Biallelic disruption of DDX41 activity is associated with distinct genomic and immunophenotypic hallmarks in acute leukemia.

Introduction: Inherited DDX41 mutations cause familial predisposition to hematologic malignancies including acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), with the majority of DDX41 mutated MDS/AMLs described to date harboring germline DDX41 and co-occurring somatic DDX41 variants. DDX41-AMLs were shown to share distinguishing clinical features such as a late AML onset and an indolent disease associated with a favorable outcome. However, genotype-phenotype correlation in DDX41-MDS/AMLs remain poorly understood. Methods: Here, we studied the genetic profile, bone marrow morphology and immunophenotype of 51 patients with DDX41 mutations. We further assessed the functional impact of ten previously uncharacterized DDX41 variants of uncertain significance. Results: Our results demonstrate that MDS/AML cases harboring two DDX41 variants share specific clinicopathologic hallmarks that are not seen in other patients with monoallelic DDX41 related hematologic malignancies. We further showed that the features seen in these individuals with two DDX41 variants were concordant with biallelic DDX41 disruption. Discussion: Here, we expand on previous clinicopathologic findings on DDX41 mutated hematologic malignancies. Functional analyses conducted in this study unraveled previously uncharacterized DDX41 alleles and further illustrate the implication of biallelic disruption in the pathophysiology of this distinct AML entity.

Cardiac MRI and Clinical Outcomes in TMEM43 Arrhythmogenic Cardiomyopathy.

Arrhythmogenic cardiomyopathy is an inherited cardiomyopathy that can involve both ventricles. Several genes have been identified as pathogenic in arrhythmogenic cardiomyopathy, including TMEM43. However, there are limited data on cardiac MRI findings in patients with TMEM43 variants to date. In this case series, cardiac MRI findings and clinical outcomes are described in 14 patients with TMEM43 variants, including eight (57%) with the pathogenic p.Ser358Leu variant (six female patients; mean age, 33 years ± 15 [SD]) and six (43%) with a TMEM43 variant of unknown significance (three female patients; mean age, 38 years ± 11). MRI findings demonstrated left ventricular systolic dysfunction in eight (57%) patients and right ventricular dysfunction in four (29%) patients. Among the nine patients with late gadolinium enhancement imaging, left ventricular late gadolinium enhancement was present in seven (78%; all subepicardial) patients. In summary, TMEM43 variants are associated with high prevalence of subepicardial late gadolinium enhancement and left ventricular dysfunction. Keywords: Arrhythmogenic Cardiomyopathy, Arrhythmogenic Right Ventricular Cardiomyopathy, TMEM43, Cardiac MRI, Genetic Variants Supplemental material is available for this article.

Validation of BRCA testing on cytologic samples of high-grade serous carcinoma.

BACKGROUND: Testing for BRCA1/2 gene alterations in patients with high-grade serous carcinoma (HGSC) is a critical determinant of treatment eligibility for poly(adenosine diphosphate-ribose) polymerase inhibitors in addition to providing vital information for genetic counselling. Many patients present with effusions necessitating therapeutic drainage, and this makes cytologic specimens (CySs) the initial diagnostic material for HGSC, often before histologic sampling. Initiating somatic BRCA testing on a CyS allows the BRCA status to be determined sooner, and this affects clinical management. METHODS: Retrospectively, 8 cases of formalin-fixed, paraffin-embedded (FFPE) CySs of peritoneal or pleural fluid from patients with HGSC and known BRCA1/2 alterations previously established by the testing of FFPE surgical specimens (SpSs) underwent next-generation sequencing (NGS). Prospectively, 11 cases of peritoneal or pleural fluid from patients with HGSC but an unknown BRCA1/2 status underwent NGS with fresh, alcohol-fixed, and FFPE CySs, and they were compared with subsequent NGS on 4 SpSs. RESULTS: CySs yielded high-quantity and high-quality DNA for NGS analysis when sufficient tumor cellularity was present. Fresh, alcohol-fixed, and FFPE CySs were all suitable for NGS and provided identical NGS results. SpS and CyS BRCA testing was concordant in 10 of 12 cases. The 2 discordant cases showed low tumor cellularity and quality in the CyS and the SpS, respectively. CONCLUSION: Effusion CySs of HGSC are excellent sources for NGS testing for BRCA1/2 genetic alterations when sufficient tumor cellularity is present. Fresh, alcohol-fixed, and FFPE CySs are equivalent for NGS of BRCA1/2. NGS testing of HGSC CySs demonstrates good concordance with SpSs for the BRCA1/2 status.

Tumor and germline next generation sequencing in high grade serous cancer: experience from a large population-based testing program.

The aim of this study was to determine the prevalence of somatic and germline pathogenic variants (PVs) in high-grade serous cancer (HGSC) and to demonstrate the technical feasibility and effectiveness of a large-scale, population-based tumor testing program. It involved a retrospective review of genetic test results in 600 consecutive HGSC tumor samples and a subsequent comparison of germline and tumor results in a subset of 200 individuals. Tumor testing was successful in 95% of samples (570/600) with at least one BRCA1/2 PV identified in 16% (93/570) of cases. Among the 200 paired cases, BRCA1/2 PVs were detected in 38 tumors (19%); 58% were somatic (22/38); and 42% were germline (16/38). There was 100% concordance between germline and tumor test results. This is the largest series of BRCA1/2 testing in HGSC (tumor-only and paired cohorts), reported to date, and our data show that an effectively designed and validated population-based tumor testing program can be used to determine both treatment eligibility and hereditary cancer risk.

Exome and genome sequencing in adults with undiagnosed disease: a prospective cohort study.

BACKGROUND: Exome and genome sequencing have been demonstrated to increase diagnostic yield in paediatric populations, improving treatment options and providing risk information for relatives. There are limited studies examining the clinical utility of these tests in adults, who currently have limited access to this technology. METHODS: Patients from adult and cancer genetics clinics across Toronto, Ontario, Canada were recruited into a prospective cohort study evaluating the diagnostic utility of exome and genome sequencing in adults. Eligible patients were ≥18 years of age and suspected of having a hereditary disorder but had received previous uninformative genetic test results. In total, we examined the diagnostic utility of exome and genome sequencing in 47 probands and 34 of their relatives who consented to participate and underwent exome or genome sequencing. RESULTS: Overall, 17% (8/47) of probands had a pathogenic or likely pathogenic variant identified in a gene associated with their primary indication for testing. The diagnostic yield for patients with a cancer history was similar to the yield for patients with a non-cancer history (4/18 (22%) vs 4/29 (14%)). An additional 24 probands (51%) had an inconclusive result. Secondary findings were identified in 10 patients (21%); three had medically actionable results. CONCLUSIONS: This study lends evidence to the diagnostic utility of exome or genome sequencing in an undiagnosed adult population. The significant increase in diagnostic yield warrants the use of this technology. The identification and communication of secondary findings may provide added value when using this testing modality as a first-line test.

Year 1: Experiences of a tertiary cancer centre following implementation of reflex BRCA1 and BRCA2 tumor testing for all high-grade serous ovarian cancers in a universal healthcare system.

OBJECTIVE: This study compares the rate and time to genetic referral, and patient uptake of germline genetic services, before and after implementation of reflex BRCA1/2 tumor testing for high-grade serous ovarian cancer (HGSOC) in a universal healthcare system. METHODS: A retrospective chart review of HSGOC patients diagnosed in the year before (PRE) and after (POST) implementation of reflex BRCA1/2 tumor testing was conducted. Clinical information (date/age at diagnosis, personal/family history of breast/ovarian cancer, cancer stage, primary treatment, tumor results) and dates of genetics referral, counseling, and germline testing were obtained. Incident rate ratios (IRR) and 95% CI were calculated using negative binomial regression. Time to referral was evaluated using Kaplan-Meier survival analysis. Fisher Exact tests were used to evaluate uptake of genetic services. RESULTS: 175 HGSOC patients were identified (81 PRE; 94 POST). Post-implementation of tumor testing, there was a higher rate of genetics referral (12.88 versus 7.10/1000 person-days; IRR = 1.60, 95% CI: 1.07-2.42) and a shorter median time from diagnosis to referral (59 days PRE, 33 days POST; p = .04). In the POST cohort, most patients were referred prior to receiving their tumor results (n = 63/77; 81.8%). Once referred, most patients attended genetic counseling (94.5% PRE, 97.6% POST; p = .418) and pursue germline testing (98.6% PRE; 100% POST; p = .455). CONCLUSIONS: Following implementation of reflex BRCA1/2 tumor testing for HGSOC, significant improvements to the rate and time to genetics referral were identified. Additional studies are needed to evaluate physician referral practices and the long-term impact of reflex tumor testing.

Genetic Testing for Diagnosis of Hypertrophic Cardiomyopathy Mimics: Yield and Clinical Significance.

Background Genetic testing is helpful for diagnosis of hypertrophic cardiomyopathy (HCM) mimics. Little data are available regarding the yield of such testing and its clinical impact. Methods The HCM genetic database at our center was used for identification of patients who underwent HCM-directed genetic testing including at least 1 gene associated with an HCM mimic (GLA, TTR, PRKAG2, LAMP2, PTPN11, RAF1, and DES). Charts were retrospectively reviewed and genetic and clinical data extracted. Results There were 1731 unrelated HCM patients who underwent genetic testing for at least 1 gene related to an HCM mimic. In 1.45% of cases, a pathogenic or likely pathogenic variant in one of these genes was identified. This included a yield of 1% for Fabry disease, 0.3% for familial amyloidosis, 0.15% for PRKAG2-related cardiomyopathy, and 1 patient with Noonan syndrome. In the majority of patients, diagnosis of the HCM mimic based on clinical findings alone would have been challenging. Accurate diagnosis of an HCM mimic led to change in management (eg, enzyme replacement therapy) or family screening in all cases. Conclusions Genetic testing is helpful in the diagnosis of HCM mimics in patients with no or few extracardiac manifestations. Adding these genes to all HCM genetic panels should be considered.

Next-Generation Service Delivery: A Scoping Review of Patient Outcomes Associated with Alternative Models of Genetic Counseling and Genetic Testing for Hereditary Cancer.

The combination of increased referral for genetic testing and the current shortage of genetic counselors has necessitated the development and implementation of alternative models of genetic counseling and testing for hereditary cancer assessment. The purpose of this scoping review is to provide an overview of the patient outcomes that are associated with alternative models of genetic testing and genetic counseling for hereditary cancer, including germline-only and tumor testing models. Seven databases were searched, selecting studies that were: (1) full-text articles published ≥2007 or conference abstracts published ≥2015, and (2) assessing patient outcomes of an alternative model of genetic counseling or testing. A total of 79 publications were included for review and synthesis. Data-charting was completed using a data-charting form that was developed by the study team for this review. Seven alternative models were identified, including four models that involved a genetic counselor: telephone, telegenic, group, and embedded genetic counseling models; and three models that did not: mainstreaming, direct, and tumor-first genetic testing models. Overall, these models may be an acceptable alternative to traditional models on knowledge, patient satisfaction, psychosocial measures, and the uptake of genetic testing; however, particular populations may be better served by traditional in-person genetic counseling. As precision medicine initiatives continue to advance, institutions should consider the implementation of new models of genetic service delivery, utilizing a model that will best serve the needs of their unique patient populations.

Structured assessment and followup for patients with hereditary kidney tumour syndromes.

INTRODUCTION: Optimal clinical assessment and subsequent followup of patients with or suspected of having a hereditary renal cell carcinoma syndrome (hRCC) is not standardized and practice varies widely. We propose protocols to optimize these processes in patients with hRCC to encourage a more uniform approach to management that can then be evaluated. METHODS: A review of the literature, including existing guidelines, was carried out for the years 1985-2015. Expert consensus was used to define recommendations for initial assessment and followup. RESULTS: Recommendations for newly diagnosed patients' assessment and optimal ages to initiate followup protocols for von Hippel Lindau disease (VHL), hereditary papillary renal cancer (HPRC), hereditary leiomyomatosis with renal cell carcinoma (HLRCC), Birt-Hogg-Dubé syndrome (BHD), familial paraganglioma-pheochromocytoma syndromes (PGL-PCC), and tuberous sclerosis (TSC) are proposed. CONCLUSIONS: Our proposed consensus for structured assessment and followup is intended as a roadmap for the care of patients with hRCC to guide healthcare providers. Although the list of syndromes included is not exhaustive, the document serves as a starting point for future updates.

Knowledge of genetic testing for hereditary kidney cancer in Canada is lacking: The results of the Canadian national hereditary kidney cancer needs assessment survey.

INTRODUCTON: Treatment of hereditary renal cell carcinoma (HRCC) requires a multidisciplinary approach that may involve medical oncologists, geneticists, genetic counsellors, and urologists. The objective of our survey was to obtain current and representative information about the use and perceived importance of genetic testing for HRCC in Canada. METHODS: A self-administered web-based survey was provided to Canadian medical oncologists, geneticists, genetic counsellors, and urologists in collaboration with their respective associations. The survey was created through an iterative process in consultation with the Kidney Cancer Research Network of Canada and contained both quantitative and qualitative components. The survey was designed to be exploratory and results were compared across regions. RESULTS: The overall response was low (6.6%). Of the respondents, 42%, 33%, 19%, 5% were genetic counsellors, urologists, medical oncologists and medical geneticists, respectively. Of the respondents, 62.7% described their practice as academic, and 37.3% described it as non-academic. Non-academic respondents tended to refer for genetic counselling less frequently than academic (48.6% vs. 67.2%). Most respondents believed that genetic testing for HRCC was available (82.8%), although 47.7% did not know which tests were available. This observation was consistent across provinces. Testing for Von Hippel-Lindau syndrome was given the highest priority among respondents. Limited provider knowledge, clinical guidelines, institutional funding, access, and poor coordination between disciplines were cited as barriers to testing. INTERPRETATION: There is a need to increase provider knowledge of genetic testing for HRCC. These findings support the development of practice guidelines and national strategies to improve coordination of specialists and access to genetics services. Limitations of the present study include low survey response which did not allow for inferential analysis by geographic region or respondent specialty.

Canadian guideline on genetic screening for hereditary renal cell cancers.

BACKGROUND: Hereditary renal cell cancer (RCC) is an ideal model for germline genetic testing. We propose a guideline of hereditary RCC specific criteria to suggest referral for genetic assessment. METHODS: A review of the literature and stakeholder resources for existing guidelines or consensus statements was performed. Referral criteria were developed by expert consensus. RESULTS: The criteria included characteristics for patients with RCC (age ≤45 years, bilateral or multifocal tumours, associated medical conditions and non-clear cell histologies with unusual features) and for patients with or without RCC, but a family history of specific clinical or genetic diagnoses. CONCLUSIONS: This guideline represents a practical RCC-specific reference to allow healthcare providers to identify patients who may have a hereditary RCC syndrome, without extensive knowledge of each syndrome. RCC survivors and their families can also use the document to guide their discussions with healthcare providers about their need for referral. The criteria refer to the most common hereditary renal tumour syndromes and do not represent a comprehensive or exclusive list. Prospective validation of the criteria is warranted.

Systolic myocardial mechanics in patients with Anderson-Fabry disease with and without left ventricular hypertrophy and in comparison to nonobstructive hypertrophic cardiomyopathy.

OBJECTIVES: Anderson-Fabry disease (AFD) is a lysosomal storage disease, which can involve the heart, mimicking hypertrophic cardiomyopathy (HCM). The underlying mechanism of disease in AFD is an infiltrative, diffuse process, whereas HCM is a primary heart muscle condition with patchy distribution, which may prompt differences in myocardial mechanics. The aim of this study was to assess myocardial mechanics in AFD according to the presence of left ventricular hypertrophy (LVH) compared to nonobstructive HCM (NHCM) and healthy controls. METHODS AND RESULTS: We carried out a single-center, retrospective study in a small, genetically confirmed AFD cohort, which was divided into a subgroup with LVH (LVH+, n = 19), and without LVH (LVH-, n = 21). Comparison groups were healthy controls (n = 40) and NHCM patients (n = 19). Vector Velocity Imaging was applied to two-dimensional echocardiography studies for assessment of longitudinal strain (LS), circumferential strain (CS), and base-to-apex CS gradients. AFD LVH+ patients had lower global LS than AFD LVH- patients (-14 ± 4% vs -17 ± 3%, P < 0.05), but similarly lowered global CS (-24 ± 5% vs -22 ± 5%, P = ns). AFD LVH+ and NHCM had similarly lowered global LS compared to normals, but significantly lower global CS was observed in AFD LVH+ (-24 ± 5% vs -28 ± 4%, P < 0.05), whereas it was significantly increased in NHCM (-31 ± 2% vs -28 ± 4%, P < 0.05). Unlike NHCM, in both AFD subgroups, patients lost their normal base-to-apex CS gradient. CONCLUSIONS: AFD patients without LVH already show abnormal systolic myocardial mechanics. Relevant differences in myocardial mechanics between AFD patients with LVH compared to NHCM reflect the different underlying mechanisms of disease.

Deletion 17q12 is a recurrent copy number variant that confers high risk of autism and schizophrenia.

Autism spectrum disorders (ASD) and schizophrenia are neurodevelopmental disorders for which recent evidence indicates an important etiologic role for rare copy number variants (CNVs) and suggests common genetic mechanisms. We performed cytogenomic array analysis in a discovery sample of patients with neurodevelopmental disorders referred for clinical testing. We detected a recurrent 1.4 Mb deletion at 17q12, which harbors HNF1B, the gene responsible for renal cysts and diabetes syndrome (RCAD), in 18/15,749 patients, including several with ASD, but 0/4,519 controls. We identified additional shared phenotypic features among nine patients available for clinical assessment, including macrocephaly, characteristic facial features, renal anomalies, and neurocognitive impairments. In a large follow-up sample, the same deletion was identified in 2/1,182 ASD/neurocognitive impairment and in 4/6,340 schizophrenia patients, but in 0/47,929 controls (corrected p = 7.37 × 10⁻5). These data demonstrate that deletion 17q12 is a recurrent, pathogenic CNV that confers a very high risk for ASD and schizophrenia and show that one or more of the 15 genes in the deleted interval is dosage sensitive and essential for normal brain development and function. In addition, the phenotypic features of patients with this CNV are consistent with a contiguous gene syndrome that extends beyond RCAD, which is caused by HNF1B mutations only.