Combining familial hypercholesterolemia and statin genetic studies as a strategy for the implementation of pharmacogenomics. A multidisciplinary approach.

The diagnostic process of familial hypercholesterolemia frequently involves the use of genetic studies. Patients are treated with lipid-lowering drugs, frequently statins. Although pharmacogenomic clinical practice guidelines focusing on genotype-based statin prescription have been published, their use in routine clinical practice remains very modest.We have implemented a new NGS strategy that combines a panel of genes related to familial hypercholesterolemia with genomic regions related to the pharmacogenomics of lipid-lowering drugs described in clinical practice guidelines and in EMA and FDA drug labels. A multidisciplinary team of doctors, biologists, and pharmacists creates a clinical report that provides diagnostic and therapeutic findings using a knowledge management and clinical decision support system, as well as an algorithm for treatment selection.For 12 months, a total of 483 genetic diagnostic studies for familial hypercholesterolemia were carried out, of which 221 (45.8%) requested a complementary pharmacogenomic test. Of these 221 patients, 66.5% were carriers of actionable variants in any of the studied pharmacogenomic pathways: 46.6% of patients in one pathway, 19.0% in two pathways, and 0.9% in three pathways. 45.7% of patients could have a response to atorvastatin different from that of the reference population, 45.7% for simvastatin and lovastatin, 29.0% for fluvastatin, and 6.7% patients for pitavastatin.This implementation approach facilitates the incorporation of pharmacogenomic studies in clinical care practice, it does not add complexity nor additional steps to laboratory processes, and improves the pharmacotherapeutic process of patients.

Genotype-phenotype correlations in hypertrophic cardiomyopathy: a multicenter study in Portugal and Spain of the TPM1 p.Arg21Leu variant.

INTRODUCTION AND OBJECTIVES: TPM1 is one of the main hypertrophic cardiomyopathy (HCM) genes. Clinical information on carriers is relatively scarce, limiting the interpretation of genetic findings in individual patients. Our aim was to establish genotype-phenotype correlations of the TPM1 p.Arg21Leu variant in a serie of pedigrees. METHODS: TPM1 was evaluated by next-generation sequencing in 10 561 unrelated probands with inherited heart diseases. Familial genetic screening was performed by the Sanger method. We analyzed TPM1 p.Arg21Leu pedigrees for cosegregation, clinical characteristics, and outcomes. We also estimated the geographical distribution of the carrier families in Portugal and Spain. RESULTS: The TPM1 p.Arg21Leu variant was identified in 25/4099 (0.61%) HCM-cases, and was absent in 6462 control individuals with other inherited cardiac phenotypes (P<.0001). In total, 83 carriers (31 probands) were identified. The combined LOD score for familial cosegregation was 3.95. The cumulative probability of diagnosis in carriers was 50% at the age of 50 years for males, and was 25% in female carriers. At the age of 70 years, 17% of males and 46% of female carriers were unaffected. Mean maximal left ventricular wall thickness was 21.4 ±7.65mm. Calculated HCM sudden death risk was low in 34 carriers (77.5%), intermediated in 8 (18%), and high in only 2 (4.5%). Survival free of cardiovascular death or heart transplant was 87.5% at 50 years. Six percent of carriers were homozygous and 18% had an additional variant. Family origin was concentrated in Galicia, Extremadura, and northern Portugal, suggesting a founder effect. CONCLUSIONS: TPM1 p.Arg21Leu is a pathogenic HCM variant associated with late-onset/incomplete penetrance and a generally favorable prognosis.

Development and validation of a next-generation sequencing panel for clinical pharmacogenetics.

The rapid clinical implementation of next generation sequencing techniques is  due to its ability to sequence a large number of genetic regions at lower costs  than conventional techniques. However, its use in the field of pharmacogenetics  is still very limited. OBJECTIVE: Design, development, implementation and validation of a clinical  pharmacogenetics next-generation sequencing panel. METHOD: We developed a panel of hybrid capture probes (SureSelect®) for the  analysis of the genetic regions of clinical interest collected by literature search  and using Illumina HiSeq 1500® sequencing platform. We developed a  bioinformatic algorithm for variant annotation, haplotype inference and  determination of structural variants in the genes of interest. The results obtained were validated with Coriell® reference material from the pharmacogenetic  repositories. RESULTS: The developed panel allows the study of a total of 12,794 regions comprised in 389 genes. Validation results showed a sensitivity greater  than 99% for single nucleotide variants and small INDELs. Haplotype imputation was consistent with the consensus results in the characterized  reference materials. Furthermore, the developed tool was able to correctly  identify different types of CYP2D6 copy number variations as well as a wide  variety of HLA-B alleles. CONCLUSIONS: This technology represents an appropriate alternative for its  clinical use with advantages over conventional techniques in its throughput and  complex gene study capabilities (CYP2D6, HLA-B).

La rápida implantación clínica de las técnicas de secuenciación masiva en  paralelo se debe a su capacidad para secuenciar un gran número de regiones  genéticas con un coste menor a las técnicas convencionales. Sin embargo, su  uso en el ámbito de la farmacogenética es, todavía, muy escaso.Objetivo: Diseño, desarrollo, implementación y validación de un panel de  secuenciación masiva en paralelo de farmacogenética orientado a la práctica  clínica.Método: Se desarrolló un panel de sondas de captura híbrida (SureSelect ®)  para el análisis de las regiones genéticas de interés clínico recopiladas mediante  búsqueda bibliográfica. Se empleó la plataforma de secuenciación Illumina HiSeq 1500®. Se desarrolló un algoritmo de análisis bioinformático para la anotación  de variantes puntuales, inferencia de haplotipos y determinación de variantes  estructurales en los genes de interés. Los resultados obtenidos se validaron con  materiales de referencia Coriell® de los repositorios de farmacogenética.Resultados: El panel desarrollado permite el estudio de un total de 12.794  regiones comprendidas en 389 genes. Los resultados de validación mostraron  una sensibilidad superior al 99% para variantes puntuales e inserciones y  deleciones pequeñas. La imputación de haplotipos fue coherente con los  resultados consenso de los materiales de referencia caracterizados. Además, la  herramienta desarrollada pudo identificar correctamente diferentes tipos de  variaciones de número de copias de CYP2D6, así como una gran variedad de  alelos de HLA-B.Conclusiones: Esta tecnología representa una alternativa adecuada para su  empleo asistencial con ventajas frente a las técnicas convencionales en su  rendimiento de producción y sus capacidades de estudio de genes complejos  (CYP2D6, HLA-B).

The R820W mutation in the MYBPC3 gene, associated with hypertrophic cardiomyopathy in cats, causes hypertrophic cardiomyopathy and left ventricular non-compaction in humans.

BACKGROUND: The R820W mutation in the MYBPC3 gene has been associated with the development of hypertrophic cardiomyopathy (HCM) in rag-doll cats, but had not been described in humans. AIMS: To describe the phenotype associated with the R820W mutation identified in a human family. METHODS: The R820W was identified by direct sequencing of the MYBPC3 gene in a 47 year old woman with HCM and left ventricular non-compaction (LVNC). Clinical and genetic studies of the R820W mutation were performed in her family. RESULTS: The index patient was homozygous for the mutation and had no additional mutations in the main sarcomeric genes (MYH7, TNNT2, TNNI3, and TPM1). She had HCM with LVNC and normal systolic function. One brother had died suddenly at age 43 years. Another brother diagnosed of LVNC with severe systolic dysfunction and a cardiac arrest was also homozygous for the mutation. One heterozygous 31 year old sister, and three heterozygous sons of the index (ages 14, 20 and 23 years old) were clinically unaffected. The father of the index was apparently healthy and her mother had atrial fibrillation and an electrocardiographic diagnosis of left ventricular hypertrophy at age 86 years. CONCLUSION: The R820W mutation in the MYBPC3 gene, previously associated with HCM in rag-doll cats, causes both HCM and LVNC in homozygous human carriers, with mild or null clinical expression in heterozygous carriers.

[Exercise echocardiography to differentiate dilated cardiomyopathy from ischemic left ventricular dysfunction]. / Ecocardiografía de ejercicio para diferenciar la miocardiopatía dilatada de la disfunción ventricualr por cardiopatía isquémica.

OBJECTIVES: Previous studies have shown the usefulness of dobutamine echocardiography to differentiate dilated cardiomyopathy (DC) from ischemic left ventricular dysfunction (ILVD), but no studies have been made using exercise echocardiography (EE). We hypothesized that most patients with DC have some contractile reserve and experience an increase in left ventricular ejection fraction (LVEF) during exercise, as opposed to patients with ILVD. Differences in response to EE may be useful to clinically differentiate between these two entities. PATIENTS AND METHOD: Between 1 March 1995 and 1 March 2001, we performed 4,133 EE studies on 3,830 patients. Of 289 patients (8%) with moderate or severe LV dysfunction (biplane LVEF < 41% and left ventricular end-diastolic diameter > 5.2 cm), 207 were excluded: 111 for a history of myocardial infarction; 28 for scarring on echocardiography (regional akinesia/dyskinesia with thinning and/or increased brightness); 13 for previous revascularization procedures; 9 for aortic valve disease; 11 for a known cause of cardiomyopathy; and 35 for not undergoing angiography. The study group was therefore composed of 82 patients who were encouraged to perform maximal treadmill EE. EE criteria for ILVD were either impaired regional wall motion (RWM) or a decrease/no change in LVEF from baseline to peak exercise, while criteria for DC were RWM improvement/no change and LVEF increase. The ILVD group was formed by 39 patients with stenosis >/= 70% diameter stenosis of a major epicardial coronary artery or major branch vessel. The remaining 43 patients constituted the DC group. RESULTS: The number of coronary risk factors (ILVD 2.0 1.1; DC 1.9 1.1), baseline LVEF (ILVD 30 7; DC 30 8), and exercise-induced angina (ILVD 23%; DC 14%) did not differ between groups (p = NS). ILVD patients achieved less Mets (6.6 3.1 vs 8.3 2.8; p < 0.05), had a lower heart rate x systolic blood pressure product (22 5 vs 27 7; p < 0.001), and developed regional and/or global LV dysfunction more frequently (79 vs 28%; p < 0.001). Sensitivity, specificity, positive and negative predictive values and global accuracy for ILVD detection were 79% (95% CI: 70-88), 72% (95% CI: 63-81), 72% (95% CI: 63-81), 79% (95% CI: 67-85), and 76% (95% CI: 69-83), respectively. CONCLUSION: Global and/or regional LV function impairment with exercise is accurate in identifying patients with ILVD. This method could reduce the need for invasive procedures.