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J Med Genet 49:644-649 doi:10.1136/jmedgenet-2012-101189
  • Methods

Use of targeted exome sequencing as a diagnostic tool for Familial Hypercholesterolaemia

Open Access
  1. UK10K4
  1. 1Centre for Cardiovascular Genetics, British Heart Foundation Laboratories, Institute of Cardiovascular Science, The Rayne Buliding University College London, London, UK
  2. 2Department of Genetics, Environment and Evolution, UCL Genetics Institute, University College London, London, UK
  3. 3Department of Primary Care Health Sciences, NIHR School of Primary Care Research, University of Oxford, Oxford, UK
  4. 4http://www.uk10k.org
  1. Correspondence to Professor Steve Eric Humphries, Centre for Cardiovascular Genetics, British Heart Foundation Laboratories, Institute Cardiovascular Science, University College London Medicine School, The Rayne Building, 5 University Street, London WC1E 6JF, UK; rmhaseh{at}ucl.ac.uk
  • Received 25 July 2012
  • Revised 2 September 2012
  • Accepted 4 September 2012

Abstract

Background Familial Hypercholesterolaemia (FH) is an autosomal dominant disease, caused by mutations in LDLR, APOB or PCSK9, which results in high levels of LDL-cholesterol (LDL-C) leading to early coronary heart disease. An autosomal recessive form of FH is also known, due to homozygous mutations in LDLRAP1. This study assessed the utility of an exome capture method and deep sequencing in FH diagnosis.

Methods Exomes of 48 definite FH patients, with no mutation detected by current methods, were captured by Agilent Human All Exon 50Mb assay and sequenced on the Illumina HiSeq 2000 platform. Variants were called by GATK and SAMtools.

Results The mean coverage of FH genes varied considerably (PCSK9=23x, LDLRAP1=36x, LDLR=56x and APOB=93x). Exome sequencing detected 17 LDLR mutations, including three copy number variants, two APOB mutations, missed by the standard techniques, two LDLR novel variants likely to be FH-causing, and five APOB variants of uncertain effect. Two variants called in PCSK9 were not confirmed by Sanger sequencing. One heterozygous mutation was found in LDLRAP1.

Conclusions High-throughput DNA sequencing demonstrated its efficiency in well-covered DNA regions, in particular LDLR. This highly automated technology is proving to be effective for heterogeneous diseases and may soon replace laborious conventional methods. However, the poor coverage of gene promoters and repetitive, or GC-rich sequences, remains problematic, and validation of all identified variants is currently required.

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