We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the United States Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for junction discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed, for these and qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings.

Abstractβ-adrenergic receptor (βAR) blockade is standard therapy for cardiac failure and ischemia. G-protein coupled receptor kinases (GRKs) desensitize βAR, suggesting that genetic GRK variants might modify outcomes in these syndromes. Re-sequencing of GRK2 and GRK5 revealed a nonsynonymous polymorphism of GRK5, common in African Americans (AA), substituting leucine (L) for glutamine (Q) at position 41. GRK5-L41 more effectively uncoupled isoproterenol-stimulated responses than GRK5-Q41 in transfected cells and transgenic mice, and like pharmacological βAR blockade, GRK5-L41 protected against experimental catecholamine-induced cardiomyopathy. Human association studies showed a pharmacogenomic interaction between GRK5-L41 and β-blocker treatment on mortality outcome in independent cohorts of AA cardiac failure (P=0.036) and ischemia (P=0.023). In 375 prospectively followed AA heart failure subjects, GRK5-L41 was protective against death/cardiac transplant (single allele: RR=0.28, 95% CI=0.12-0.66; two alleles: RR=0.08, 95% CI=0.04-0.19; P=0.004). The gain-of-function GRK5-L41 polymorphism facilitates βAR desensitization during catecholamine excess, imparting "genetic β-blockade" and improving survival in heart failure.

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Objective To identify genetic modifiers of β-blocker (BB) response and long-term survival in heart failure (HF). Background Differences in BB treatment effect between Caucasians and African Americans with HF have been reported. Methods Prospective cohort study of 2,460 patients (711 African American; 1,749 Caucasian) enrolled between 1999 and 2007. 2039 (81.7%) were treated with BB. Each was genotyped for β1-adrenergic receptor (ADRB1) Arg389>Gly and G-protein receptor kinase 5 (GRK5) Gln41>Leu polymorphisms, which are more prevalent among African Americans than Caucasians. Primary endpoint was survival time from HF onset. Results There were 765 deaths during follow up (median 46 months). BB treatment increased survival in Caucasians (Log Rank P=0.00038) but not African Americans (Log Rank P=0.327). Among patients not taking BB, ADRB1 Gly389 was associated with decreased survival in Caucasians (HR = 1.98, 95% CI = 1.1 − 3.7, P = 0.03) while GRK5 Leu41 was associated with improved survival in African Americans (HR = 0.325, CI = 0.133 − 0.796, P = 0.01). ADRB1 Gly389 GRK5 Gln41Gln African Americans derived similar survival benefit from BB therapy (HR = 0.385 95% CI = 0.182 − 0.813, P = 0.012) as ADRB1 Gly389 GRK5 Gln41Gln Caucasians (HR = 0.529, 95% CI = 0.326 − 0.858, P=0.0098). Conclusions These data demonstrate that differences caused by β-adrenergic receptor signaling pathway gene polymorphisms, rather than race, are the major factors contributing to apparent differences in BB treatment effect between Caucasians and African Americans; proper evaluation of treatment response should account for genetic variance.