformatics online.

Phase I study of conformal radiotherapy and concurrent full-dose gemcitabine with erlotinib for unresected pancreatic cancer

PURPOSE

To determine the recommended dose of radiotherapy when combined with full-dose gemcitabine and erlotinib for unresected pancreas cancer.

METHODS AND MATERIALS

Patients with unresected pancreatic cancer (Zubrod performance status 0-2) were eligible for the present study. Gemcitabine was given weekly for 7 weeks (1,000 mg/m(2)) with erlotinib daily for 8 weeks (100 mg). A final toxicity assessment was performed in Week 9. Radiotherapy (starting at 30 Gy in 2-Gy fractions, 5 d/wk) was given to the gross tumor plus a 1-cm margin starting with the first dose of gemcitabine. A standard 3 plus 3 dose escalation (an additional 4 Gy within 2 days for each dose level) was used, except for the starting dose level, which was scheduled to contain 6 patients. In general, Grade 3 or greater gastrointestinal toxicity was considered a dose-limiting toxicity, except for Grade 3 anorexia or Grade 3 fatigue alone.

RESULTS

A total of 20 patients were treated (10 men and 10 women). Nausea, vomiting, and infection were significantly associated with the radiation dose (p = .01, p = .03, and p = .03, respectively). Of the 20 patients, 5 did not complete treatment and were not evaluable for dose-escalation purposes (3 who developed progressive disease during treatment and 2 who electively discontinued it). Dose-limiting toxicity occurred in none of 6 patients at 30 Gy, 2 of 6 at 34 Gy, and 1 of 3 patients at 38 Gy.

CONCLUSION

The results of the present study have indicated that the recommended Phase II dose is 30 Gy in 15 fractions.

Composite Biclonal Marginal Zone Lymphoma of Lung and Chronic Lymphocytic Leukemia: Pathologic, Phenotypic, Cytogenetic, and Molecular Study

The simultaneous diagnosis of marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT) and chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) is rare. This study reports a patient with composite synchronous biclonal occurrence of MALT lymphoma of the lung and CLL/SLL. The morphology of the lung and peripheral blood showed features of MALT lymphoma and CLL, respectively. The cytogenetic evaluation of the lung specimen revealed a t(1;14) (p22;q32), a frequent genetic abnormality in MALT lymphoma. Flow cytometry analysis of the lung tissue showed features of MALT lymphoma and CLL/SLL with different light chain restriction, whereas the blood showed phenotypic evidence of CLL/SLL. Fluorescence in situ hybridization study of the blood showed a deletion of 13q14 and 17p13. Immunoglobulin heavy chain (IgH) gene rearrangement study of the lung tissue and blood showed a monoclonal IgH gene rearrangement with distinct light chain restriction, suggesting that the immunophenotypically different cell populations originated from separate clones.