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Identification of a novel LDLR disease-causing variant using capture-based next-generation sequencing screening of familial hypercholesterolemia patients in Taiwan

  • Author Footnotes
    1 The authors contributed equally to this work.
    Yun-Chieh Hsiung
    Footnotes
    1 The authors contributed equally to this work.
    Affiliations
    Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
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  • Author Footnotes
    1 The authors contributed equally to this work.
    Po-Chih Lin
    Footnotes
    1 The authors contributed equally to this work.
    Affiliations
    Department of Internal Medicine and Cardiovascular Center, National Taiwan University Hospital, Taipei, Taiwan
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  • Chih-Shan Chen
    Affiliations
    Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
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  • Yi-Ching Tung
    Affiliations
    Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan

    Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
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  • Wei-Shiung Yang
    Affiliations
    Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan

    Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan

    Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan

    Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan

    Department of Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
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  • Pei-Lung Chen
    Correspondence
    Corresponding author. Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, 2 Xuzhou Rd, Zhongzheng Dist, Taipei, 10055, Taiwan.
    Affiliations
    Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan

    Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan

    Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan

    Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan

    Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
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  • Ta-Chen Su
    Correspondence
    Corresponding author. Department of Internal Medicine, National Taiwan University Hospital, 7 Chung-Shan South Road, Taipei, 10002, Taiwan.
    Affiliations
    Department of Internal Medicine and Cardiovascular Center, National Taiwan University Hospital, Taipei, Taiwan

    Institute of Occupational Medicine and Industrial Hygiene, National Taiwan University College of Public Health, Taipei, Taiwan
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  • Author Footnotes
    1 The authors contributed equally to this work.

      Highlights

      • This is the first capture-based NGS testing for FH to cover the whole LDLR genomic region.
      • It can detect from small-size variants to large structural variants accounting for ∼10% of disease-causing LDLR variants.
      • Our genetic diagnosis rate was 75%.
      • We identified LDLR c.1186+2T>G as a novel and common disease-causing variant in Taiwan.

      Abstract

      Background and aims

      Familial hypercholesterolemia (FH) is an autosomal dominant disorder with paramount health impacts. However, less than 1% FH patients in Taiwan were formally diagnosed, partly due to the lack of reliable cost-effective genetic testing. We aimed at using a next-generation sequencing (NGS) platform as the clinical genetic testing method for FH.

      Methods

      We designed probes to capture the whole LDLR gene and all coding sequences of APOB and PCSK9, and then sequenced with Illumina MiSeq platform (2 × 300 bps). The entire pipeline was tested on 13 DNA samples with known causative variants (including 3 large duplications and 2 large deletions). Then we enrolled a new cohort of 28 unrelated FH patients with Dutch Lipid Clinic Network score ≥5. Relatives were included in the cascade screening.

      Results

      From the 13 DNA samples, we correctly identify all the variants, including big duplications and deletions. From the new cohort, we identified the causative variants in 21 of the 28 unrelated probands; five of them carrying a novel splice site variant c.1186+2T>G in LDLR. Among the family members, the concentration of LDL cholesterol was 7.82 ± 2.13 mmol/l in LDLR c.1186+2T>G carrier group (n = 26), and was significantly higher than 3.18 ± 1.36 mmol/l in the non-carrier group (n = 25).

      Conclusions

      This is the first capture-based NGS testing for FH to cover the whole LDLR genomic region, and therefore making reliable structural variation detection. This panel can comprehensively detect disease-causing variants in LDLR, APOB, and PCSK9 for FH patients.

      Keywords

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