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Thorax 67:A21 doi:10.1136/thoraxjnl-2012-202678.045
  • Spoken sessions
  • Pathophysiology of pulmonary vascular remodelling

S39 Whole Exome Sequencing in Chronic Thromboembolic Pulmonary Hypertension Reveals Biologically Plausible Novel Genetic Variation

  1. N Morrell
  1. Papworth Hospital, Cambridge, United Kingdom

Abstract

Chronic thromboembolic pulmonary hypertension (CTEPH) is a disease with no known heritability, the cumulative incidence of which has been placed at between 0.5 and 9.1% following acute pulmonary embolism [1,2]. A majority consensus on its development has emerged predicated on the theory of disordered thrombus resolution following venous thromboembolism. This in part stems from epidemiological data but is also based on studies implicating established clinical and laboratory factors, a central theorem being that individuals respond differently to acute thrombotic insult.

Given traditional prothrombotic factors explain less than 10% of reported cases of CTEPH, we hypothesised a significant burden of disease is accounted for by unidentified genetic factors. Using an unbiased approach of exome capture, we selected 20, deeply phenotyped, young individuals (11 female) who had suffered large PE that subsequently developed haemodynamically confirmed CTEPH despite anticoagulation. Individuals with known prothrombotic tendency and significant comorbidity were excluded. Selected patients were White Caucasian origin.

Following ethical approval, DNA was extracted from 20 whole blood samples and libraries prepared. Whole exome sequencing was undertaken using Agilent’s Sure Select Exome capture kit on the Hiseq 2000 platform prior to bioinformatic analysis. 75 bp paired-end reads were aligned to the H19 Reference genome and the pipeline annotated for SNPs and indels. Intergenic, intronic and UTR variants were removed from the dataset with minimum mapping quality score and 20x read-depth coverage stipulated for variant calls.

Consecutive filtres were applied, firstly retaining those predicted to be pathogenic flagged as splice-site, essential splice-site, missense, frameshift-coding, non-synonymous coding, NMD-transcript, within-mature-miRNA, STOP-gained and STOP-lost. Variants also present in twenty locally sourced normal controls were discarded. Additional filtres were subsequently applied to exclude variants already listed in dbSNP/1000 genomes data with remaining variants split into heterozygous and homozygous groups (Table 1). Our final candidate list contains novel DNA variants lying within pathways known to mediate both inflammation and endothelial dysfunction in the pulmonary vasculature. Detailed downstream biological analysis of our variant effects following validation measures may lead to the uncovering of novel mechanisms in this difficult disease.

Abstract S39 Table 1

References

  1. Surie S, Gibson NS, Gerdes VE, Bouma BJ, van Eck-Smit BL, Buller HR, Bresser P. Active search for chronic thromboembolic pulmonary hypertension does not appear indicated after acute pulmonary embolism. Thromb Res. 2010; 125: 202–5.

  2. Becattini C, Agnelli G, Pesavento R, Silingardi M, Poggio R, Taliani MR, Ageno W. Incidence of chronic thromboembolic pulmonary hypertension after a first episode of pulmonary embolism. Chest. 2006; 130:172–5.