Cancer screening with multicancer detection tests: A translational science review

Multicancer detection (MCD) tests use a single, easily obtainable biospecimen, such as blood, to screen for more than one cancer concurrently. MCD tests can potentially be used to improve early cancer detection, including cancers that currently lack effective screening methods. However, these tests have unknown and unquantified benefits and harms. MCD tests differ from conventional cancer screening tests in that the organ responsible for a positive test is unknown, and a broad diagnostic workup may be necessary to confirm the location and type of underlying cancer. Among two prospective studies involving greater than 16,000 individuals, MCD tests identified those who had some cancers without currently recommended screening tests, including pancreas, ovary, liver, uterus, small intestine, oropharyngeal, bone, thyroid, and hematologic malignancies, at early stages. Reported MCD test sensitivities range from 27% to 95% but differ by organ and are lower for early stage cancers, for which treatment toxicity would be lowest and the potential for cure might be highest. False reassurance from a negative MCD result may reduce screening adherence, risking a loss in proven public health benefits from standard-of-care screening. Prospective clinical trials are needed to address uncertainties about MCD accuracy to detect different cancers in asymptomatic individuals, whether these tests can detect cancer sufficiently early for effective treatment and mortality reduction, the degree to which these tests may contribute to cancer overdiagnosis and overtreatment, whether MCD tests work equally well across all populations, and the appropriate diagnostic evaluation and follow-up for patients with a positive test.

Challenges to Using Big Data in Cancer

Big data in healthcare can enable unprecedented understanding of diseases and their treatment, particularly in oncology. These data may include electronic health records, medical imaging, genomic sequencing, payor records, and data from pharmaceutical research, wearables, and medical devices. The ability to combine datasets and use data across many analyses is critical to the successful use of big data and is a concern for those who generate and use the data. Interoperability and data quality continue to be major challenges when working with different healthcare datasets. Mapping terminology across datasets, missing and incorrect data, and varying data structures make combining data an onerous and largely manual undertaking. Data privacy is another concern addressed by the Health Insurance Portability and Accountability Act, the Common Rule, and the General Data Protection Regulation. The use of big data is now included in the planning and activities of the FDA and the European Medicines Agency. The willingness of organizations to share data in a precompetitive fashion, agreements on data quality standards, and institution of universal and practical tenets on data privacy will be crucial to fully realizing the potential for big data in medicine.

Quantitating and assessing interoperability between electronic health records

OBJECTIVES

Electronic health records (EHRs) contain a large quantity of machine-readable data. However, institutions choose different EHR vendors, and the same product may be implemented differently at different sites. Our goal was to quantify the interoperability of real-world EHR implementations with respect to clinically relevant structured data.

MATERIALS AND METHODS

We analyzed de-identified and aggregated data from 68 oncology sites that implemented 1 of 5 EHR vendor products. Using 6 medications and 6 laboratory tests for which well-accepted standards exist, we calculated inter- and intra-EHR vendor interoperability scores.

RESULTS

The mean intra-EHR vendor interoperability score was 0.68 as compared to a mean of 0.22 for inter-system interoperability, when weighted by number of systems of each type, and 0.57 and 0.20 when not weighting by number of systems of each type.

DISCUSSION

In contrast to data elements required for successful billing, clinically relevant data elements are rarely standardized, even though applicable standards exist. We chose a representative sample of laboratory tests and medications for oncology practices, but our set of data elements should be seen as an example, rather than a definitive list.

CONCLUSIONS

We defined and demonstrated a quantitative measure of interoperability between site EHR systems and within/between implemented vendor systems. Two sites that share the same vendor are, on average, more interoperable. However, even for implementation of the same EHR product, interoperability is not guaranteed. Our results can inform institutional EHR selection, analysis, and optimization for interoperability.

OUP accepted manuscript

Objective

Assess the effectiveness of providing Logical Observation Identifiers Names and Codes (LOINC®)-to-In Vitro Diagnostic (LIVD) coding specification, required by the United States Department of Health and Human Services for SARS-CoV-2 reporting, in medical center laboratories and utilize findings to inform future United States Food and Drug Administration policy on the use of real-world evidence in regulatory decisions.

Materials and Methods

We compared gaps and similarities between diagnostic test manufacturers’ recommended LOINC® codes and the LOINC® codes used in medical center laboratories for the same tests.

Results

Five medical centers and three test manufacturers extracted data from laboratory information systems (LIS) for prioritized tests of interest. The data submission ranged from 74 to 532 LOINC® codes per site. Three test manufacturers submitted 15 LIVD catalogs representing 26 distinct devices, 6956 tests, and 686 LOINC® codes. We identified mismatches in how medical centers use LOINC® to encode laboratory tests compared to how test manufacturers encode the same laboratory tests. Of 331 tests available in the LIVD files, 136 (41%) were represented by a mismatched LOINC® code by the medical centers (chi-square 45.0, 4 df, P < .0001).

Discussion

The five medical centers and three test manufacturers vary in how they organize, categorize, and store LIS catalog information. This variation impacts data quality and interoperability.

Conclusion

The results of the study indicate that providing the LIVD mappings was not sufficient to support laboratory data interoperability. National implementation of LIVD and further efforts to promote laboratory interoperability will require a more comprehensive effort and continuing evaluation and quality control.

The FDA Oncology Center of Excellence Scientific Collaborative: Charting a Course for Applied Regulatory Science Research in Oncology

The FDA Oncology Center of Excellence (OCE) is a leader within the agency in scientific outreach activities and regulatory science research. On the basis of analysis of scientific workshops, internal meetings, and publications, the OCE identified nine scientific priority areas and one cross-cutting area of high interest for collaboration with external researchers. This article describes the process for identifying these scientific interest areas and highlights funded and unfunded opportunities for external researchers to work with FDA staff on critical regulatory science challenges.

Impact of Broadening Trial Eligibility Criteria for Patients with Advanced Non-Small Cell Lung Cancer: Real-World Analysis of Select ASCO-Friends Recommendations

PURPOSE

Cancer clinical trials often accrue slowly or miss enrollment targets. Strict eligibility criteria are a major reason. Restrictive criteria also limit opportunities for patient participation while compromising external validity of trial results. We examined the impact of broadening select eligibility criteria on characteristics and number of patients eligible for trials, using recommendations of the American Society of Clinical Oncology (ASCO) and Friends of Cancer Research.

EXPERIMENTAL DESIGN

A retrospective, observational analysis used electronic health record data from ASCO's CancerLinQ Discovery database. Study cohort included patients with advanced non-small cell lung cancer treated from 2011 to 2018. Patients were grouped by traditional criteria [no brain metastases, no other malignancies, and creatinine clearance (CrCl) ≥ 60 mL/minute] and broadened criteria (including brain metastases, other malignancies, and CrCl ≥ 30 mL/minute).

RESULTS

The analysis cohort included 10,500 patients. Median age was 68 years, and 73% of patients were White. Most patients had stage IV disease (65%). A total of 5,005 patients (48%) would be excluded from trial participation using the traditional criteria. The broadened criteria, however, would allow 98% of patients (10,346) to be potential participants. Examination of patients included by traditional criteria (5,495) versus those added (4,851) by broadened criteria showed that the number of women, patients aged 75+ years, and those with stage IV cancer was significantly greater using broadened criteria.

CONCLUSIONS

This analysis of real-world data demonstrated that broadening three common eligibility criteria has the potential to double the eligible patient population and include trial participants who are more representative of those encountered in practice.See related commentary by Giantonio, p. 2369.

Development of CancerLinQ, a Health Information Learning Platform From Multiple Electronic Health Record Systems to Support Improved Quality of Care

PURPOSE

ASCO, through its wholly owned subsidiary, CancerLinQ LLC, developed CancerLinQ, a learning health system for oncology. A learning health system is important for oncology patients because less than 5% of patients with cancer enroll in clinical trials, leaving evidence gaps for patient populations not enrolled in trials. In addition, clinical trial populations often differ from the overall cancer population with respect to age, race, performance status, and other clinical parameters.

MATERIALS AND METHODS

Working with subscribing practices, CancerLinQ accepts data from electronic health records and transforms the local representation of a patient's care into a standardized representation on the basis of the Quality Data Model from the National Quality Forum. CancerLinQ provides this information back to the subscribing practice through a series of tools that support quality improvement. CancerLinQ also creates de-identified data sets for secondary research use.

RESULTS

As of March 2020, CancerLinQ includes data from 63 organizations across the United States that use nine different electronic health records. The database includes 1,426,015 patients with a primary cancer diagnosis, of which 238,680 have had additional information abstracted from unstructured content.

CONCLUSION

As CancerLinQ continues to onboard subscribing practices, the breadth of potential applications for a learning health care system widen. Future practice-facing tools could include real-world data visualization, recommendations for treatment of patients with actionable genetic variations, and identification of patients who may be eligible for clinical trials. Feeding these insights back into oncology practice ensures that we learn how to treat patients with cancer not just on the basis of the selective experience of the 5% that enroll in clinical trials, but from the real-world experience of the entire spectrum of patients with cancer in the United States.

Next-Generation Sequencing and the Clinical Oncology Workflow: Data Challenges, Proposed Solutions, and a Call to Action

PURPOSE

Next-generation sequencing (NGS) of tumor and germline DNA is foundational for precision oncology, with rapidly expanding diagnostic, prognostic, and therapeutic implications. Although few question the importance of NGS in modern oncology care, the process of gathering primary molecular data, integrating it into electronic health records, and optimally using it as part of a clinical workflow remains far from seamless. Numerous challenges persist around data standards and interoperability, and clinicians frequently face difficulties in managing the growing amount of genomic knowledge required to care for patients and keep up to date.

METHODS

This review provides a descriptive analysis of genomic data workflows for NGS data in clinical oncology and issues that arise from the inconsistent use of standards for sharing data across systems. Potential solutions are described.

RESULTS

NGS technology, especially for somatic genomics, is well established and widely used in routine patient care, quality measurement, and research. Available genomic knowledge bases play an evolving role in patient management but lack harmonization with one another. Questions about their provenance and timeliness of updating remain. Potentially useful standards for sharing genomic data, such as HL7 FHIR and mCODE, remain primarily in the research and/or development stage. Nonetheless, their impact will likely be seen as uptake increases across care settings and laboratories. The specific use case of ASCO CancerLinQ, as a clinicogenomic database, is discussed.

CONCLUSION

Because the electronic health records of today seem ill suited for managing genomic data, other solutions are required, including universal data standards and applications that use application programming interfaces, along with a commitment on the part of sequencing laboratories to consistently provide structured genomic data for clinical use.

Impact of broadening clinical trial eligibility criteria for advanced non-small cell lung cancer patients: Real-world analysis

LBA108

Background: Restrictive trial eligibility criteria limit data generalizability and patient opportunity to participate. We compared numbers and characteristics of patients (pts) eligible using traditional vs expanded criteria recommended by ASCO and Friends of Cancer Research. Methods: A retrospective, observational analysis used deidentified EHR data from ASCO’s CancerLinQ database. Study cohort included adult aNSCLC pts with ≥2 visits and ≥1 dose of systemic treatment post-advanced-disease diagnosis from 2011-2018. Recorded creatinine clearance (CrCl) or Cockcroft-Gault variables were required. Pts were grouped by traditional criteria (no brain metastases, no other malignancies and CrCl >60 mL/min) and expanded criteria (brain metastases and other malignancies allowed and CrCl >30 mL/min). Results: 10,500 pts were identified (Table). Median age 67.6 years [IQR 60.3-74.4]. 56% were male, and 65% white. 60% were Stage IV, 80% former or current smokers. 5005 (47.7%) pts were excluded by traditional exclusion criteria, while only 154 (1.5%) pts were excluded by expanded criteria. Expanded criteria patients were older (67.5 v 66.1, p<0.001); and more likely to be female (44% v 40%), Stage IV (60% v 55%), have non-squamous histology (47% v 45%), and never smokers (16% v 13%). Additional analysis is needed to differentiate treated/stable vs. active brain metastases. Conclusions: Use of the ASCO-Friends expanded criteria would enable nearly twice as many aNSCLC pts to be considered for trial participation (4,851 patients, 46.2%). Narrower criteria should only be used based on compelling scientific rationale for exclusion. [Table: see text]

Characteristics of patients receiving immune checkpoint inhibitors (ICI) in ASCO’s CancerLinQ

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Background: ICI’s have demonstrated significant clinical benefit since the first FDA approval in 2011 of ipilimumab for metastatic melanoma. Five additional ICI therapies have since been approved across several indications. The objectives of this study were to describe the clinical and demographic features of patients receiving ICI treatment along with utilization patterns in real-world settings. Methods: We conducted a retrospective, observational cohort study using statistically de-identified data from January 2011 to November 2018 in CancerLinQ, ASCO’s real-world oncology database, which now contains EHR data from 49 diverse oncology practices in the U.S. Adult patients diagnosed with any cancer type who received ≥1 dose of an ICI (see Table) and had ≥2 clinical visits were eligible for inclusion. Patients were excluded if they received an ICI prior to its first FDA approval date to avoid inclusion of clinical trial patients. Descriptive statistics were used to examine treatment patterns and clinical characteristics of patients receiving ICIs. Results: This analysis included 12,712 patients who received an ICI. Median patient age was 67.4 years [IQR 59.3, 75.3]; 58% were male. White race made up the highest percent (83%) of ICI patients, followed by Black race (9%) and Other (8%). The most common primary cancers at the start of treatment were lung cancer (36%), melanoma (8%), urothelial cancer (2%) and renal cell carcinoma (2%). Of the 8,444 patients with known disease stage, 5,446 (64%) had Stage IV cancer. Breakdown of ICI treatment patterns can be found in the accompanying table. Uptake of ICIs was the most rapid for nivolumab, which had the highest use (49%), followed by pembrolizumab for rapid adoption and use (30%). Conclusions: This analysis gives insights into patient characteristics and real-world treatment patterns for ICIs. ICIs were used most widely in males, lung cancer patients and patients with advanced disease. These baseline characteristics inform our analyses of ICI use in patients with autoimmune disease, also reported herein.[Table: see text]

Laboratory and clinical data integration: Toward an evidence development framework

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Background: Decision making in precision oncology relies on the timeliness of diagnostic testing. Uncertainty surrounding the clinical utility of laboratory developed molecular and next generation sequencing (NGS) tests (LDTs) has engendered a predominantly manual claims review process. Denials and delays may create hurdles for optimally treating patients, and denials may contribute to financial toxicity. ASCO’s CancerLinQ aggregates clinical data from EHRs of participating oncology practices to improve the quality of care for patients. We hypothesized that standardized clinical data could be used in the short term to appeal denials of NGS LDTs and in the long run, lead to evidence-based coverage decisions. Methods: Using National Provider Index IDs, CancerLinQ participating physicians were cross-walked to ordering physicians of tests offered from 100 U.S. laboratories using XIFIN for billing services in 2018 to evaluate the feasibility of using CancerLinQ clinical data for claims adjudication. We determined the proportion of molecular and NGS tests (based on CPT coding) initially denied and the proportion of successful appeals through a manual submission process for clinical documentation (not including CancerLinQ data). CancerLinQ clinical data were evaluated for key elements necessary for successful appeals. Results: Sixty-five percent of CancerLinQ participating physicians ordered tests from the laboratories identified. Approximately 80% of NGS and 40% of molecular services were initially denied. After appealing with clinical information through the manual process, 55% of denials were successfully overturned. Key clinical data provided manually could be automatically extracted from CancerLinQ at high rates, such as ICD-9/ICD-10 cancer diagnosis (100% of 1,082,606 patients), Stage Group (47.6 %), and treatment plan (35.9%). Metastatic disease status is available through M1-stage (23.2% of total M-Stage), AJCC Stage IV (29.0% of total AJCC Stage) and Metastatic diagnosis codes (17.2%). Conclusions: CancerLinQ contains key data elements necessary for successful appeals and can streamline the claims adjudication process, ultimately helping to build the evidence base for coverage decisions.

Quantifying interoperability: An analysis of oncology practice electronic health record data variability

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Background: Implementation of electronic health records (EHRs) has engendered a large quantity of machine-readable data. However, different practices choose different EHR vendors and the same vendor product may be implemented differently at each practice. Motivated by the desire to facilitate appropriate integration of data, our goal was to describe and quantify the consistency and variation of structured data within EHRs. Methods: De-identified and aggregated CancerLinQ data from 47 practices regarding the standards and variability of structured data including race, diagnoses, encounters, cancer staging, selected cancer-relevant medications, lab values and biomarkers were analyzed. EHR represented included ARIA, MOSAIQ, Allscripts, Centricity, Epic, Intellidose, NextGen, and OncoEMR. Results: De-identified EHR implementations included 23 A, 12 B, C and 5 other vendors. Only 6 practices (13%) used non-standard race representation. All practices used ICD-9/10 for diagnoses. There was variability in coding of encounters. Sixteen practices always used CPT, 5 practices always used SNOMED CT and 26 practices used multiple standards. Multiple staging systems were used. An average of 48% (range 11%-; including patients staged more than once) of patient records included coded staging information. Only one practice used a standard (LOINC) for laboratory data. No standards were used for medications ordered/administered or biomarkers. The table shows the number of distinct names for selected lab tests, medications and biomarkers across systems. Conclusions: In this cross-sectional sample, standards are used consistently for diagnoses and encounter data, often for race and rarely for medications, laboratory tests or biomarkers.[Table: see text]

NCI and ASCO CancerLinQ collaboration to advance quality of cancer care and surveillance

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Background: The National Cancer Institute (NCI) Surveillance, Epidemiology, and End Results (SEER) Program curates population-based cancer data representing 34% of the US population. CancerLinQ is an ASCO initiative that collects and analyzes electronic health record (EHR) data to give oncologists opportunities to improve the quality of patient care. With the shared goal of understanding care delivery, NCI SEER and CancerLinQ launched a pilot linkage. Purpose: Establish data exchange between registries and oncology practices to a) provide clinicians with SEER data to more effectively evaluate care within their practices, and b) enhance ability of SEER registries to capture cancer-related data and facilitate compliance of legally mandated public health reporting requirements while supporting metrics for quality reporting to providers. Methods: The SEER Iowa Cancer Registry is developing bidirectional linkages with CancerLinQ practices. The initial pilot in Iowa establishes connectivity and a data pipeline to capture discrete data elements in EHRs. The linkage methods are securely conducted by IMS, an honest broker for the Registry and ASCO. Patterns of care will be evaluated in the matched patient population. Analysis of shared data elements will provide comparative validation of data captured electronically (EHR) and manually (abstraction). Enhancing the patient care quality through efficient utilization of shared data was paramount when selecting treatment-related Quality Oncology Practice Initiative (QOPI) measures for calculation focusing on breast (QPP 449, QPP 450) and prostate cancer (QPP 102, QPP 104). Results: Publicly available SEER data for cohort evaluation is available to providers via SEERLinQ. The two-way exchange data pipeline complies with reporting requirements. Validation of shared data elements, statistics for matched patients, improved data completeness measures, and automated calculation of QOPI measures will be demonstrated. Conclusions: This collaboration builds an initial foundation of curated Registry-EHR linked data to automate cancer reporting to lower the physician burden, improve SEER evaluation of clinical care patterns, and enhance patient care quality.

Real-world characteristics and outcomes of patients with advanced non-small cell lung cancer (aNSCLC) receiving immune checkpoint inhibitor

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Background: Immune Checkpoint Inhibitors (ICIs) were first approved for the treatment of aNSCLC in 2014, and since this time have seen rapid adoption in the marketplace. We sought to describe the characteristics of patients with aNSCLC receiving ICIs in the real-world, as well as to examine treatment patterns and outcomes in the time since initial ICI approval. Methods: We conducted a retrospective, observational cohort study using statistically de-identified data from January 2011 to November 2018 in CancerLinQ, ASCO’s real-world oncology database. Adult patients with a curated diagnosis of Stage III or IV NSCLC who received ≥1 dose of an ICI and had ≥2 clinical visits were eligible for inclusion. Stage III patients were excluded if they received any local therapy < 1 year prior to receiving ICI. Patients were also excluded if they received ICI prior to the first FDA approval date. Demographic and clinical characteristics of aNSCLC patients receiving ICI are reported. Outcomes including time to treatment discontinuation (TTD), time to next treatment (TTNT), real-world progression free survival (rwPFS) and overall survival (OS) were examined via the Kaplan Meier method. Results: Among 2,425 aNSCLC ICI patients included in this analysis, median age was 68.0 years (IQR 60.7, 75.2], 54% were male and 73% of patients were white. Non-squamous histology accounted for 64% of aNSCLC ICI users, and 81% had Stage IV disease. Eastern Cooperative Oncology Group (ECOG) performance status was 0-1 in 77% and 2+ in 23% of patients, and 70% were current or former smokers. The majority (75%) of patients received ICI as second-line or later therapy. Treatment outcomes and survival are reported in the Table. Conclusions: This analysis demonstrates that aNSCLC patients receiving ICI therapy in the real-world are older than what was reported in some clinical trials, though survival outcomes were similar. Further research to examine impact of covariates on outcomes is warranted. [Table: see text]

Real-world prevalence of autoimmune disease (AD) among patients (pts) receiving immune checkpoint inhibitors (ICI) in ASCO’s CancerLinQ database

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Background: Although pts with AD are routinely excluded from ICI clinical trials, evidence suggests they may be receiving ICI therapy once approved. We sought to understand the prevalence of AD among all pts receiving ICIs in real world clinical care, as well as in advanced non-small cell lung cancer (aNSCLC) alone, and to describe the characteristics of ICI pts with and without evidence of AD. Methods: We conducted a retrospective, observational cohort study using statistically de-identified data from January 2011 to November 2018 in CancerLinQ, ASCO’s real-world oncology database. Adult pts who received ≥ 1 dose of an ICI and had ≥ 2 clinical visits were eligible for inclusion. A sub-analysis examining only aNSCLC pts was also carried out. To reduce the likelihood of capturing pts who may have been on a clinical trial, pts were excluded if they received the ICI prior to its first FDA approval date. AD status was determined by the presence of select ICD-9/ICD-10 codes or a medication used to treat autoimmune disease (including steroids) prior to ICI treatment start date. Symphony claims data were linked to CLQ via tokenization to build out cohorts. Characteristics of pts with and without autoimmune disease were compared using Chi-square or Fisher’s exact tests. Results: Prevalence of AD was 23% (538/2425 pts) in the aNSCLC population and 27% (3407/12712 pts) in the all ICI patient population. Median age did not differ between AD pts and those with no evidence of AD (All ICI: 67.6 v 67.3 years; aNSCLC: 68.5 v 67.9). AD pts were more likely to be female (All ICI: 46% v 40%, p < 0.001; aNSCLC: 55% v 44%, p < 0.001). Among all ICI pts, AD pts were less likely to be Stage IV (62% v 65%) or to have melanoma (4.6% versus 8.7%) compared to pts with no evidence of AD. The most common ADs among all ICI and aNSCLC patients were glucocorticoid deficiency (6.3% and 3.9%), rheumatoid arthritis (4.2% and 5.8%), and sacroiliitis (2.7% and 3.9%), respectively. Conclusions: This analysis of real-world data finds that a large proportion of pts receiving ICI may have pre-existing AD. Further examination is warranted to examine how AD status may impact outcomes.

Hypertension and use of bevacizumab among patients treated in community settings

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Background: CancerLinQ Discovery (CLQD) is a real-world dataset (RWD) derived from electronic health records across the US. This analysis builds on the prior observation of cautioned use of bevacizumab (Bev) among older adults using Medicare claims data. The goals of this study are to estimate the prevalence and incidence of hypertension (HT) and blood pressure (BP) patterns among patients (pts) with breast cancer (BC) or lung cancer (LC) treated with Bev. Methods: The cohort consists of all BC and LC pts in the platform at the time of CLQD dataset creation. At least one administration of Bev was required for inclusion as was diagnosis date and date of first Bev use. Elevated BP was defined as > 140 mmHg for systolic and > 90 mmHg for diastolic BP; elevated and max BP within 90 days of first Bev and 120 after were calculated for each pt. Summary statistics and proportions were calculated within these subgroups: baseline HT, race, age, and ECOG performance status (PS). Results: Overall, 1941 pts with BC and 4590 pts with LC treated from 2005 to 2017 were included. Baseline characteristics included % female (99 BC, 48 LC); % white (71 BC, 81 LC); % age > 65 years (34 BC, 52 LC). PS was available for N = 2118; most pts were PS 0-1 (88% BC, 82% LC). At baseline, more than half of pts were hypertensive (57% BC, 52% LC). An increase of at least 10mmHg in systolic BP within 120 days of treatment occurred in over half of pts with a normal baseline BP (54% BC, 56% LC) and in one-third of those with baseline HT (34% BC, 32% LC.) A significant proportion experienced at least a 20mmHg increase in systolic BP among those normotensive (29% BC, 32% LC) or hypertensive at baseline (16% BC, 16% LC). A majority of pts > 65 years had at least one elevated BP prior to Bev treatment (81% BC, 72% LC) although there were no clinically significant differences in rates of post treatment HT by age, race or PS. Conclusions: RWD provides important insights regarding the use and safety of medications outside the clinical trial population. Bev administration among pts with baseline (or pre-existent) HT is common in these practices. BP elevation post Bev exposure is also common, particularly among those with normal BP at baseline.

Real-world outcomes of patients with advanced non-small cell lung cancer (aNSCLC) and autoimmune disease (AD) receiving immune checkpoint inhibitors (ICIs)

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Background: Anecdotal and early evidence suggest ICIs are being used in patients with advanced malignancies and history of AD, despite such patients being typically excluded from traditional clinical trials. We compared the outcomes of patients with or without AD, all of whom had ICI treatment for aNSCLC. Methods: We conducted a retrospective, observational cohort study using de-identified, curated data in ASCO’s CancerLinQ. Patients with Stage III or IV NSCLC who received ≥1 dose of an ICI and had ≥2 visits from Jan 2011 to Nov 2018 were included. AD status prior to ICI treatment was identified using ICD-9/ICD-10 codes or AD medications (including steroids). Symphony claims data were linked via tokenization to build cohorts. Time to treatment discontinuation (TTD), time to next treatment (TTNT), real-world progression-free survival (rwPFS) and overall survival (OS) were compared across the two cohorts using the log-rank test. Cox Proportional Hazards Model was used to adjust for covariates. Adverse events (AEs) were compared using Chi-Square and Fisher’s Exact Test. Active AD was defined as evidence of autoimmune disease in the year prior to starting ICIs. Results: Among 2425 patients with aNSCLC treated with ICIs, AD was present in 22% (N=538). Median OS in all patients was 12.4 months (95% CI 11.3-13.5). TTD, TTNT, rwPFS and OS did not differ between the two cohorts (Table). There was no association between AD status and outcomes. There was no increased incidence of AEs in the AD group; however a sub-analysis among patients with active AD showed higher rates of select AEs including endocrine, GI and blood disorders. Conclusions: This analysis demonstrates that patients with evidence of AD prior to receiving ICI have similar outcomes compared to patients with no evidence of AD. Further research is needed to better understand the impact of active AD on the risk of AEs and patient outcomes. [Table: see text]

Electronic but overly eclectic: Disciplined EHR data management is needed to automate MIPS reporting

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Background: Physician reimbursement for care delivered to Medicare beneficiaries fundamentally changed with the 2015 MACRA legislation, requiring eligible clinicians to report quality measures in the Merit-Based Incentive Payment System (MIPS). To determine whether structured data in electronic health records (EHRs) were adequate to report MIPS results, EHR data ingested by ASCO’s CancerLinQ (CLQ) was analyzed. Methods: Nineteen MIPS measures specified for medical oncology, including 8 shared by other specialties, were retrieved from qpp.cms.gov and systematically evaluated to determine data elements necessary to satisfy each measure. The existence of corresponding data fields and completion of these fields with clinical data was analyzed according to EHR implementation in de-identified and aggregated CLQ data. Results: Five clinician informaticists reviewed the 19 oncology MIPS measures, and identified a consensus list of 52 discrete EHR data elements (DEs) that would be needed. CLQ-processed data from 4 commercial EHR systems implemented at 47 CLQ practices found structured data fields for 84% (43 of 52) of the DE, but fewer than half (46%) of these fields were ever populated and only 32% (17 of 52) of DE were recorded for > 20% of cases. Only 3-5 of 19 MIPS measures could be reliably reported based on data element availability by most practices in this sample set. There were minimal differences between the EHRs ability to encode MIPS DE. Elements most likely to be encoded were those for registration (birthdate, gender), billing (diagnosis, meds), vital signs and smoking status, while those seldom or never encoded related to care plans (tobacco, alcohol, pain management). Other DE rarely encoded were patient events occurring outside the oncology practice (receipt/completion of consultations, dates of hospice enrollment and death), which would be dependent on data exchange between work units and practice entities or, more likely, re-entry by oncology practices. Conclusions: Only a minority of DE required to satisfy MIPS criteria are available as discrete data fields in current EHRs, limiting automated reporting efforts. Improved data quality and completeness is needed to satisfy mandated reporting.

BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2

The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data to support highly collaborative research activities. Its goal is to generate an informed and current understanding of the impact of genetic variation on cancer risk across the iconic cancer predisposition genes, BRCA1 and BRCA2. Initially, reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org. The purpose of the BRCA Exchange is to provide the community with a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype. More than 20,000 variants have been aggregated, three times the number found in the next-largest public database at the project’s outset, of which approximately 7,250 have expert classifications. The data set is based on shared information from existing clinical databases—Breast Cancer Information Core (BIC), ClinVar, and the Leiden Open Variation Database (LOVD)—as well as population databases, all linked to a single point of access. The BRCA Challenge has brought together the existing international Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium expert panel, along with expert clinicians, diagnosticians, researchers, and database providers, all with a common goal of advancing our understanding of BRCA1 and BRCA2 variation. Ongoing work includes direct contact with national centers with access to BRCA1 and BRCA2 diagnostic data to encourage data sharing, development of methods suitable for extraction of genetic variation at the level of individual laboratory reports, and engagement with participant communities to enable a more comprehensive understanding of the clinical significance of genetic variation in BRCA1 and BRCA2.

The goal of this study and paper has been to develop an international resource to generate an informed and current understanding of the impact of genetic variation on cancer risk across the cancer predisposition genes, BRCA1 and BRCA2. Reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org, to provide a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype.

Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research

Genome sequencing has revolutionized the diagnosis of genetic diseases. Close collaborations between basic scientists and clinical genomicists are now needed to link genetic variants with disease causation. To facilitate such collaborations, we recommend prioritizing clinically relevant genes for functional studies, developing reference variant-phenotype databases, adopting phenotype description standards, and promoting data sharing.

Integrating Genomic Resources with Electronic Health Records using the HL7 Infobutton Standard

BACKGROUND

The Clinical Genome Resource (ClinGen) Electronic Health Record (EHR) Workgroup aims to integrate ClinGen resources with EHRs. A promising option to enable this integration is through the Health Level Seven (HL7) Infobutton Standard. EHR systems that are certified according to the US Meaningful Use program provide HL7-compliant infobutton capabilities, which can be leveraged to support clinical decision-making in genomics.

OBJECTIVES

To integrate genomic knowledge resources using the HL7 infobutton standard. Two tactics to achieve this objective were: (1) creating an HL7-compliant search interface for ClinGen, and (2) proposing guidance for genomic resources on achieving HL7 Infobutton standard accessibility and compliance.

METHODS

We built a search interface utilizing OpenInfobutton, an open source reference implementation of the HL7 Infobutton standard. ClinGen resources were assessed for readiness towards HL7 compliance. Finally, based upon our experiences we provide recommendations for publishers seeking to achieve HL7 compliance.

RESULTS

Eight genomic resources and two sub-resources were integrated with the ClinGen search engine via OpenInfobutton and the HL7 infobutton standard. Resources we assessed have varying levels of readiness towards HL7-compliance. Furthermore, we found that adoption of standard terminologies used by EHR systems is the main gap to achieve compliance.

CONCLUSION

Genomic resources can be integrated with EHR systems via the HL7 Infobutton standard using OpenInfobutton. Full compliance of genomic resources with the Infobutton standard would further enhance interoperability with EHR systems.

Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant

Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) is an autosomal-dominant cancer-predisposition syndrome with a significant risk of gastric, but not colorectal, adenocarcinoma. We mapped the gene to 5q22 and found loss of the wild-type allele on 5q in fundic gland polyps from affected individuals. Whole-exome and -genome sequencing failed to find causal mutations but, through Sanger sequencing, we identified point mutations in APC promoter 1B that co-segregated with disease in all six families. The mutations reduced binding of the YY1 transcription factor and impaired activity of the APC promoter 1B in luciferase assays. Analysis of blood and saliva from carriers showed allelic imbalance of APC, suggesting that these mutations lead to decreased allele-specific expression in vivo. Similar mutations in APC promoter 1B occur in rare families with familial adenomatous polyposis (FAP). Promoter 1A is methylated in GAPPS and sporadic FGPs and in normal stomach, which suggests that 1B transcripts are more important than 1A in gastric mucosa. This might explain why all known GAPPS-affected families carry promoter 1B point mutations but only rare FAP-affected families carry similar mutations, the colonic cells usually being protected by the expression of the 1A isoform. Gastric polyposis and cancer have been previously described in some FAP-affected individuals with large deletions around promoter 1B. Our finding that GAPPS is caused by point mutations in the same promoter suggests that families with mutations affecting the promoter 1B are at risk of gastric adenocarcinoma, regardless of whether or not colorectal polyps are present.

A Clinical Service to Support the Return of Secondary Genomic Findings in Human Research

Human genome and exome sequencing are powerful research tools that can generate secondary findings beyond the scope of the research. Most secondary genomic findings are of low importance, but some (for a current estimate of 1%-3% of individuals) confer high risk of a serious disease that could be mitigated by timely medical intervention. The impact and scope of secondary findings in genome and exome sequencing will only increase in the future. There is considerable agreement that high-impact findings should be returned to participants, but many researchers performing genomic research studies do not have the background, skills, or resources to identify, verify, interpret, and return such variants. Here, we introduce a proposal for the formation of a secondary-genomic-findings service (SGFS) that would support researchers by enabling the return of clinically actionable sequencing results to research participants in a standardized manner. We describe a proposed structure for such a centralized service and evaluate the advantages and challenges of the approach. We suggest that such a service would be of greater benefit to all parties involved than present practice, which is highly variable. We encourage research centers to consider the adoption of a centralized SGFS.

Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting

This article provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward.

Impact of family history assessment on communication with family members and health care providers: A report from the Family Healthware™ Impact Trial (FHITr)

OBJECTIVE

This study examines the impact of Family Healthware™ on communication behaviors; specifically, communication with family members and health care providers about family health history.

METHODS

A total of 3786 participants were enrolled in the Family Healthware™ Impact Trial (FHITr) in the United States from 2005-7. The trial employed a two-arm cluster-randomized design, with primary care practices serving as the unit of randomization. Using generalized estimating equations (GEE), analyses focused on communication behaviors at 6month follow-up, adjusting for age, site and practice clustering.

RESULTS

A significant interaction was observed between study arm and baseline communication status for the family communication outcomes (p's<.01), indicating that intervention had effects of different magnitude between those already communicating at baseline and those who were not. Among participants who were not communicating at baseline, intervention participants had higher odds of communicating with family members about family history risk (OR=1.24, p=0.042) and actively collecting family history information at follow-up (OR=2.67, p=0.026). Family Healthware™ did not have a significant effect on family communication among those already communicating at baseline, or on provider communication, regardless of baseline communication status. Greater communication was observed among those at increased familial risk for a greater number of diseases.

CONCLUSION

Family Healthware™ prompted more communication about family history with family members, among those who were not previously communicating. Efforts are needed to identify approaches to encourage greater sharing of family history information, particularly with health care providers.

ClinVar: public archive of relationships among sequence variation and human phenotype

ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/) provides a freely available archive of reports of relationships among medically important variants and phenotypes. ClinVar accessions submissions reporting human variation, interpretations of the relationship of that variation to human health and the evidence supporting each interpretation. The database is tightly coupled with dbSNP and dbVar, which maintain information about the location of variation on human assemblies. ClinVar is also based on the phenotypic descriptions maintained in MedGen (http://www.ncbi.nlm.nih.gov/medgen). Each ClinVar record represents the submitter, the variation and the phenotype, i.e. the unit that is assigned an accession of the format SCV000000000.0. The submitter can update the submission at any time, in which case a new version is assigned. To facilitate evaluation of the medical importance of each variant, ClinVar aggregates submissions with the same variation/phenotype combination, adds value from other NCBI databases, assigns a distinct accession of the format RCV000000000.0 and reports if there are conflicting clinical interpretations. Data in ClinVar are available in multiple formats, including html, download as XML, VCF or tab-delimited subsets. Data from ClinVar are provided as annotation tracks on genomic RefSeqs and are used in tools such as Variation Reporter (http://www.ncbi.nlm.nih.gov/variation/tools/reporter), which reports what is known about variation based on user-supplied locations.

The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency

The National Institutes of Health Genetic Testing Registry (GTR; available online at http://www.ncbi.nlm.nih.gov/gtr/) maintains comprehensive information about testing offered worldwide for disorders with a genetic basis. Information is voluntarily submitted by test providers. The database provides details of each test (e.g. its purpose, target populations, methods, what it measures, analytical validity, clinical validity, clinical utility, ordering information) and laboratory (e.g. location, contact information, certifications and licenses). Each test is assigned a stable identifier of the format GTR000000000, which is versioned when the submitter updates information. Data submitted by test providers are integrated with basic information maintained in National Center for Biotechnology Information’s databases and presented on the web and through FTP (ftp.ncbi.nih.gov/pub/GTR/_README.html).

Alcohol and tobacco lower the age of presentation in sporadic pancreatic cancer in a dose-dependent manner: a multicenter study

OBJECTIVES

The objective of this study was to examine the association between tobacco and alcohol dose and type and the age of onset of pancreatic adenocarcinoma (PancCa).

METHODS

Prospective data from the Pancreatic Cancer Collaborative Registry were used to examine the association between age of onset and variables of interest including: gender, race, birth country, educational status, family history of PancCa, diabetes status, and tobacco and alcohol use. Statistical analysis included logistic and linear regression, Cox proportional hazard regression, and time-to-event analysis.

RESULTS

The median age to diagnosis for PancCa was 66.3 years (95% confidence intervals (CIs), 64.5-68.0). Males were more likely than females to be smokers (77% vs. 69%, P=0.0002) and heavy alcohol and beer consumers (19% vs. 6%, 34% vs. 19%, P<0.0001). In univariate analysis for effects on PancCa presentation age, the following were significant: gender, alcohol and tobacco use (amount, status and type), family history of PancCa, and body mass index. Both alcohol and tobacco had dose-dependent effects. In multivariate analysis, alcohol status and dose were independently associated with increased risk for earlier PancCa onset with greatest risk occurring in heavy drinkers (HR 1.62, 95% CI 1.04-2.54). Smoking status had the highest risk for earlier onset pancreatic cancer with a HR of 2.69 (95% CI, 1.97-3.68) for active smokers and independent effects for dose (P=0.019). The deleterious effects for alcohol and tobacco appear to resolve after 10 years of abstinence.

CONCLUSIONS

Alcohol and tobacco use are associated with a dose-related increased risk for earlier age of onset of PancCa. Although beer drinkers develop pancreatic cancer at an earlier age than nondrinkers, alcohol type did not have a significant effect after controlling for alcohol dose.

Family history assessment: impact on disease risk perceptions

BACKGROUND

Family Healthware™, a tool developed by the CDC, is a self-administered web-based family history tool that assesses familial risk for six diseases (coronary heart disease; stroke; diabetes; and colon, breast, and ovarian cancers) and provides personalized prevention messages based on risk. The Family Healthware Impact Trial (FHITr) set out to examine the clinical utility of presenting personalized preventive messages tailored to family history risk for improving health behaviors.

PURPOSE

The purpose of this study was to examine the impact of Family Healthware on modifying disease risk perceptions, particularly among those who initially underestimated their risk for certain diseases.

DESIGN

A total of 3786 patients were enrolled in a cluster-randomized trial to evaluate the clinical utility of Family Healthware.

SETTING/PARTICIPANTS

Participants were recruited from 41 primary care practices among 13 states between 2005 and 2007.

MAIN OUTCOME MEASURES

Perceived risk for each disease was assessed at baseline and 6-month follow-up using a single-item comparative risk question. Analyses were completed in March 2012.

RESULTS

Compared to controls, Family Healthware increased risk perceptions among those who underestimated their risk for heart disease (15% vs 9%, p<0.005); stroke (11% vs 8%, p<0.05); diabetes (18% vs 11%, p<0.05); and colon cancer (17% vs 10%, p=0.05) but not breast or ovarian cancers. The majority of underestimators did not shift in their disease risk perceptions.

CONCLUSIONS

Family Healthware was effective at increasing disease risk perceptions, particularly for metabolic conditions, among those who underestimated their risk. Results from this study also demonstrate the relatively resistant nature of risk perceptions.

TRIAL REGISTRATION

This study is registered at clinicaltrials.govNCT00164658.

A nonsynonymous polymorphism in IRS1 modifies risk of developing breast and ovarian cancers in BRCA1 and ovarian cancer in BRCA2 mutation carriers

BACKGROUND

We previously reported significant associations between genetic variants in insulin receptor substrate 1 (IRS1) and breast cancer risk in women carrying BRCA1 mutations. The objectives of this study were to investigate whether the IRS1 variants modified ovarian cancer risk and were associated with breast cancer risk in a larger cohort of BRCA1 and BRCA2 mutation carriers.

METHODS

IRS1 rs1801123, rs1330645, and rs1801278 were genotyped in samples from 36 centers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Data were analyzed by a retrospective cohort approach modeling the associations with breast and ovarian cancer risks simultaneously. Analyses were stratified by BRCA1 and BRCA2 status and mutation class in BRCA1 carriers.

RESULTS

Rs1801278 (Gly972Arg) was associated with ovarian cancer risk for both BRCA1 (HR, 1.43; 95% confidence interval (CI), 1.06-1.92; P = 0.019) and BRCA2 mutation carriers (HR, 2.21; 95% CI, 1.39-3.52, P = 0.0008). For BRCA1 mutation carriers, the breast cancer risk was higher in carriers with class II mutations than class I mutations (class II HR, 1.86; 95% CI, 1.28-2.70; class I HR, 0.86; 95%CI, 0.69-1.09; P(difference), 0.0006). Rs13306465 was associated with ovarian cancer risk in BRCA1 class II mutation carriers (HR, 2.42; P = 0.03).

CONCLUSION

The IRS1 Gly972Arg single-nucleotide polymorphism, which affects insulin-like growth factor and insulin signaling, modifies ovarian cancer risk in BRCA1 and BRCA2 mutation carriers and breast cancer risk in BRCA1 class II mutation carriers.

IMPACT

These findings may prove useful for risk prediction for breast and ovarian cancers in BRCA1 and BRCA2 mutation carriers.

Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes

Genome- and exome-sequencing costs are continuing to fall, and many individuals are undergoing these assessments as research participants and patients. The issue of secondary (so-called incidental) findings in exome analysis is controversial, and data are needed on methods of detection and their frequency. We piloted secondary variant detection by analyzing exomes for mutations in cancer-susceptibility syndromes in subjects ascertained for atherosclerosis phenotypes. We performed exome sequencing on 572 ClinSeq participants, and in 37 genes, we interpreted variants that cause high-penetrance cancer syndromes by using an algorithm that filtered results on the basis of mutation type, quality, and frequency and that filtered mutation-database entries on the basis of defined categories of causation. We identified 454 sequence variants that differed from the human reference. Exclusions were made on the basis of sequence quality (26 variants) and high frequency in the cohort (77 variants) or dbSNP (17 variants), leaving 334 variants of potential clinical importance. These were further filtered on the basis of curation of literature reports. Seven participants, four of whom were of Ashkenazi Jewish descent and three of whom did not meet family-history-based referral criteria, had deleterious BRCA1 or BRCA2 mutations. One participant had a deleterious SDHC mutation, which causes paragangliomas. Exome sequencing, coupled with multidisciplinary interpretation, detected clinically important mutations in cancer-susceptibility genes; four of such mutations were in individuals without a significant family history of disease. We conclude that secondary variants of high clinical importance will be detected at an appreciable frequency in exomes, and we suggest that priority be given to the development of more efficient modes of interpretation with trials in larger patient groups.

Health beliefs among individuals at increased familial risk for type 2 diabetes: implications for prevention

AIM

To evaluate perceived risk, control, worry, and severity about diabetes, coronary heart disease (CHD) and stroke among individuals at increased familial risk of diabetes.

METHODS

Data analyses were based on the Family Healthware™ Impact Trial. Baseline health beliefs were compared across three groups: (1) no family history of diabetes, CHD or stroke (n=836), (2) family history of diabetes alone (n=267), and (3) family history of diabetes and CHD and/or stroke (n=978).

RESULTS

After adjusting for age, gender, race, education and BMI, scores for perceived risk for diabetes (p<0.0001), CHD (p<0.0001) and stroke (p<0.0001) were lowest in Group 1 and highest in Group 3. Similar results were observed about worry for diabetes (p<0.0001), CHD (p<0.0001) and stroke (p<0.0001). Perceptions of control or severity for diabetes, CHD or stroke did not vary across the three groups.

CONCLUSIONS

Among individuals at increased familial risk for diabetes, having family members affected with CHD and/or stroke significantly influenced perceived risk and worry. Tailored lifestyle interventions for this group that assess health beliefs and emphasize approaches for preventing diabetes, as well as its vascular complications, may be an effective strategy for reducing the global burden of these serious but related chronic disorders.

Breast and ovarian cancer risk and risk reduction in Jewish BRCA1/2 mutation carriers

PURPOSE

Mutations in BRCA1/2 dramatically increase the risk of both breast and ovarian cancers. Three mutations in these genes (185delAG, 5382insC, and 6174delT) occur at high frequency in Ashkenazi Jews. We evaluated how these common Jewish mutations (CJMs) affect cancer risks and risk reduction.

METHODS

Our cohort comprised 4,649 women with disease-associated BRCA1/2 mutations from 22 centers in the Prevention and Observation of Surgical End Points Consortium. Of these women, 969 were self-identified Jewish women. Cox proportional hazards models were used to estimate breast and ovarian cancer risks, as well as risk reduction from risk-reducing salpingo-oophorectomy (RRSO), by CJM and self-identified Jewish status.

RESULTS

Ninety-one percent of Jewish BRCA1/2-positive women carried a CJM. Jewish women were significantly more likely to undergo RRSO than non-Jewish women (54% v 41%, respectively; odds ratio, 1.87; 95% CI, 1.44 to 2.42). Relative risks of cancer varied by CJM, with the relative risk of breast cancer being significantly lower in 6174delT mutation carriers than in non-CJM BRCA2 carriers (hazard ratio, 0.35; 95% CI, 0.18 to 0.69). No significant difference was seen in cancer risk reduction after RRSO among subgroups.

CONCLUSION

Consistent with previous results, risks for breast and ovarian cancer varied by CJM in BRCA1/2 carriers. In particular, 6174delT carriers had a lower risk of breast cancer. This finding requires additional confirmation in larger prospective and population-based cohort studies before being integrated into clinical care.

Common variants at the 19p13.1 and ZNF365 loci are associated with ER subtypes of breast cancer and ovarian cancer risk in BRCA1 and BRCA2 mutation carriers

BACKGROUND

Genome-wide association studies (GWAS) identified variants at 19p13.1 and ZNF365 (10q21.2) as risk factors for breast cancer among BRCA1 and BRCA2 mutation carriers, respectively. We explored associations with ovarian cancer and with breast cancer by tumor histopathology for these variants in mutation carriers from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA).

METHODS

Genotyping data for 12,599 BRCA1 and 7,132 BRCA2 mutation carriers from 40 studies were combined.

RESULTS

We confirmed associations between rs8170 at 19p13.1 and breast cancer risk for BRCA1 mutation carriers [HR, 1.17; 95% confidence interval (CI), 1.07-1.27; P = 7.42 × 10(-4)] and between rs16917302 at ZNF365 (HR, 0.84; 95% CI, 0.73-0.97; P = 0.017) but not rs311499 at 20q13.3 (HR, 1.11; 95% CI, 0.94-1.31; P = 0.22) and breast cancer risk for BRCA2 mutation carriers. Analyses based on tumor histopathology showed that 19p13 variants were predominantly associated with estrogen receptor (ER)-negative breast cancer for both BRCA1 and BRCA2 mutation carriers, whereas rs16917302 at ZNF365 was mainly associated with ER-positive breast cancer for both BRCA1 and BRCA2 mutation carriers. We also found for the first time that rs67397200 at 19p13.1 was associated with an increased risk of ovarian cancer for BRCA1 (HR, 1.16; 95% CI, 1.05-1.29; P = 3.8 × 10(-4)) and BRCA2 mutation carriers (HR, 1.30; 95% CI, 1.10-1.52; P = 1.8 × 10(-3)).

CONCLUSIONS

19p13.1 and ZNF365 are susceptibility loci for ovarian cancer and ER subtypes of breast cancer among BRCA1 and BRCA2 mutation carriers.

IMPACT

These findings can lead to an improved understanding of tumor development and may prove useful for breast and ovarian cancer risk prediction for BRCA1 and BRCA2 mutation carriers.

Clinical utility of family history for cancer screening and referral in primary care: a report from the Family Healthware Impact Trial

PURPOSE

To assess the effectiveness of computerized familial risk assessment and tailored messages for identifying individuals for targeted cancer prevention strategies and motivating behavior change.

METHODS

We conducted a randomized clinical trial in primary care patients aged 35-65 years using Family Healthware, a self-administered, internet-based tool that collects family history for six common diseases including breast cancer, colon cancer, and ovarian cancer, stratifies risk into three tiers, and provides tailored prevention messages. Cancer screening adherence and consultation were measured at baseline and 6-month follow-up.

RESULTS

Of 3283 participants, 34% were at strong or moderate risk of at least one of the cancers. Family Healthware identified additional participants for whom earlier screening (colon cancer, 4.4%; breast cancer, women ages: 35-39 years, 9%) or genetic assessment (colon cancer, 2.5%; breast cancer, 10%; and ovarian cancer, 4%) may be indicated. Fewer than half were already adherent with risk-based screening. Screening adherence improved for all risk categories with no difference between intervention and control groups. Consultation with specialists did not differ between groups.

CONCLUSION

Family Healthware identified patients for intensified cancer prevention. Engagement of clinicians and patients, integration with clinical decision support, and inclusion of nonfamilial risk factors may be necessary to achieve the full potential of computerized risk assessment.

Genetic variation in IGF2 and HTRA1 and breast cancer risk among BRCA1 and BRCA2 carriers

BACKGROUND

BRCA1 and BRCA2 mutation carriers have a lifetime breast cancer risk of 40% to 80%, suggesting the presence of risk modifiers. We previously identified significant associations in genetic variants in the insulin-like growth factor (IGF) signaling pathway. Here, we investigate additional IGF signaling genes as risk modifiers for breast cancer development in BRCA carriers.

METHODS

A cohort of 1,019 BRCA1 and 500 BRCA2 mutation carriers were genotyped for 99 single-nucleotide polymorphisms (SNP) in 13 genes. Proportional hazards regression was used to model time from birth to diagnosis of breast cancer for BRCA1 and BRCA2 carriers separately. For linkage disequilibrium (LD) blocks with multiple SNPs, an additive genetic model was used. For an SNP analysis, no additivity assumptions were made.

RESULTS

Significant associations were found between risk of breast cancer and LD blocks in IGF2 for BRCA1 and BRCA2 mutation carriers (global P values of 0.009 for BRCA1 and 0.007 for BRCA2), HTRA1 for BRCA1 carriers (global P value of 0.005), and MMP3 for BRCA2 carriers (global P = 0.0000007 for BRCA2).

CONCLUSIONS

We identified significant associations of genetic variants involved in IGF signaling. With the known interaction of BRCA1 and IGF signaling and the loss of PTEN in a majority of BRCA1 tumors, this suggests that signaling through AKT may modify breast cancer risk in BRCA1 carriers.

IMPACT

These results suggest potential avenues for future research targeting the IGF signaling pathway in modifying risk in BRCA1and BRCA2 mutation carriers.

Modification of BRCA1-Associated Breast and Ovarian Cancer Risk by BRCA1-Interacting Genes

Inherited BRCA1 mutations confer elevated cancer risk. Recent studies have identified genes that encode proteins that interact with BRCA1 as modifiers of BRCA1-associated breast cancer. We evaluated a comprehensive set of genes that encode most known BRCA1 interactors to evaluate the role of these genes as modifiers of cancer risk. A cohort of 2,825 BRCA1 mutation carriers was used to evaluate the association of haplotypes at ATM, BRCC36, BRCC45 (BRE), BRIP1 (BACH1/FANCJ), CTIP, ABRA1 (FAM175A), MERIT40, MRE11A, NBS1, PALB2 (FANCN), RAD50, RAD51, RAP80, and TOPBP1, and was associated with time to breast and ovarian cancer diagnosis. Statistically significant false discovery rate (FDR) adjusted P values for overall association of haplotypes (P(FDR)) with breast cancer were identified at ATM (P(FDR) = 0.029), BRCC45 (P(FDR) = 0.019), BRIP1 (P(FDR) = 0.008), CTIP (P(FDR) = 0.017), MERIT40 (P(FDR) = 0.019), NBS1 (P(FDR) = 0.003), RAD50 (P(FDR) = 0.014), and TOPBP1 (P(FDR) = 0.011). Haplotypes at ABRA1 (P(FDR) = 0.007), BRCC45 (P(FDR) = 0.016 and P(FDR) = 0.005 in two haplotype blocks), and RAP80 (P(FDR) < 0.001) were associated with ovarian cancer risk. Overall, the data suggest that genomic variation at multiple loci that encode proteins that interact biologically with BRCA1 are associated with modified breast cancer and ovarian cancer risk in women who carry BRCA1 mutations.

Long-term outcomes, branch-specific expressivity, and disease-related mortality in von Hippel-Lindau type 2A

Although a large kindred with familial pheochromocytoma (Pheo) and paraganglioma (PGL) was discovered in 1962 and later found to represent von Hippel-Lindau (VHL) type 2A (mutation Y112H), the phenotype lacks current characterization. Branch-specific expressivity was suspected based on oral family history. Family pedigree analysis, prospective interviews, and extensive record review were used to extend the pedigree, determine phenotype, examine branch-specific expression, and analyze mortality rates over 5 decades. In its 3 known affected branches the kindred now comprises 107 people with or at-risk for VHL, of whom 49 have been diagnosed and 35/49 (71%) are clinically affected. Phenotypic cumulative lifetime risk was 71% for Pheo/PGL, 15% for hemangioblastoma, 33% for retinal angioma, 3% for renal cell carcinoma, and 3% for pancreatic cysts. The mean ages for VHL and Pheo/PGL diagnosis were younger in successive generations. Branch II-4 predominately expressed RA, while branch II-5 predominantly expressed Pheo/PGL. Disease-specific mortality occurred early and was less frequent in successive generations. This analysis of Y112H VHL confirms a high cumulative risk for pheochromocytoma/paraganglioma. Over time, both age at diagnosis and disease-specific mortality have decreased. The observed branch-specific expressivity prompts further study of genetic and environmental disease modifiers in this large family.

Haplotype structure in Ashkenazi Jewish BRCA1 and BRCA2 mutation carriers

Three founder mutations in BRCA1 and BRCA2 contribute to the risk of hereditary breast and ovarian cancer in Ashkenazi Jews (AJ). They are observed at increased frequency in the AJ compared to other BRCA mutations in Caucasian non-Jews (CNJ). Several authors have proposed that elevated allele frequencies in the surrounding genomic regions reflect adaptive or balancing selection. Such proposals predict long-range linkage disequilibrium (LD) resulting from a selective sweep, although genetic drift in a founder population may also act to create long-distance LD. To date, few studies have used the tools of statistical genomics to examine the likelihood of long-range LD at a deleterious locus in a population that faced a genetic bottleneck. We studied the genotypes of hundreds of women from a large international consortium of BRCA1 and BRCA2 mutation carriers and found that AJ women exhibited long-range haplotypes compared to CNJ women. More than 50% of the AJ chromosomes with the BRCA1 185delAG mutation share an identical 2.1 Mb haplotype and nearly 16% of AJ chromosomes carrying the BRCA2 6174delT mutation share a 1.4 Mb haplotype. Simulations based on the best inference of Ashkenazi population demography indicate that long-range haplotypes are expected in the context of a genome-wide survey. Our results are consistent with the hypothesis that a local bottleneck effect from population size constriction events could by chance have resulted in the large haplotype blocks observed at high frequency in the BRCA1 and BRCA2 regions of Ashkenazi Jews.

PCCR: Pancreatic Cancer Collaborative Registry

The Pancreatic Cancer Collaborative Registry (PCCR) is a multi-institutional web-based system aimed to collect a variety of data on pancreatic cancer patients and high-risk subjects in a standard and efficient way. The PCCR was initiated by a group of experts in medical oncology, gastroenterology, genetics, pathology, epidemiology, nutrition, and computer science with the goal of facilitating rapid and uniform collection of critical information and biological samples to be used in developing diagnostic, prevention and treatment strategies against pancreatic cancer. The PCCR is a multi-tier web application that utilizes Java/JSP technology and has Oracle 10 g database as a back-end. The PCCR uses a “confederation model” that encourages participation of any interested center, irrespective of its size or location. The PCCR utilizes a standardized approach to data collection and reporting, and uses extensive validation procedures to prevent entering erroneous data. The PCCR controlled vocabulary is harmonized with the NCI Thesaurus (NCIt) or Systematized Nomenclature of Medicine-Clinical Terms (SNOMED-CT). The PCCR questionnaire has accommodated standards accepted in cancer research and healthcare. Currently, seven cancer centers in the USA, as well as one center in Italy are participating in the PCCR. At present, the PCCR database contains data on more than 2,700 subjects (PC patients and individuals at high risk of getting this disease). The PCCR has been certified by the NCI Center for Biomedical Informatics and Information Technology as a cancer Biomedical Informatics Grid (caBIG^®) Bronze Compatible product. The PCCR provides a foundation for collaborative PC research. It has all the necessary prerequisites for subsequent evolution of the developed infrastructure from simply gathering PC-related data into a biomedical computing platform vital for successful PC studies, care and treatment. Studies utilizing data collected in the PCCR may engender new approaches to disease prognosis, risk factor assessment, and therapeutic interventions.

Effect of preventive messages tailored to family history on health behaviors: the Family Healthware Impact Trial

PURPOSE

We wanted to determine the impact of automated family history assessment and tailored messages for coronary heart disease, stroke, diabetes, colorectal, breast, and ovarian cancer on preventive behaviors compared with a standard preventive message.

METHODS

The study was a cluster-randomized clinical trial that included 41 primary care practices, the majority in the Midwest, using Family Healthware, a self-administered, Web-based tool that assesses familial risk for the diseases and provides personalized risk-tailored messages. Patients in the control group received an age- and sex-specific health message related to lifestyle and screening. Smoking cessation, fruit and vegetable intake, physical activity, aspirin use, blood pressure, and cholesterol and blood glucose screening were assessed at baseline and 6 months after the intervention.

RESULTS

Of 4,248 participants, 3,344 (78%) completed the study. Participants were white (91%), female (70%), and insured (97%), and had a mean age of 50.6 years (range 35-65 years). Intervention participants were more likely to increase daily fruit and vegetable consumption from 5 or fewer servings a day to 5 or more servings a day (OR = 1.29; 95% confidence interval [CI], 1.05-1.58) and to increase physical activity (OR = 1.47; 95% CI, 1.08-1.98) to 5 to 6 times a week for 30 minutes or more a week. The absolute differences in proportion were 3% and 4%, respectively. Intervention participants were less likely to move from not having cholesterol screening in the last 5 years to having their cholesterol measured within 5 years (OR = 0.34; 95% CI, 0.17-0.67), with an absolute difference of 15%.

CONCLUSIONS

Messages tailored to an individual's familial risk for 6 common diseases modestly increased self-reported physical activity and fruit and vegetable intake but reduced the likelihood of receiving cholesterol screening.

Genotype-phenotype correlations of pheochromocytoma in two large von Hippel-Lindau (VHL) type 2A kindreds with different missense mutations

Von Hippel-Lindau (VHL) disease type 2A is an inherited tumor syndrome characterized by predisposition to pheochromocytoma (pheo), retinal hemangioma (RA), and central nervous system hemangioblastoma (HB). Specific VHL subtypes display genotype-phenotype correlations but, unlike other familial syndromes such as MEN-2, the phenotype in VHL has not yet been stratified at the codon level. Over decades, we have managed two very large VHL type 2A regional kindreds with nearly adjacent but distinct VHL missense mutations. We determined the phenotype of Family 2 and compared the clinical and pathologic parameters of pheo between 30 members of Family 1 (Y112H mutation) and 33 members of Family 2 (Y98H mutation) with mean follow-up of 15.5 and 12.1 years, respectively (P = 0.24). In Family 2, pheo was the most frequent VHL manifestation (79%) and all pheo diagnoses occurred by age 50. Age at first diagnosis was younger in Family 2 than in Family 1 (mean 19.7 vs. 28.8 years; P = 0.02). Pheo expressivity differed by genotype: Family 1 pheo was more likely to be multifocal (P = 0.04), as well as malignant (P < 0.01) and lethal (P = 0.02). Family 1 pheo was also more likely to secrete vanillylmandelic acid (VMA) alone (P = 0.05). This analysis of 130 pheochromocytomas in 63 VHL type 2A patients demonstrates that mutation-specific malignancy and expression patterns exist within the VHL type 2A subtype, and provides information that may help tailor the screening and management algorithms of affected members and those at risk.

Components of family history associated with women's disease perceptions for cancer: a report from the Family Healthware™ Impact Trial

PURPOSE

To determine the specific components of family history and personal characteristics related to disease perceptions about breast, colon, and ovarian cancers.

METHODS

Baseline, cross-sectional data on 2,505 healthy women aged 35-65 years enrolled from 41 primary care practices in the cluster-randomized Family Healthware™ Impact Trial, assessed for detailed family history and perceived risk, perceived severity, worry, and perceived control over getting six common diseases including breast, colon, and ovarian cancers.

RESULTS

Participants provided family history information on 41,841 total relatives. We found evidence of underreporting of paternal family history and lower perceived breast cancer risk with cancer in the paternal versus maternal lineage. We observed cancer-specific perceived risks and worry for individual family history elements and also found novel "spillover" effects where a family history of one cancer was associated with altered disease perceptions of another. Having a mother with early-onset breast or ovarian cancer was strongly associated with perceived risk of breast cancer. Age, parenthood, and affected lineage were associated with disease perceptions and ran counter to empiric risks.

CONCLUSIONS

Understanding patients' formulation of risk for multiple diseases is important for public health initiatives that seek to inform risk appraisal, influence disease perceptions, or match preventive interventions to existing risk perceptions.

The rs10993994 risk allele for prostate cancer results in clinically relevant changes in microseminoprotein-beta expression in tissue and urine

Background

Microseminoprotein-beta (MSMB) regulates apoptosis and using genome-wide association studies the rs10993994 single nucleotide polymorphism in the MSMB promoter has been linked to an increased risk of developing prostate cancer. The promoter location of the risk allele, and its ability to reduce promoter activity, suggested that the rs10993994 risk allele could result in lowered MSMB in benign tissue leading to increased prostate cancer risk.

Methodology/Principal Findings

MSMB expression in benign and malignant prostate tissue was examined using immunohistochemistry and compared with the rs10993994 genotype. Urinary MSMB concentrations were determined by ELISA and correlated with urinary PSA, the presence or absence of cancer, rs10993994 genotype and age of onset. MSMB levels in prostate tissue and urine were greatly reduced with tumourigenesis. Urinary MSMB was better than urinary PSA at differentiating men with prostate cancer at all Gleason grades. The high risk allele was associated with heterogeneity of MSMB staining and loss of MSMB in both tissue and urine in benign prostate.

Conclusions

These data show that some high risk alleles discovered using genome-wide association studies produce phenotypic effects with potential clinical utility. We provide the first link between a low penetrance polymorphism for prostate cancer and a potential test in human tissue and bodily fluids. There is potential to develop tissue and urinary MSMB for a biomarker of prostate cancer risk, diagnosis and disease monitoring.