Array-based resequencing for mutations causing familial hypercholesterolemia

• Published in: Atherosclerosis Vol. 216; no. 2; pp. 383 - 389
• Main Authors: Chiou, Kuan-Rau, Charng, Min-Ji, Chang, Hua-Mei
• Format: Journal Article
• Language: English
• Published: Amsterdam Elsevier Ireland Ltd 01.06.2011; Elsevier
• Subjects: Adult; apolipoprotein B; Apolipoproteins B; Apolipoproteins B - genetics; Array; atherosclerosis; Atherosclerosis (general aspects, experimental research); Automation; Biological and medical sciences; Blood and lymphatic vessels; Cardiology. Vascular system; Cardiovascular; computer software; disease prevalence; DNA; DNA Mutational Analysis; DNA Mutational Analysis - methods; Familial defective apolipoprotein B; Familial hypercholesterolemia; Female; Gene Deletion; genes; genetic heterogeneity; genetics; Humans; hypercholesterolemia; Hyperlipoproteinemia Type II; Hyperlipoproteinemia Type II - genetics; low density lipoprotein; Male; Medical sciences; methods; microarray technology; Middle Aged; Mutation; Oligonucleotide Array Sequence Analysis; patients; point mutation; Prevalence; Proprotein Convertase 9; Proprotein Convertases; Receptors, LDL; Receptors, LDL - genetics; Resequence; screening; Serine Endopeptidases; Serine Endopeptidases - genetics; subtilisin; Familial defective apolipoprotein B; Array; FH; Resequence; MLPA; PCSK9; Familial hypercholesterolemia; APOB; LDLR; PCR; proprotein convertase subtilisin/kexin type 9; low-density lipoprotein receptor; multiple ligation-dependent probe amplification; familial hypercholesterolemia; apolipoprotein B; polymerase chain reaction; Metabolic diseases; Lipids; Cardiovascular disease; Hyperlipoproteinemia; Lipoprotein; Cholesterol; Genetic disease; Vascular disease; Apolipoprotein B; Hypercholesterolemia; Atherosclerosis; Mutation; Dyslipemia
• ISSN: 0021-9150; 1879-1484; 1879-1484
• DOI: 10.1016/j.atherosclerosis.2011.02.006

Familial hypercholesterolemia (FH) is a heterogeneous autosomal dominant disease with a prevalence of 1 in 500. To date, over 1200 unique pathogenic mutations have been identified in at least 3 genes. The large allelic and genetic heterogeneity of FH requires high-throughput, rapid, and affordable mutation detection technology to efficiently integrate molecular screening into clinical practice. We developed an array-based resequencing assay to facilitate genetic testing in FH patients. We designed a custom DNA resequencing array to detect mutations on all 3 FH-causing genes – LDL receptor (LDLR), apolipoprotein B (APOB), and proprotein convertase subtilisin/kexin type 9 gene (PCSK9) – and 290 known insertion/deletion mutations on LDLR. We verified FH array performance by analyzing 35 previously sequenced subjects (21 with point mutations, 2 insertions, 7 deletions, and 5 healthy controls) and blindly screening 125 FH patients. The average microarray call rate was 98.45% and the agreement between microarray and capillary sequencing was 99.99%. The FH array detected mutations by using automated software analysis, followed by manual review in 28 of the 30 subjects (pickup rate, 93.3%). In the blinded study, the FH array detected at least 1 mutation in 77.5% of patients clinically diagnosed with definite FH according to Simon Broome FH criteria and in 52.9% with probable FH diagnosis. The high-throughput FH resequencing array detects LDLR, APOB, and PCSK9 with high efficiency and accuracy and identifies disease-causing mutations. Thus, it facilitates large-scale screening of the heterogeneous FH populations.