Alleviating misclassified germline variants in underrepresented populations: A strategy using popmax.

PURPOSE: Germline variant interpretation often depends on population-matched control cohorts. This is not feasible for population groups that are underrepresented in current population reference databases. METHODS: We classify germline variants with population-matched controls for 2 ancestrally diverse cohorts of patients: 132 early-onset or familial colorectal carcinoma patients from Singapore and 100 early-onset colorectal carcinoma patients from the United States. The effects of using a population-mismatched control cohort are simulated by swapping the control cohorts used for each patient cohort, with or without the popmax computational strategy. RESULTS: Population-matched classifications revealed a combined 62 pathogenic or likely pathogenic (P/LP) variants in 34 genes across both cohorts. Using a population-mismatched control cohort resulted in misclassification of non-P/LP variants as P/LP, driven by the absence of ancestry-specific rare variants in the control cohort. Popmax was more effective in alleviating misclassifications for the Singapore cohort than the US cohort. CONCLUSION: Underrepresented population groups can suffer from higher rates of false-positive P/LP results. Popmax can partially alleviate these misclassifications, but its efficacy still depends on the degree with which the population groups are represented in the control cohort.

Landscape of germline pathogenic variants in patients with dual primary breast and lung cancer.

BACKGROUND: Cancer predisposition is most often studied in the context of single cancers. However, inherited cancer predispositions can also give rise to multiple primary cancers. Yet, there is a paucity of studies on genetic predisposition in multiple primary cancers, especially those outside of well-defined cancer predisposition syndromes. This study aimed to identify germline variants associated with dual primary cancers of the breast and lung. METHODS: Exome sequencing was performed on germline DNA from 55 Singapore patients (52 [95%] never-smokers) with dual primaries in the breast and lung, confirmed by histopathology. Using two large control cohorts: the local SG10K_Health (n = 9770) and gnomAD non-cancer East Asians (n = 9626); and two additional local case cohorts of early-onset or familial breast cancer (n = 290), and lung cancer (n = 209), variants were assessed for pathogenicity in accordance with ACMG/AMP guidelines. In particular, comparisons were made with known pathogenic or likely pathogenic variants in the ClinVar database, pathogenicity predictions were obtained from in silico prediction software, and case-control association analyses were performed. RESULTS: Altogether, we identified 19 pathogenic or likely pathogenic variants from 16 genes, detected in 17 of 55 (31%) patients. Six of the 19 variants were identified using ClinVar, while 13 variants were classified pathogenic or likely pathogenic using ACMG/AMP guidelines. The 16 genes include well-known cancer predisposition genes such as BRCA2, TP53, and RAD51D; but also lesser known cancer genes EXT2, WWOX, GATA2, and GPC3. Most of these genes are involved in DNA damage repair, reaffirming the role of impaired DNA repair mechanisms in the development of multiple malignancies. These variants warrant further investigations in additional populations. CONCLUSIONS: We have identified both known and novel variants significantly enriched in patients with primary breast and lung malignancies, expanding the body of known cancer predisposition variants for both breast and lung cancer. These variants are mostly from genes involved in DNA repair, affirming the role of impaired DNA repair in the predisposition and development of multiple cancers.

Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility.

BACKGROUND: For the majority of individuals with early-onset or familial breast cancer referred for genetic testing, the genetic basis of their familial breast cancer remains unexplained. To identify novel germline variants associated with breast cancer predisposition, whole-exome sequencing (WES) was performed. METHODS: WES on 290 BRCA1/BRCA2-negative Singaporeans with early-onset breast cancer and/or a family history of breast cancer was done. Case-control analysis against the East-Asian subpopulation (EAS) from the Genome Aggregation Database (gnomAD) identified variants enriched in cases, which were further selected by occurrence in cancer gene databases. Variants were further evaluated in repeated case-control analyses using a second case cohort from the database of Genotypes and Phenotypes (dbGaP) comprising 466 early-onset breast cancer patients from the United States, and a Singapore SG10K_Health control cohort. RESULTS: Forty-nine breast cancer-associated germline pathogenic variants in 37 genes were identified in Singapore cases versus gnomAD (EAS). Compared against SG10K_Health controls, 13 of 49 variants remain significantly enriched (False Discovery Rate (FDR)-adjusted p < 0.05). Comparing these 49 variants in dbGaP cases against gnomAD (EAS) and SG10K_Health controls revealed 23 concordant variants that were significantly enriched (FDR-adjusted p < 0.05). Fourteen variants were consistently enriched in breast cancer cases across all comparisons (FDR-adjusted p < 0.05). Seven variants in GPRIN2, NRG1, MYO5A, CLIP1, CUX1, GNAS and MGA were confirmed by Sanger sequencing. CONCLUSIONS: In conclusion, we have identified pathogenic variants in genes associated with breast cancer predisposition. Importantly, many of these variants were significant in a second case cohort from dbGaP, suggesting that the strategy of using case-control analysis to select variants could potentially be utilized for identifying variants associated with cancer susceptibility.

Development and validation of a circulating microRNA panel for the early detection of breast cancer.

BACKGROUND: Mammography is widely used for breast cancer screening but suffers from a high false-positive rate. Here, we perform the largest comprehensive, multi-center study to date involving diverse ethnic groups, for the identification of circulating miRNAs for breast cancer screening. METHODS: This study had a discovery phase (n = 289) and two validation phases (n = 374 and n = 379). Quantitative PCR profiling of 324 miRNAs was performed on serum samples from breast cancer (all stages) and healthy subjects to identify miRNA biomarkers. Two-fold cross-validation was used for building and optimising breast cancer-associated miRNA panels. An optimal panel was validated in cohorts with Caucasian and Asian samples. Diagnostic ability was evaluated using area under the curve (AUC) analysis. RESULTS: The study identified and validated 30 miRNAs dysregulated in breast cancer. An optimised eight-miRNA panel showed consistent performance in all cohorts and was successfully validated with AUC, accuracy, sensitivity, and specificity of 0.915, 82.3%, 72.2% and 91.5%, respectively. The prediction model detected breast cancer in both Caucasian and Asian populations with AUCs ranging from 0.880 to 0.973, including pre-malignant lesions (stage 0; AUC of 0.831) and early-stage (stages I-II) cancers (AUC of 0.916). CONCLUSIONS: Our panel can potentially be used for breast cancer screening, in conjunction with mammography.

Continuity of supervision: Does it mean what we think it means?

CONTEXT: Continuity of supervision (CoS) is generally accepted as an important element of competency-based medical education (CBME). However, collecting and interpreting evidence for its effectiveness are a challenge because we lack a shared understanding of CoS. Translating the available evidence about CoS into practice is an even greater challenge because the evidence largely exists in the undergraduate medical education (UME) literature, whereas literature about CBME is mostly situated in postgraduate medical education (PGME). PROPOSAL: We explore the potential dangers of basing assumptions of the importance of CoS in CBME on evidence from the UME level where CBME is yet to be widely implemented. First, we discuss current understandings of what is meant by CoS and examine some of its evidence and where such evidence comes from. Next, we consider relevant theories related to CoS in the context of CBME and review how it is conceptualised in different educational models. We then discuss some contextual and pedagogical differences between UME and PGME when CoS is considered. Finally, we propose a shared understanding of CoS and outline implications and next steps to determine if the benefits of CoS seen at the UME level will also manifest with PGME learners. CONCLUSIONS: We have the opportunity to undertake research to close our gap in knowledge about CoS at the PGME level using data emerging from our experiences with CBME. Selecting specific dimensions of CoS will allow research that is necessary to determine that what works at the UME level will also work at the PGME level as we continue to march towards CBME.

Breast cancer in women with neurofibromatosis type 1 (NF1): a comprehensive case series with molecular insights into its aggressive phenotype.

PURPOSE: The purpose of the study was to improve the understanding of NF1-associated breast cancer, given the increased risk of breast cancer in this tumour predisposition syndrome and the limited data. METHODS: We identified 18 women with NF1 and breast cancer at our institution. Clinical and pathologic characteristics of NF1-associated breast cancers were compared with 7132 breast cancers in patients without NF1 from our institutional database. Next generation sequencing was performed on DNA from blood and breast cancer specimens available. Blood specimens negative for NF1 mutation were subjected to multiplex ligation-dependent probe amplification (MLPA) to identify complete/partial deletions or duplications. Expression of neurofibromin in the NF1-associated breast cancers was evaluated using immunohistochemistry. RESULTS: There was a higher frequency of grade 3 (83.3% vs 45.4%, p = 0.005), oestrogen receptor (ER) negative (66.7% vs 26.3%, p < 0.001) and human epidermal growth factor receptor 2 (HER2)-positive (66.7% vs 23.4%, p < 0.001) tumours among NF1 patients compared to non-NF1 breast cancers. Overall survival was inferior in NF1 patients in multivariable analysis (hazard ratio 2.25, 95% CI 1.11-4.60; p = 0.025). Apart from germline NF1 mutations (11/16; 69%), somatic mutations in TP53 (8/10; 80%), second-hit NF1 (2/10; 20%), KMT2C (4/10; 40%), KMT2D (2/10; 20%), and PIK3CA (2/10; 20%) were observed. Immunohistochemical expression of neurofibromin was seen in the nuclei and/or cytoplasm of all specimens, but without any consistent pattern in the intensity or extent. CONCLUSIONS: This comprehensive series of NF1-associated breast cancers suggests that their aggressive features are related to germline NF1 mutations in cooperation with somatic mutations in TP53, KMT2C and other genes.

Comprehensive spectrum of BRCA1 and BRCA2 deleterious mutations in breast cancer in Asian countries.

Approximately 5%-10% of breast cancers are due to genetic predisposition caused by germline mutations; the most commonly tested genes are BRCA1 and BRCA2 mutations. Some mutations are unique to one family and others are recurrent; the spectrum of BRCA1/BRCA2 mutations varies depending on the geographical origins, populations or ethnic groups. In this review, we compiled data from 11 participating Asian countries (Bangladesh, Mainland China, Hong Kong SAR, Indonesia, Japan, Korea, Malaysia, Philippines, Singapore, Thailand and Vietnam), and from ethnic Asians residing in Canada and the USA. We have additionally conducted a literature review to include other Asian countries mainly in Central and Western Asia. We present the current pathogenic mutation spectrum of BRCA1/BRCA2 genes in patients with breast cancer in various Asian populations. Understanding BRCA1/BRCA2 mutations in Asians will help provide better risk assessment and clinical management of breast cancer.

Machine learning unveils an immune-related DNA methylation profile in germline DNA from breast cancer patients.

BACKGROUND: There is an unmet need for precise biomarkers for early non-invasive breast cancer detection. Here, we aimed to identify blood-based DNA methylation biomarkers that are associated with breast cancer. METHODS: DNA methylation profiling was performed for 524 Asian Chinese individuals, comprising 256 breast cancer patients and 268 age-matched healthy controls, using the Infinium MethylationEPIC array. Feature selection was applied to 649,688 CpG sites in the training set. Predictive models were built by training three machine learning models, with performance evaluated on an independent test set. Enrichment analysis to identify transcription factors binding to regions associated with the selected CpG sites and pathway analysis for genes located nearby were conducted. RESULTS: A methylation profile comprising 51 CpGs was identified that effectively distinguishes breast cancer patients from healthy controls achieving an AUC of 0.823 on an independent test set. Notably, it outperformed all four previously reported breast cancer-associated methylation profiles. Enrichment analysis revealed enrichment of genomic loci associated with the binding of immune modulating AP-1 transcription factors, while pathway analysis of nearby genes showed an overrepresentation of immune-related pathways. CONCLUSION: This study has identified a breast cancer-associated methylation profile that is immune-related to potential for early cancer detection.

Management of Multiple Myeloma: A Review for General Practitioners in Oncology.

Multiple myeloma (MM) is a malignant clonal plasma cell disorder in the bone marrow and is the second-most common hematologic malignancy in adults. Although patients with MM have a moderate life expectancy, it remains a heterogeneous disease that often requires multiple lines of chemotherapy for durable control and long-term survival. This review outlines current management strategies for both transplant-eligible and transplant-ineligible patients as well as for relapsed and refractory disease. Advances in drug therapies have widened management options and improved survival. In this paper, we also discuss implications for special populations and survivorship care.

Degradation of methylation signals in cryopreserved DNA.

BACKGROUND: Blood-based DNA methylation has shown great promise as a biomarker in a wide variety of diseases. Studies of DNA methylation in blood often utilize samples which have been cryopreserved for years or even decades. Therefore, changes in DNA methylation associated with long-term cryopreservation can introduce biases or otherwise mislead methylation analyses of cryopreserved DNA. However, previous studies have presented conflicting results with studies reporting hypomethylation, no effect, or even hypermethylation of DNA following long-term cryopreservation. These studies may have been limited by insufficient sample sizes, or by their profiling of methylation only on an aggregate global scale, or profiling of only a few CpGs. RESULTS: We analyzed two large prospective cohorts: a discovery (n = 126) and a validation (n = 136) cohort, where DNA was cryopreserved for up to four years. In both cohorts there was no detectable change in mean global methylation across increasing storage durations as DNA. However, when analysis was performed on the level of individual CpG methylation both cohorts exhibited a greater number of hypomethylated than hypermethylated CpGs at q-value < 0.05 (4049 hypomethylated but only 50 hypermethylated CpGs in discovery, and 63 hypomethylated but only 6 hypermethylated CpGs in validation). The results were the same even after controlling for age, storage duration as buffy coat prior to DNA extraction, and estimated cell type composition. Furthermore, we find that in both cohorts, CpGs have a greater likelihood to be hypomethylated the closer they are to a CpG island; except for CpGs at the CpG islands themselves which are less likely to be hypomethylated. CONCLUSION: Cryopreservation of DNA after a few years results in a detectable bias toward hypomethylation at the level of individual CpG methylation, though when analyzed in aggregate there is no detectable change in mean global methylation. Studies profiling methylation in cryopreserved DNA should be mindful of this hypomethylation bias, and more attention should be directed at developing more stable methods of DNA cryopreservation for biomedical research or clinical use.

Using Learning Analytics to Examine Differences in Assessment Forms From Continuous Versus Episodic Supervisors of Family Medicine Residents.

Background: It is assumed that there is a need for continuity of supervision within competency-based medical education, despite most evidence coming from the undergraduate medical education rather than the graduate medical education (GME) context. This evidence gap must be addressed to justify the time and effort needed to redesign GME programs to support continuity of supervision. Objective: To examine differences in assessment behaviors of continuous supervisors (CS) versus episodic supervisors (ES), using completed formative assessment forms, FieldNotes, as a proxy. Methods: The FieldNotes CS- and ES-entered for family medicine residents (N=186) across 3 outpatient teaching sites over 3 academic years (2015-2016, 2016-2017, 2017-2018) were examined using 2-sample proportion z-tests to determine differences on 3 FieldNote elements: competency (Sentinel Habit [SH]), Clinical Domain (CD), and Progress Level (PL). Results: Sixty-nine percent (6104 of 8909) of total FieldNotes were analyzed. Higher proportions of CS-entered FieldNotes indicated SH3 (Managing patients with best practices), z=-3.631, P<.0001; CD2 (Care of adults), z=-8.659, P<.0001; CD3 (Care of the elderly), z=-4.592, P<.0001; and PL3 (Carry on, got it), z=-4.482, P<.0001. Higher proportions of ES-entered FieldNotes indicated SH7 (Communication skills), z=4.268, P<.0001; SH8 (Helping others learn), z=20.136, P<.0001; CD1 (Doctor-patient relationship/ethics), z=14.888, P<.0001; CD9 (Not applicable), z=7.180, P<.0001; and PL2 (In progress), z=5.117, P<.0001. Conclusions: The type of supervisory relationship impacts assessment: there is variability in which competencies are paid attention to, which contexts or populations are included, and which progress levels are chosen.

In-Person or Online? The Effect of Delivery Mode on Team-Based Learning of Clinical Reasoning in a Family Medicine Clerkship.

In health professions education, team-based learning (TBL) has been used to help learners develop clinical reasoning and decision-making skills. The COVID-19 pandemic has challenged institutions to move curriculum delivery from largely in-person to online. With the anticipated return to in-person instruction and arguments made in favor of online instruction in certain circumstances, evidence is needed to support decision making in curriculum planning. The purpose of this study was to examine the effect of delivery mode (in-person vs. online) on student learning of clinical reasoning and clinical decision-making (CR/CDM) in the family medicine clerkship. Data from three cohorts of third-year medical students were included in the study: 2018/2019 cohort, in-person; 2019/2020 cohort, half of the cohort in-person, half of the cohort online; 2020/2021 cohort, online. Students' performance data-individual readiness assurance test (IRAT) and group readiness assurance test (GRAT) scores-were used. The Generalized Estimating Equations (GEE) analysis was performed. As expected, students scored higher in GRAT than IRAT across the three cohorts. No significant IRAT-GRAT differences were observed between in-person and online delivery of TBL sessions. Student learning of CR/CDM in TBL is comparable between the two modes of delivery in the family medicine clerkship. Future research in other clerkships, years of medical education, and professional programs is needed to inform decision making regarding the TBL delivery mode.

An Evaluation of the Quality of Environmental Impact Assessment Reports in the Mobile Telecommunications Infrastructure Sector: The Case of Plateau State in Nigeria.

Environmental impact assessment reports meant for proposed development actions can be evaluated to reveal their quality and fitness for the purpose of environmental decision-making. Therefore, this study evaluated the quality and identified strengths and weaknesses in environmental impact assessment reports of telecommunications infrastructure proposed for Plateau State in Nigeria. To this end, 80 reports were evaluated using the modified version of the Lee and Colley review package. The results revealed the following points. In Review Area 1.0 (Description of the proposed telecommunications facilities) and Review Area 5.0 (Communication of results), the quality of environmental impact assessment reports was found to be generally satisfactory. However, the quality of all reports was considered 'very unsatisfactory' ('F') regarding their overall legal compliance with the requirements stipulated in the remaining three Review Areas, namely, Review Area 2.0 (Terrain susceptibility in the proposed project areas), Review Area 3.0 (Associated and potential environmental impacts), and Review Area 4.0 (Mitigation measures/alternatives). This 'F' rating was assigned to 65% (52/80) of reports regarding Review Area 3.0 because the information provided was 'very unsatisfactory'; important tasks were poorly carried out or not attempted at all. Moreover, in review areas such as Review Area 2.0 and Review Area 4.0, all reports in the evaluation were assigned an 'F' quality. Such an unsatisfactory quality rating is ascribable to the very unsatisfactory manner in which the reports were populated, especially as important task(s) were poorly performed or not attempted at all. Historically, only Review Area 1.0 and Review Area 5.0 indicated improvements in quality over time, whereas the remaining three review areas (Review Area 2.0, Review Area 3.0 and Review Area 4.0) did not improve. Based on the results obtained from the study, we recommend that there should be periodic reviews of environmental impact assessment reports by independent reviewers and environmental consultants should adhere to the sectoral guidelines for telecommunication infrastructure during the production of these reports. Moreover, in order to build technical capacity, more studies on report quality must be conducted in all sectors in Nigeria.

Toward a Regional Gerontological Agenda: The Use of Empowerment Evaluation.

This article describes the application of an empowerment evaluation approach to nurturing the growth and priority setting of a regional organization. A model is provided of the processes whereby the Southern Gerontological Society (SGS) identified research and service priorities by conducting a survey of stakeholder perceptions of regional needs. The survey goal was to identify important issues faced by older adults in the South as a prelude to refining SGS research and service priorities and developing its contemporary regional gerontological agenda. We trace how the survey findings were translated into actions including shaping the annual meeting program, creating new standing committees, and developing service activities. Underlying the process of developing and refining this agenda are a set of key principles that have come to characterize the operation of SGS. These principles are discussed and provide a model for comparable organizations seeking to develop agendas consistent with their mission and identity.