A DNA Microarray for the Detection of Point Mutations and Copy Number Variation Causing Familial Hypercholesterolemia in Europe

Abstract

To facilitate genetic cascade screening for familial hypercholesterolemia (FH) in Europe, two versions (7 and 9) of a DNA microarray were developed to detect the most frequent point mutations in the low-density lipoprotein receptor (LDLR), apolipoprotein B (APOB), and proprotein convertase subtilisin/kexin 9 (PCSK9) genes. The design of these microarrays is based on LIPOchip, version 4, which detects 191 LDLR and APOB mutations identified in Spanish patients with FH. A major improvement of LIPOchip, versions 7 and 9, is the ability to detect copy number variation (deletions or duplications of entire exons) in LDLR, thus abolishing the need to perform multiplex ligase-dependent probe amplification in patients with FH. The aim of this study was to validate a tool capable of detecting point mutations and copy number variations simultaneously and to evaluate its use and the newly developed software for analysis in clinical practice by reanalysis of several patients with known mutations causing FH. With the help of these validations, several aspects were analyzed, improved, and implemented in a newer version, which was evaluated through an internal validation.

Effect of LDL cholesterol, statins and presence of mutations on the prevalence of type 2 diabetes in heterozygous familial hypercholesterolemia

“…The platform consists of two consecutive steps: the first is LIPOchip® microarray analysis for the detection of the most frequent Spanish point mutations in the LDLR gene and in the APOB exon 26, as well as CNVs in LDLR. When the LIPOchip® microarray yielded a negative result (no mutation is found), the LDLR, APOB (binding domain) and PCSK9 gene coding sequences, exon-intron boundaries, and short proximal intronic sequences were sequenced with a GS Junior system (Roche Diagnostics Corporation, Basel, Switzerland) 12 .…”

Bile acid synthesis precursors in subjects with genetic hypercholesterolemia negative for LDLR/APOB/PCSK9/APOE mutations. Association with lipids and carotid atherosclerosis

“…The platform consists of two consecutive steps: the first one is the LIPOchip 1 microarray analysis for the detection of the most frequent Spanish point mutations in the LDLR gene and in the APOB exon 26, as well as CNVs in LDLR. When the LIPOchip 1 microarray gives a negative result (no mutation is found), the LDLR, APOB (binding domain) and PCSK9 gene coding sequences, exon-intron boundaries, and short proximal intronic sequences were sequenced with a GS Junior system (Roche Diagnostics Corporation, Basel, Switzerland) [32].…”

Recent advances in the understanding and care of familial hypercholesterolaemia: significance of the biology and therapeutic regulation of proprotein convertase subtilisin/kexin type 9

“…This is reasonable based on the wide mutation spectrum seen in FH in the U.S.A., the inability to identify pathogenic mutations in a significant proportion of people with phenotypically obvious FH, the currently high cost of DNA testing [12,16] and the complexity of care that a genetic screening programme generates [17]. However, advances in genetic testing and its inclusion in cascade screening will allow the detection of new mutations and become cheaper over time [19][20][21]. This can substantially change the architecture and efficiency of a cascade screening strategy.…”