Breast imaging, breast surgery, and cancer genetics in the age of COVID-19.

BACKGROUND: The objective of the current study was to provide insight into the effect of coronavirus disease 2019 (COVID-19) on breast cancer screening, breast surgery, and genetics consultations. METHODS: User data from a risk assessment company were collected from February 2 to April 11, 2020. The use of risk assessment was used as a proxy for the use of 3 breast cancer services, namely, breast imaging, breast surgery, and genetics consultation. Changes in the use of these services during the study period were analyzed. RESULTS: All 3 services experienced significant declines after the COVID-19 outbreak. The decline in breast surgery began during the week of March 8, followed by breast imaging and genetics consultation (both of which began during the week of March 15). Breast imaging experienced the most significant reduction, with an average weekly decline of 61.7% and a maximum decline of 94.6%. Breast surgery demonstrated an average weekly decline of 20.5%. When surgical consultation was stratified as breast cancer versus no breast cancer, the decrease among in non-breast cancer patients was more significant than that of patients with breast cancer (a decline of 66.8% vs 11.5% from the pre-COVID average weekly volume for non-breast cancer patients and patients with breast cancer, respectively). During the week of April 5, use of genetics consultations dropped to 39.9% of the average weekly volumes before COVID-19. CONCLUSIONS: COVID-19 has had a significant impact on the number of patients undergoing breast cancer prevention, screening, diagnosis, and treatment.

Implementation of an electronic genomic and family health history tool in primary prenatal care.

"The Pregnancy and Health Profile," (PHP) is a free genetic risk assessment software tool for primary prenatal providers that collects patient-entered family (FHH), personal, and obstetrical health history, performs risk assessment, and presents the provider with clinical decision support during the prenatal encounter. The tool is freely available for download at www.hughesriskapps.net. We evaluated the implementation of PHP in four geographically diverse clinical sites. Retrospective chart reviews were conducted for patients seen prior to the study period and for patients who used the PHP to collect data on documentation of FHH, discussion of cystic fibrosis (CF) and hemoglobinopathy (HB) carrier screening, and CF and HB interventions (tests, referrals). Five hundred pre-implementation phase and 618 implementation phase charts were reviewed. Documentation of a 3-generation FHH or pedigree improved at three sites; patient race/ethnicity at three sites, father of the baby (FOB) race/ethnicity at all sites, and ancestry for the patient and FOB at three sites (P < 0.001-0001). CF counseling improved for implementation phase patients at one site (8% vs. 48%, P < 0.0001) and CF screening/referrals at two (2% vs. 14%, P < 0.0001; 6% vs. 14%; P = 0.05). Counseling and intervention rates did not increase for HB. This preliminary study suggests that the PHP can improve documentation of FHH, race, and ancestry, as well as the compliance with current CF counseling and intervention guidelines in some prenatal clinics. Future evaluation of the PHP should include testing in a larger number of clinical environments, assessment of additional performance measures, and evaluation of the system's overall clinical utility.

Evaluation of a novel electronic genetic screening and clinical decision support tool in prenatal clinical settings.

"The Pregnancy and Health Profile" (PHP) is a free prenatal genetic screening and clinical decision support (CDS) software tool for prenatal providers. PHP collects family health history (FHH) during intake and provides point-of-care risk assessment for providers and education for patients. This pilot study evaluated patient and provider responses to PHP and effects of using PHP in practice. PHP was implemented in four clinics. Surveys assessed provider confidence and knowledge and patient and provider satisfaction with PHP. Data on the implementation process were obtained through semi-structured interviews with administrators. Quantitative survey data were analyzed using Chi square test, Fisher's exact test, paired t tests, and multivariate logistic regression. Open-ended survey questions and interviews were analyzed using qualitative thematic analysis. Of the 83% (513/618) of patients that provided feedback, 97% felt PHP was easy to use and 98% easy to understand. Thirty percent (21/71) of participating physicians completed both pre- and post-implementation feedback surveys [13 obstetricians (OBs) and 8 family medicine physicians (FPs)]. Confidence in managing genetic risks significantly improved for OBs on 2/6 measures (p values ≤0.001) but not for FPs. Physician knowledge did not significantly change. Providers reported value in added patient engagement and reported mixed feedback about the CDS report. We identified key steps, resources, and staff support required to implement PHP in a clinical setting. To our knowledge, this study is the first to report on the integration of patient-completed, electronically captured and CDS-enabled FHH software into primary prenatal practice. PHP is acceptable to patients and providers. Key to successful implementation in the future will be customization options and interoperability with electronic health records.

Providing access to risk prediction tools via the HL7 XML-formatted risk web service.

Cancer risk prediction tools provide valuable information to clinicians but remain computationally challenging. Many clinics find that CaGene or HughesRiskApps fit their needs for easy- and ready-to-use software to obtain cancer risks; however, these resources may not fit all clinics' needs. The HughesRiskApps Group and BayesMendel Lab therefore developed a web service, called "Risk Service", which may be integrated into any client software to quickly obtain standardized and up-to-date risk predictions for BayesMendel tools (BRCAPRO, MMRpro, PancPRO, and MelaPRO), the Tyrer-Cuzick IBIS Breast Cancer Risk Evaluation Tool, and the Colorectal Cancer Risk Assessment Tool. Software clients that can convert their local structured data into the HL7 XML-formatted family and clinical patient history (Pedigree model) may integrate with the Risk Service. The Risk Service uses Apache Tomcat and Apache Axis2 technologies to provide an all Java web service. The software client sends HL7 XML information containing anonymized family and clinical history to a Dana-Farber Cancer Institute (DFCI) server, where it is parsed, interpreted, and processed by multiple risk tools. The Risk Service then formats the results into an HL7 style message and returns the risk predictions to the originating software client. Upon consent, users may allow DFCI to maintain the data for future research. The Risk Service implementation is exemplified through HughesRiskApps. The Risk Service broadens the availability of valuable, up-to-date cancer risk tools and allows clinics and researchers to integrate risk prediction tools into their own software interface designed for their needs. Each software package can collect risk data using its own interface, and display the results using its own interface, while using a central, up-to-date risk calculator. This allows users to choose from multiple interfaces while always getting the latest risk calculations. Consenting users contribute their data for future research, thus building a rich multicenter resource.

Hereditary breast and ovarian cancer and other hereditary syndromes: using technology to identify carriers.

PURPOSE AND METHODS: Most patients who harbor a genetic mutation for hereditary breast cancer have not been identified, despite the availability of genetic testing. Developing an effective approach to the identification of high-risk individuals is the key to preventing and/or providing early diagnosis of cancer in this patient population. This educational review addresses these issues. RESULTS AND DISCUSSION: Using data available on the internet, and making assumptions regarding the types and results of genetic testing, we have estimated the number of mutation carriers in the country and the number who have been tested and identified as such. Overall, our ability to fund and more effectively manage carriers is weak. A technological solution is discussed.

Bias in the reporting of family history: implications for clinical care.

Family history of cancer is critical for identifying and managing patients at risk for cancer. However, the quality of family history data is dependent on the accuracy of patient self reporting. Therefore, the validity of family history reporting is crucial to the quality of clinical care. A retrospective review of family history data collected at a community hospital between 2005 and 2009 was performed in 43,257 women presenting for screening mammography. Reported numbers of breast, colon, prostate, lung, and ovarian cancer were compared in maternal relatives vs. paternal relatives and in first vs. second degree relatives. Significant reporting differences were found between maternal and paternal family history of cancer, in addition to degree of relative. The number of paternal family histories of cancer was significantly lower than that of maternal family histories of cancer. Similarly, the percentage of grandparents' family histories of cancer was significantly lower than the percentage of parents' family histories of cancer. This trend was found in all cancers except prostate cancer. Self-reported family history in the community setting is often influenced by both bloodline of the cancer history and the degree of relative affected. This is evident by the underreporting of paternal family histories of cancer, and also, though to a lesser extent, by degree. These discrepancies in reporting family history of cancer imply we need to take more care in collecting accurate family histories and also in the clinical management of individuals in relation to hereditary risk.

Natural variation in Drosophila stressed locomotion meets or exceeds variation caused by hsp70 mutation: analysis of behavior and performance.

Thermotolerance involves more than life or death. Investigating the complexity of this trait will aid identification of its genetic contributors. We examined variation in thermally stressed walking behavior and performance in natural Drosophila melanogaster strains and strains mutant for the heat shock protein Hsp70, to determine which aspects of locomotion are affected by heat shock and genotype. We developed software for the large-scale capture, analysis, and visualization of locomotion, and determined: (1) Heat shock and thermal pretreatment significantly and differentially impact fly locomotor behavior and performance. (2) Stressed locomotion traits vary extensively among natural strains. (3) Interactions among treatments, strains, and traits are substantial and often counterintuitive. (4) Hsp70 overexpressing flies are faster and more basally thermoprotected in performance than Hsp70 null flies, but null flies are more unidirectional. (5) Natural variation in most stressed locomotion traits exceeds that caused by Hsp70 mutation, reveals uncoupling between thermoprotection of behavior and performance, and suggests significant genetic variation for trait-specific modifiers of thermotolerance.

Electronic health records and the management of women at high risk of hereditary breast and ovarian cancer.

Currently, management strategies exist that can decrease the morbidity and mortality associated with having a BRCA1 or BRCA2 mutation. Unfortunately, the task of identifying these patients at high risk is a daunting challenge. This problem is intensified because Electronic Health Records (EHRs) today lack the functionality needed to identify these women and to manage those women once they have been identified. Numerous niche software programs have been developed to fill this gap. Unfortunately, these extremely valuable niche programs are prevented from being interoperable with the EHRs, on the premise that each EHR vendor will build their own programs. Effectively, in our efforts to adopt EHRs, we have lost sight of the fact that they can only have a major impact on quality of care if they contain structured data and if they interact with robust Clinical Decision Support (CDS) tools. We are at a cross roads in the development of the health care Information Technology infrastructure. We can choose a path where each EHR vendor develops each CDS module independently. Alternatively, we can choose a path where experts in each field develop external niche software modules that are interoperable with any EHR vendor. We believe that the modular approach to development of niche software programs that are interoperable with current EHRs will markedly increase the speed at which useful and functional EHRs that improve quality of care become a reality. Thus, in order to realize the benefits of CDS, we suggest vendors develop means to become interoperable with external modular niche programs.

Identification and management of women at high risk for hereditary breast/ovarian cancer syndrome.

Despite advances in identifying genetic markers of high risk patients and the availability of genetic testing, it remains challenging to efficiently identify women who are at hereditary risk and to manage their care appropriately. HughesRiskApps, an open-source family history collection, risk assessment, and Clinical Decision Support (CDS) software package, was developed to address the shortcomings in our ability to identify and treat the high risk population. This system is designed for use in primary care clinics, breast centers, and cancer risk clinics to collect family history and risk information and provide the necessary CDS to increase quality of care and efficiency. This paper reports on the first implementation of HughesRiskApps in the community hospital setting. HughesRiskApps was implemented at the Newton-Wellesley Hospital. Between April 1, 2007 and March 31, 2008, 32,966 analyses were performed on 25,763 individuals. Within this population, 915 (3.6%) individuals were found to be eligible for risk assessment and possible genetic testing based on the 10% risk of mutation threshold. During the first year of implementation, physicians and patients have fully accepted the system, and 3.6% of patients assessed have been referred to risk assessment and consideration of genetic testing. These early results indicate that the number of patients identified for risk assessment has increased dramatically and that the care of these patients is more efficient and likely more effective.

Inducible and constitutive heat shock gene expression responds to modification of Hsp70 copy number in Drosophila melanogaster but does not compensate for loss of thermotolerance in Hsp70 null flies.

BACKGROUND: The heat shock protein Hsp70 promotes inducible thermotolerance in nearly every organism examined to date. Hsp70 interacts with a network of other stress-response proteins, and dissecting the relative roles of these interactions in causing thermotolerance remains difficult. Here we examine the effect of Hsp70 gene copy number modification on thermotolerance and the expression of multiple stress-response genes in Drosophila melanogaster, to determine which genes may represent mechanisms of stress tolerance independent of Hsp70. RESULTS: Hsp70 copy number in four strains is positively associated with Hsp70 expression and inducible thermotolerance of severe heat shock. When assayed at carefully chosen temperatures, Hsp70 null flies are almost entirely deficient in thermotolerance. In contrast to expectations, increasing Hsp70 expression levels induced by thermal pretreatment are associated with increasing levels of seven other inducible Hsps across strains. In addition, complete Hsp70 loss causes upregulation of the inducible Hsps and six constitutive stress-response genes following severe heat shocks. CONCLUSION: Modification of Hsp70 copy number quantitatively and qualitatively affects the expression of multiple other stress-response genes. A positive association between absolute expression levels of Hsp70 and other Hsps after thermal pretreatment suggests novel regulatory mechanisms. Severe heat shocks induce both novel gene expression patterns and almost total mortality in the Hsp70 null strain: alteration of gene expression in this strain does not compensate for Hsp70 loss but suggests candidates for overexpression studies.

Which risk model to use? Clinical implications of the ACS MRI screening guidelines.

The American Cancer Society (ACS) guidelines define the appropriate use of MRI as an adjunct to mammography for breast cancer screening. Three risk assessment models are recommended to determine if women are at sufficient risk to warrant the use of this expensive screening tool, however, the real-world application of these models has not been explored. We sought to understand how these models behave in a community setting for women undergoing mammography screening. We conducted a retrospective analysis of 5,894 women, who received mammography screening at a community hospital and assessed their eligibility for MRI according to the ACS guidelines. Of the 5,894 women, 342 (5.8%) were eligible for MRI, but we found significant differences in the number of eligible women identified by each model. Our results indicate that these models identify very different populations, implying that the ACS guidelines deserve further development and consideration.

Personalizing prenatal care using family health history: identifying a panel of conditions for a novel electronic genetic screening tool.

In the age of genomic medicine, family health history (FHH) remains an important tool for personalized risk assessment as it can inform approaches to disease prevention and management. In primary care, including in prenatal settings, providers recognize that FHH enables them to assess the risk for birth defects and complex conditions that not only affect the fetus health, but also the mother's. However, many providers lack the time to gather FHH or the knowledge to confidently interpret the data. Electronic tools providing clinical decision support using FHH data can aid the busy provider with data collection and interpretation. We describe the scope of conditions included in a patient-entered FHH tool that provides clinical decision support and point-of-care education to assist with patient management. This report details how we selected the conditions for which it is appropriate to use FHH as a means to promote personalized medicine in primary prenatal care.

The feasibility of using natural language processing to extract clinical information from breast pathology reports.

OBJECTIVE: The opportunity to integrate clinical decision support systems into clinical practice is limited due to the lack of structured, machine readable data in the current format of the electronic health record. Natural language processing has been designed to convert free text into machine readable data. The aim of the current study was to ascertain the feasibility of using natural language processing to extract clinical information from >76,000 breast pathology reports. APPROACH AND PROCEDURE: Breast pathology reports from three institutions were analyzed using natural language processing software (Clearforest, Waltham, MA) to extract information on a variety of pathologic diagnoses of interest. Data tables were created from the extracted information according to date of surgery, side of surgery, and medical record number. The variety of ways in which each diagnosis could be represented was recorded, as a means of demonstrating the complexity of machine interpretation of free text. RESULTS: There was widespread variation in how pathologists reported common pathologic diagnoses. We report, for example, 124 ways of saying invasive ductal carcinoma and 95 ways of saying invasive lobular carcinoma. There were >4000 ways of saying invasive ductal carcinoma was not present. Natural language processor sensitivity and specificity were 99.1% and 96.5% when compared to expert human coders. CONCLUSION: We have demonstrated how a large body of free text medical information such as seen in breast pathology reports, can be converted to a machine readable format using natural language processing, and described the inherent complexities of the task.

The American Cancer Society guidelines for breast screening with magnetic resonance imaging: an argument for genetic testing.

BACKGROUND: The American Cancer Society (ACS) guidelines for screening with breast magnetic resonance imaging (MRI) recommend MRI for women who have a lifetime risk > or = 20% of developing breast cancer. Genetic testing for breast cancer gene (BRCA) mutations is offered to women who have a risk > or = 10% of carrying a mutation. The objectives of the current study were 1) to identify the number of women in a breast cancer screening population who had > or = 20% lifetime breast cancer risk and, thus, were candidates for screening MRI; and 2) to determine the number of women who had > or = 10% risk of BRCA mutation yet had <20% lifetime risk of breast cancer and, thus, may not have been identified as candidates for MRI screening. METHODS: From 2003 to 2005, women who underwent screening mammography completed a self-administered questionnaire regarding breast cancer risk factors. For each patient, the lifetime breast cancer risk and the risk of BRCA mutation was determined by using the computerized BRCAPRO breast cancer risk-assessment model. RESULTS: Of 18,190 women, 78 (0.43%) had > or = 20% lifetime risk of breast cancer, all of whom had > or = 10% risk of carrying a BRCA mutation. An additional 374 women (2.06%) had <20% lifetime breast cancer risk but > or = 10% risk of mutation. Overall, there were 183 (1%) predicted mutation carriers, 27 women (0.15%) who had > or = 20% lifetime risk of breast cancer, and 62 women (0.34%) who had > or = 10% risk of mutation but <20% lifetime breast cancer risk. CONCLUSIONS: The ACS guidelines for breast MRI screening may systematically exclude MRI screening for many women who have a substantial risk for BRCA mutation. The current results demonstrated a need for greater awareness of breast cancer risk factors in the screening mammography population, so that high-risk women can be identified and given access to genetic testing and counseling regarding all risk-reducing interventions.

Accuracy of self-reported personal history of cancer in an outpatient breast center.

The self-reporting of cancer history is becoming increasingly important, as it frequently guides medical decision-making. We studied the accuracy of personal cancer history using a self-administered questionnaire, comparing the results with the Tumor Registry at our institution. Among 39,662 records, we identified 3614 women with a single cancer in the Tumor Registry who reported none or one cancer on their questionnaire. The sensitivity in self-reporting cancers was 85.7%, ranging from 92.1% for breast cancer to 42.9% for leukemia. The accuracy for breast cancer and Hodgkin's Lymphoma was significantly better than other cancers (p=0.00027, CI: 1.4-3.88). Analysis of patient's characteristics showed that Caucasians reported breast cancer more accurately than Asian/Pacific Islanders (p=0.008), and those with Jewish ancestry more accurately than non-Jewish (p=0.0435). These results will help us to improve data collection and thus improve medical decision-making.