Improve Cancer Risk Assessment Research Articles

Variant curation and interpretation in hereditary cancer genes: An institutional experience in Latin America.

Variant curation refers to the application of evidence-based methods for the interpretation of genetic variants. Significant variability in this process among laboratories affects clinical practice. For admixed Hispanic/Latino populations, underrepresented in genomic databases, the interpretation of genetic variants for cancer risk is challenging. We retrospectively evaluated 601 sequence variants detected in patients participating in the largest Institutional Hereditary Cancer Program in Colombia. VarSome and PathoMAN were used for automated curation, and ACMG/AMP and Sherloc criteria were applied for manual curation. Regarding the automated curation, 11% of the variants (64/601) were reclassified, 59% (354/601) had no changes in its interpretation, and the other 30% (183/601) presented conflicting interpretations. With respect to manual curation, of the 183 variants with conflicting interpretations, 17% (N= 31) were reclassified, 66% (N= 120) had no changes in their initial interpretation, and 17% (N= 32) remained with conflicting interpretation status. Overall, 91% of the VUS were downgraded and 9% were upgraded. Most VUS were reclassified as benign/likely benign. Since false-positive and -negative results can be obtained with automated tools, manual curation should also be used as a complement. Our results contribute to improving cancer risk assessment and management for a broad range of hereditary cancer syndromes in Hispanic/Latino populations.

Preferences for a polygenic test to estimate cancer risk in a general Australian population.

There is significant interest in the use of polygenic risk score (PRS) tests to improve cancer risk assessment and stratified prevention. Our current understanding of preferences regarding different aspects of this novel testing approach is limited. This study examined which attributes of a PRS test most influence the likelihood of testing. A discrete choice experiment was developed to elicit preferences for different aspects of a PRS test by surveying an online sample of the Australian population. Preferences were assessed using mixed logistic regression, latent class analysis, and marginal willingness to pay. The 1002 surveyed respondents were more likely to choose a PRS test that was more accurate, tested for multiple cancer types, and enabled cancer risk reduction through lifestyle modification, screening, or medication. There was also a preference for testing through a primary care physician rather than online or through a genetic specialist. A test that did not impact life insurance eligibility or premiums was preferred over the one that did. This study found that the Australian population prefer a PRS test that is highly accurate, tests for multiple cancers, has noninvasive risk reduction measures, and is performed through primary care.

Assessing Breast Cancer Risks to Improve Care for an Increased-Risk Population within Eastern North Carolina.

BACKGROUND The average lifetime risk of breast cancer for an American woman is 12.5%, but individual risks vary significantly. Risk modeling is a standard of care for breast cancer screening and prevention with recommended tools to stratify individual risks based on age, family history, breast density, and a host of other known risk factors. Because of a lack of resources rurally, we have not consistently met this standard of care within all of North Carolina.METHODS We implemented a quality improvement project to assess the risk for breast cancer by gathering data on community risks. We implemented an evidence-based tool (Tyrer-Cuzick) for quantifying risk within a mostly rural population of Eastern North Carolina and developed customized services for women meeting elevated-risk definition. These services included additional imaging for elevated-risk women and a risk-reduction program. We also assessed genetic risks for hereditary breast and ovarian cancer in our at-risk population using National Comprehensive Cancer Network (NCCN) guidelines based on family history and added local genetics extenders to help test more women. We analyzed data regularly using Plan-Do-Study-Act methods to improve outcomes over 1 year.RESULTS We screened a population of 4500 women at a community hospital over a 1-year period for their individual lifetime cancer risk and genetic risk. Breast cancer risk was quantitated at the time of mammography, and women were stratified into 3 groups for risk management. Within our screening population, 6.3% of women were at high risk (defined by a lifetime breast cancer risk greater than or equal to 20%) and another 8.1% were above-average risk (defined by a lifetime breast cancer risk of 15%-20%). These women (14.4%) could potentially benefit from additional risk-management strategies. Additionally, 20% of all unaffected women within a typical screening population of Eastern North Carolina met NCCN guidelines for hereditary breast cancer and ovarian cancer testing independent of their cancer risk score. Using a model of targeted intervention within a population with elevated risks can be helpful in improving outcomes.LIMITATIONS This population within Eastern North Carolina is mostly rural and represents a potentially biased population, as it involves older women undergoing annual mammography. It may not be broadly applicable to the entire population based on age, geography, and other risks.CONCLUSIONS This model for improving cancer risk assessment and testing at a small community hospital in Eastern North Carolina was successful and addressed a community need. We discovered a high rate of increased-risk women who can benefit from individualized risk management, and a higher percentage of women who potentially benefit from genetic testing. These higher cumulative risks may in part explain some of the disparities seen for breast-cancer-specific outcomes in some parts of the state.

The stanford prostate cancer calculator: Development and external validation of online nomograms incorporating PIRADS scores to predict clinically significant prostate cancer.

While multiparametric MRI (mpMRI) has high sensitivity for detection of clinically significant prostate cancer (CSC), false positives and negatives remain common. Calculators that combine mpMRI with clinical variables can improve cancer risk assessment, while providing more accurate predictions for individual patients. We sought to create and externally validate nomograms incorporating Prostate Imaging Reporting and Data System (PIRADS) scores and clinical data to predict the presence of CSC in men of all biopsy backgrounds. Data from 2125 men undergoing mpMRI and MR fusion biopsy from 2014 to 2018 at Stanford, Yale, and UAB were prospectively collected. Clinical data included age, race, PSA, biopsy status, PIRADS scores, and prostate volume. A nomogram predicting detection of CSC on targeted or systematic biopsy was created. Biopsy history, Prostate Specific Antigen (PSA) density, PIRADS score of 4 or 5, Caucasian race, and age were significant independent predictors. Our nomogram-the Stanford Prostate Cancer Calculator (SPCC)-combined these factors in a logistic regression to provide stronger predictive accuracy than PSA density or PIRADS alone. Validation of the SPCC using data from Yale and UAB yielded robust AUC values. The SPCC combines pre-biopsy mpMRI with clinical data to more accurately predict the probability of CSC in men of all biopsy backgrounds. The SPCC demonstrates strong external generalizability with successful validation in two separate institutions. The calculator is available as a free web-based tool that can direct real-time clinical decision-making.

Mapping genomic and epigenomic evolution in cancer ecosystems.

Cancer is a major cause of global mortality underpinned by genomic and epigenomic derangements. Here, we highlight the importance of multimodal data integration in understanding the molecular evolution of malignant cell states across the cancer life cycle. The widespread presence of driver mutations and epigenetic alterations in normal-appearing tissues is prompting a reassessment of how cancer initiation is defined. In later-stage cancers, studying the roles of clonal selection, epigenomic adaptation, and persister cells in metastasis and therapy resistance is an emerging field. Finally, the importance of tumor ecosystems in driving cancer development is being unraveled by single-cell and spatial technologies at unprecedented resolution. Improving cancer risk assessment and accelerating therapeutic discovery for patients will require robust, comprehensive, and integrated temporal, spatial, and multilevel tumor atlases across the cancer life cycle.

Pan-cancer analysis demonstrates that integrating polygenic risk scores with modifiable risk factors improves risk prediction

Cancer risk is determined by a complex interplay of environmental and heritable factors. Polygenic risk scores (PRS) provide a personalized genetic susceptibility profile that may be leveraged for disease prediction. Using data from the UK Biobank (413,753 individuals; 22,755 incident cancer cases), we quantify the added predictive value of integrating cancer-specific PRS with family history and modifiable risk factors for 16 cancers. We show that incorporating PRS measurably improves prediction accuracy for most cancers, but the magnitude of this improvement varies substantially. We also demonstrate that stratifying on levels of PRS identifies significantly divergent 5-year risk trajectories after accounting for family history and modifiable risk factors. At the population level, the top 20% of the PRS distribution accounts for 4.0% to 30.3% of incident cancer cases, exceeding the impact of many lifestyle-related factors. In summary, this study illustrates the potential for improving cancer risk assessment by integrating genetic risk scores.

Abstract B090: Exploring the roles of CHWs in improving uptake of family health history assessment among patients and providers: Implications for cancer risk reduction and prevention among minority populations

Abstract The collection of family health history (FHH) is integral to the implementation of population screening that could identify those at high cancer risk who could benefit most from life-saving interventions. Although most individuals believe FHH is important to their health, few actually collect or know their FHH. Recent findings have identified a reduced likelihood of FHH collection among minority populations who may already be at an increased risk for familial cancers such as kidney, cervical, prostate, ovarian, and triple-negative breast cancer. The community health worker (CHW) workforce is especially well positioned to address these challenges in FHH collection, as they are trusted members of their community and well recognized for their work in creating community-clinical linkages. Engaging CHWs in promoting FHH collection could help improve cancer risk assessment utilization among minority populations. We conducted 30 semistructured interviews with CHWs in Georgia to understand their current roles and opportunities to expand their roles to include the gathering and sharing FHH information. Interview questions were guided by the Consolidated Framework for Implementation Research and also included current engagement in FHH collection, beliefs and understanding of FHH collection, and perceived training needs to complete an FHH record using an FHH collection tool. All interviews were double coded in MAXQDA using a codebook developed, adapted, and agreed upon by the research team. Findings demonstrate that most CHWs believe that there is value in collecting FHH and that they are well suited to gather basic FHH information, but the majority had no experience collecting FHH, either formally as part of their jobs or from their own family members. Some concerns raised about this role include the potential for community members to be resistant to providing the information, CHWs' lack of medical knowledge required to address questions from clients about genetics, and the potential complexity of information needed to complete FHH tools. CHWs also provided recommendations for reducing the burden of FHH collection such as tutorials about how to gather accurate and complete information. They also suggested providing resources to clients that focus on the importance of knowing FHH and how it can be used to improve health and become knowledgeable about cancer risk-reduction resources and prevention strategies. Understanding opportunities for CHWs to extend their role in this way could help improve health care delivery and access by enhancing patient-provider communication about FHH in order to tailor recommendations, prevention, and treatment of diseases. Results from this study may inform efforts to strengthen the utility of existing FHH collection tools and accompanying materials to promote the uptake of FHH assessment among patients and providers. Citation Format: Caitlin G. Allen, Lawrence McKinney, Brittaney Bethea, Cam Escoffery, Gail McCray, Colleen McBride, Tabia Akintobi. Exploring the roles of CHWs in improving uptake of family health history assessment among patients and providers: Implications for cancer risk reduction and prevention among minority populations [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr B090.

Comparative genotoxic potential of 27 polycyclic aromatic hydrocarbons in three human cell lines

Polycyclic Aromatic Hydrocarbons (PAHs) form a family of compounds that are generally found in complex mixtures. PAHs can lead to the development of carcinogenesis. The Toxicity Equivalent Factor (TEF) approach has been suggested for estimating the toxicity of PAHs, however, due to the relative weakness of available data, TEF have not been applied for the risk characterization of PAHs as food contaminants in Europe. The determination of new TEFs for a large number of PAHs could overcome some limitations of the current method and improve cancer risk assessment. The present investigation aimed at deriving new TEFs for PAHs, based on their genotoxic effect measured in vitro and analyzed with mathematical models. For this purpose, we used a genotoxicity assay (γH2AX) with three human cell lines to analyze the genotoxic properties of 27 selected PAHs after 24 h treatment. For 11 compounds, we did not detect any genotoxic potential. For the remaining 16 PAHs, the concentration-response for genotoxic effect was modelled with the Hill equation; equivalency between PAHs at low dose was assessed by applying constraints to the model parameters. We developed for each compound, in each cell line, Genotoxic Equivalent Factor (GEF). Calculated GEF for the tested PAHs were similar in all cell lines and generally higher than the TEF usually used. These new equivalent factors for PAHs should improve cancer risk assessment.

Serum albumin adducts, DNA adducts and micronuclei frequency measured in benzo[a]pyrene-exposed mice for estimation of genotoxic potency

The environmental and food contaminant, benzo[a]pyrene {B[a]P, a polycyclic aromatic hydrocarbon (PAH)}, is classified as a human carcinogen by the International Agency for Research on Cancer. The carcinogenicity of B[a]P is linked to the formation of electrophilic metabolites, namely B[a]P-diol epoxides (BPDEs) occurring as stereoisomers. In this work, we quantified the metabolic formation of BPDE isomers and the genotoxic effect in B[a]P-exposed mice, with an aim to estimate the genotoxic potency of B[a]P per in vivo dose of its most potent metabolite [i.e. (+)-anti-BPDE]. The increase in frequency of micronuclei (fMN) in erythrocytes was measured as a biomarker for genotoxic effect. Covalent adducts to serum albumin (SA) and those to DNA from the BPDEs were analysed using liquid chromatography tandem mass spectrometry (LC–MS/MS), as adducts to histidine (BPDE-His-Pro) and deoxyguanosine (BPDE-dG), respectively. For the first time in animal experiments it was possible to resolve adducts to SA from (+)-anti-, (-)-anti- and (±)-syn-BPDE isomers by LC–MS/MS. The adduct levels in the protein were about 16 fmol/mg SA, which was orders of magnitude lower than that in the nucleic acid, 28 pmol/mg DNA, in mice exposed to 100 mg B[a]P per kg body weight (bw). Using SA adduct levels, the in vivo dose of (+)-anti-BPDE was calculated to be approximately 50 nM·h per mg B[a]P per kg bw. This allowed to make a preliminary estimate of the genotoxic potency as 2‰ fMN per μM·h of (+)-anti-BPDE. This estimate was compared to that from another food toxicant, glycidol, studied with similar methods, which indicated that the BPDE has several orders of magnitude higher genotoxic potency. The demonstrated approach on integrating biomarkers of internal dose of a causative agent and that of genotoxic effect for assessing genotoxic potency, using B[a]P as a model, has a potential for improving cancer risk assessment procedures for PAHs.

Evaluation of confocal endoscopic microscopy for detection of early-stage gastric cancer in hereditary diffuse gastric cancer (HDGC) syndrome.

Hereditary diffuse gastric cancer (HDGC) syndrome results most often from a mutation in the CDH1 tumor suppressor gene and confers a 56-70% lifetime risk of gastric cancer. In asymptomatic carriers HDGC is characterized by multiple foci of signet ring cancer cells (SRCC) throughout the gastric mucosa. Because SRCC foci are less than 1 mm in diameter, and often make up less than 2% of the gastric mucosa, they are undetectable on standard screening endoscopy. International consensus guidelines recommend thorough white light endoscopic gastric mapping with a systematic method for gastric biopsies. Despite a painstaking approach to gastric mapping, retrospective analyses have demonstrated a low rate of detection and poor sensitivity of standard white light endoscopy for detecting occult cancer cells. Therefore, a more sensitive cancer screening tool is needed for these high-risk patients. Confocal endoscopic microscopy (CEM) allows for real-time, in vivo histologic imaging of gastrointestinal mucosa during upper endoscopy. Clinical application has demonstrated the ability of CEM to differentiate normal mucosal cells and cancer cells. A phase II clinical trial is currently underway to compare CEM to standard endoscopic gastric mapping in an effort to reduce the false negative detection rate of SRCC in patients diagnosed with HDGC. After an upper endoscopy with gastric mapping is performed, patients will undergo probe-based CEM. The endoscopist will scan the anatomic zones of the stomach in a similar fashion to the systematic gastric mapping approach. Any abnormal areas visualized with the CEM probe will be biopsied and sent for permanent pathologic analysis. The primary endpoint is to determine if CEM affords a higher sensitivity for detection of SRCC in CDH1 germline mutation carriers compared to white light endoscopy with gastric mapping. This novel screening technique is expected to provide greater sensitivity for detecting occult cancer in patients with HDGC, thereby improving cancer risk-assessment and overall cancer care. ClinicalTrials.gov NCT03648879 (registration date: August 28, 2018, clinicaltrials.gov).

The Changing Landscape of Genetic Testing for Inherited Breast Cancer Predisposition.

The advent of multiple-gene germline panel testing has led to significant advances in hereditary breast and ovarian cancer risk assessment. These include guideline-specific cancer risk management recommendations for patients and their families, such as screening with breast magnetic resonance imaging and risk-reducing surgeries, which have the potential to reduce substantially the morbidity and mortality associated with a hereditary cancer predisposition. However, controversy remains about the clinical validity and actionability of genetic testing in a broader patient population. We discuss events leading to the wider availability of commercialized multiple-gene germline panel testing, the recent data that support using this powerful tool to improve cancer risk assessment and reduction strategies, and remaining challenges to clinical optimization of this new genetic technology.

Comparative potency approach based on H2AX assay for estimating the genotoxicity of polycyclic aromatic hydrocarbons

Polycyclic Aromatic Hydrocarbons (PAHs) constitute a family of over one hundred compounds and can generally be found in complex mixtures. PAHs metabolites cause DNA damage which can lead to the development of carcinogenesis. Toxicity assessment of PAH complex mixtures is currently expressed in terms of toxic equivalents, based on Toxicity Equivalent Factors (TEFs). However, the definition of new TEFs for a large number of PAH could overcome some limitations of the current method and improve cancer risk assessment. The current investigation aimed at deriving the relative potency factors of PAHs, based on their genotoxic effect measured in vitro and analyzed with mathematical models. For this purpose, we used a new genotoxic assay (γH2AX) with two human cell lines (HepG2 and LS-174T) to analyze the genotoxic properties of 13 selected PAHs at low doses after 24h treatment. The dose–response for genotoxic effects was modeled with a Hill model; equivalency between PAHs at low dose was assessed by applying constraints to the model parameters. In the two cell lines tested, we observed a clear dose–response for genotoxic effects for 11 tested compounds. LS-174T was on average ten times more sensitive than HepG2 towards PAHs regarding genotoxicity. We developed new TEFs, which we named Genotoxic Equivalent Factor (GEF). Calculated GEF for the tested PAHs were generally higher than the TEF usually used. Our study proposed a new in vitro based method for the establishment of relevant TEFs for PAHs to improve cancer risk assessment.

Abstract SS01-01: Using genomic technologies to improve cancer risk assessment

Abstract The heritable fraction of human cancers, estimated from genetic and epidemiologic approaches, is 21–42%. Heritable cancers include common adult onset malignancies (e.g. prostate, colon, breast cancers) as well as rarer cancers. During past decades, genetic approaches (e.g. linkage analysis and positional cloning) identified rare genetic mutations associated with markedly elevated cancer risk, with subsequent translation of these findings into effective preventive interventions. Recently genomic approaches (e.g. genome wide association studies [GWAS] exploiting linkage disequilibrium between single nucleotide polymorphisms in the human genome) have identified common variants of lower disease risk, as well as common variants which modify the risk of high-penetrance rare alleles. Ongoing studies are utilizing next-generation massively parallel sequencing (NGS) of whole exomes and genomes to identify the “missing heritability” of human cancer. The status GWAS and NGS approaches to cancer risk assessment will be reviewed. The large sample sizes required for GWAS will be emphasized; a case example of our recent consortium effort to identify genomic modifiers of BRCA2 penetrance will be cited. While the methods of identification of genomic variants are distinct, the principles of biomarker identification and clinical translation to preventive oncology are shared. These similarities include: the use of clinically validated variants that may not be functionally characterized; the segregation of these variants in non-Mendelian as well as Mendelian patterns; the role of gene–environment interactions; the dependence on evidence for clinical utility; the critical translational role of behavioral science; and common ethical considerations. It will be emphasized that during the current period of transition from investigation to practice, consumers must also be protected from harms of premature translation of research findings, while encouraging the innovative and cost-effective application of genomic discoveries that improve personalized oncologic care. Citation Information: Cancer Prev Res 2011;4(10 Suppl):SS01-01.

Genetic alteration in hereditary colorectal cancer

Colorectal cancer is a major cause of morbidity and mortality. Both genetic and environmental factors contribute to cancer aetiology. About 15-20% of all colorectal cancers are familial. Approximately 6% of colorectal cancers can be attributed to recognizable heritable germline mutations. The discovery of genes responsible for inherited forms of colorectal cancer have the potential to improve cancer risk assessment and counselling. Genetic testing for hereditary forms of colorectal cancer can confirm or reject diagnoses at the molecular level, determine surveillance intervals for at-risk persons, decrease the cost of surveillance by risk stratification, aid in surgical and chemoprevention decision-making, and help patients in family and career planning. This paper reviews the genetics behind genes and molecular study of the hereditary colorectal cancer. This may help the medical professionals especially internists, gastroenterologists, and oncologists to update their knowledge in this field.

Biomarkers in Molecular Medicine: Cancer Detection and Diagnosis

In spite of advances in diagnostics and therapeutics, cancer remains the second leading cause of death in the U.S. Successful cancer treatment depends not only on better therapies but also on improved methods to assess an individual's risk of developing cancer and to detect cancers at early stages when they can be more effectively treated. Current cancer diagnostic imaging methods are labor-intensive and expensive, especially for screening large asymptomatic populations. Effective screening strategies depend on methods that are noninvasive and detect cancers in their early stages of development. There is increasing interest and enthusiasm in molecular markers as tools for cancer detection and prognosis. It is hoped that newly discovered cancer biomarkers and advances in high-throughput technologies would revolutionize cancer therapies by improving cancer risk assessment, early detection, diagnosis, prognosis, and monitoring therapeutic response. These biomarkers will be used either as stand-alone tests or to complement existing imaging methods.