Identification of a novel LDLR disease-causing variant using capture-based next-generation sequencing screening of...

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.

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.

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).

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.