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Getting Personal: Omics of the Heart

Mar 22, 2019

Jane Ferguson:                Hello, and welcome to episode 26 of Getting Personal: Omics of the Heart, the podcast from Circulation: Genomic and Precision Medicine. I'm Jane Ferguson. It's March 2019, and I'm ready to spring into this month's papers, and apparently make really bad seasonal related jokes. Sorry all. Okay, let's get started.

                                           First up, is a paper from Oren Akerborg, Rapolas Spalinskas, Sailendra Pradhananga, Pelin Sahlén and colleagues from the Royal Institute of Technology in Solna, Sweden entitled "High Resolution Regulatory Maps Connect Vascular Risk Variants to Disease Related Pathways." Their goal was to identify non-coding variants associated with coronary artery disease, particularly those with putative enhancers and to map these to changes in gene function. They generated genomic interaction maps using Hi-C chromosome confirmation capture, coupled with sequence capture in several cell types, including aortic and ethelial cells, smooth muscle cells and LPS stimulated THP-1 macrophages.

                                           They captured over 25,000 features and they additionally sequenced the cellular transcriptomes and looked at epigenetic signatures using chromatin immunoprecipitation. They looked at regions interacting with gene promoters and found significant enrichment for enhancer elements. Looking at variants previously implicated in genome-wide associated studies, they identified 727 variants with promoter interactions and they were able to assign potential target genes for 398 GWAS variants.

                                           In many cases, the gene associated with a particular variant was not the closest neighbor, highlighting the importance of considering chromatin lupane when assigning intergenic variants to a gene. They identified several variants that interacted with multiple promoters, influencing expression of several genes simultaneously.

                                           Overall, this paper is a great resource for the community and takes many of these GWAS hits to the next level in starting to understand their biological relevance. They have a lot of supplemental material available online so it's definitely worth checking that out and taking a look for your favorite non-coding variant or chromosomal region to see if you can get some more information on it.

                                           Next up, Pierrick Henneton, Michael Frank and colleagues from the Hopital Europeen Georges-Pompidou in Paris bring us "Accuracy of Clinical Diagnostic Criteria For Patients with Vascular Ehlers-Danlos Syndrome in a Tertiary Referral Center." The authors were interested in determining the accuracy of the diagnostic criteria used to select patients for genetic testing for suspected vascular Ehlers-Danlos syndrome. This is because, despite the Villefrench criteria being recommended for diagnosis, the accuracy of the diagnostic criteria was never formally tested.

                                           They selected 519 subjects, including 384 probands and 135 relatives who had been seen between 2001 and 2016. They assessed the sensitivity and specificity of the Villefrench classification. Almost 32% of tested individuals carried a pathogenic COL3A1 variant. The sensitivity of the Villefrench criteria was 79% with a negative predictor value of 87%. Symptomatic probands had the highest accuracy at 92% sensitivity and 95% negative predictive value. However, the specificity was just 60%.

                                           Applying revised diagnostic criteria from 2017, it was actually less accurate because even though there was an increase in specificity, the sensitivity was reduced. Overall diagnostic performance was worst in individuals under 25 and neither set of diagnostic classifications allowed for early clinical diagnosis in individuals without a family history.

                                           Our next paper is a Mendelian randomization analysis from Susanna Larsson, Stephen Burgess and colleagues from Uppsala University and the University of Cambridge. This paper entitled "Thyroid Function And Dysfunction In Relation to Sixteen Cardiovascular Diseases: A Mendelian Randomization Study" aims to understand how subclinical thyroid dysfunction relates to risk of cardiovascular diseases. They generated genetic predictors for thyroid stimulating hormone, or TSH, through a GWAS meta-analysis in over 72,000 individuals. They then analyzed the association of genetically predicted TSH with cardiovascular outcomes in large GWAS studies of atrial fibrillation, coronary artery disease, and ischemic stroke, and further assessed associations with phenotypes in the UK Biobank.

                                           They found genetically decreased TSH levels and hyperthyroidism were associated with increased risk of atrial fibrillation but not other tested phenotypes. Overall, these data support a causal role for TSH and thyroid dysfunction in atrial fibrillation but not in other cardiovascular diseases.

                                           The next paper is also a Mendelian randomization analysis from members of the same group, Susanna Larsson, Stephen Burgess and colleagues published "Resting Heart Rate and Cardiovascular Diseases: A Mendelian Randomization Analysis." In this letter, they describe a study of the relationship between genetically increased resting heart rate and cardiovascular diseases. They constructed genetic predictors of resting heart rate and similarly to the previous study, used that as an instrument to test for associations with coronary artery disease, atrial fibrillation, and ischemic stroke in the cardiogram, atrial fibrillation, and mega stroke consortia respectively.

                                           They also looked at 13 CVD outcomes in the UK Biobank. They found that genetically predicted heart rate was inversely associated with atrial fibrillation with suggestive evidence for an inverse association with ischemic, cardioembolic, and large artery stroke. The inverse association with AF was replicated in the UK Biobank, supporting previous reports linking resting heart rate to atrial fibrillation.

                                           Next up, we have a letter from Robyn Hylind, Dominic Abrams, and colleagues from Boston Children's Hospital. This study entitled "Phenotypic Characterization of Individuals with Variants in Cardiovascular Genes in the Absence of a Primary Cardiovascular Indication For Testing" describes their work to probe incidental findings for potential cardiovascular disease variants in individuals undergoing clinical genomic sequencing for non-cardiac indications.

                                           They included 33 individuals who had been referred as carrying variants that were indicated as being associated with cardiovascular disease in primary or secondary findings. The variants were reclassified using the 2015 ACMG guidelines, and then were compared to the original classification report obtained at the time of sequencing.

                                           Of 10 pathogenic or likely pathogenic variants, only four of these were actually considered pathogenic or likely pathogenic after reclassification under the 2015 ACMG criteria, and none of these were associated with a cardiac phenotype. None of the variants could be definitively linked to any cardiac phenotype.

                                           The costs ranged from $75 to over $3700 per subject with a cost per clinical cardiac finding estimated at almost $14,000. This study highlights the relatively high cost and low yield of investigating potential cardiovascular variants and prompts consideration of how to implement strategies to ensure that variant reporting maximizes clinical return but minimizes the financial, time, and psychological burdens inherent in lengthy follow-ups.

                                           The next paper is a clinical letter from Serwet Demirdas, Gerben Schaaf and colleagues from Erasmus University Rotterdam  entitled "Delayed Diagnosis of Danon Disease in Patients Presenting with Isolated Cardiomyopathy." They report on a clinical case of a 14-year-old boy presenting with cardiac arrest due to ventricular fibrillation during exercise. Echocardiography and MRI showed cardiac concentric hypertrophy, particularly in the left ventricle. The boy's mother had died at age 31 after being diagnosed with peripartum dilated cardiomyopathy.

                                           Sequencing in the boy revealed a variant in the LAMP2 gene, known to be responsible for Danon disease, which typically presents as cardiomyopathy, skeletal myopathy, and intellectual disability. This same LAMP2 variant was found in preserved maternal tissue, but not in other family members. In this case, there was no evidence of muscle or intellectual abnormalities. However, sequencing had allowed for this diagnosis of Danon disease in the child and posthumously in his mother. This study demonstrates a utility of using extended gene panels in clinical sequencing to aid in diagnosis and to inform management of patients.

                                           The next letter is from Alvaro Roldan, Julian Palomino-Doza, Fernando Arribas and colleagues from University Hospital of the 12th of October in Madrid and is entitled "Missense Mutations in the FLNC Causing Familial Restrictive Cardiomyopathy: Growing Evidence." This report also highlights clinical cases. In this case, two individuals with variants in the filamin C, or FLNC gene. Two unrelated individuals presenting with restricting cardiomyopathy were sequenced and found to carry two different variants in the FLNC gene, one of which had not been previously reported.

                                           This expands the number of reported cases of filamin C mutations in restrictive cardiomyopathy and highlights the need for further study of the pathophysiology linking filamin C to cardiac function.

                                           Finally, we have some correspondence related to a previously published article. In the letter, Christopher Chung, Briana Davies, and Andrew Krahn comment on the recently published article from Jody Ingles on concealed arrhythmogenic right ventricular cardiomyopathy in sudden unexplained cardiac death events. In that paper earlier this year, they had reported on four cases of individuals presenting with cardiac arrest or sudden cardiac death, attributable to concealed arrhythmogenic right ventricular cardiomyopathy with underlying mutations in the plakophilin-2 gene. In the letter from Chung et al, they report similar findings where individuals may first experience electrical phenotypes before manifesting structurally detectable disease. Indeed, in their response to this letter, Ingles et al report identification of an additional case since publication of their original article.

                                           Taken together, this further strengthens the case for development of additional strategies to identify at risk individuals and predict and prevent disease events.

                                           That's all for the papers for March 2019. Go online to check them out and follow us on Twitter @Circ_Gen to see new papers as they are published online. Thanks for listening. Until next month everyone. This podcast was brought to you by Circulation Genomic and Precision Medicine and the American Heart Association Council on Genomic and Precision Medicine. This program is copyright American Heart Association 2019.