Genomic characterization of large rearrangements of the LDLR gene in Czech patients with familial hypercholesterolemia

Abstract

Background: Mutations in the LDLR gene are the most frequent cause of Familial hypercholesterolemia, an autosomal dominant disease characterised by elevated concentrations of LDL in blood plasma. In many populations, large genomic rearrangements account for approximately 10% of mutations in the LDLR gene.

Methods: DNA diagnostics of large genomic rearrangements was based on Multiple Ligation dependent Probe Amplification (MLPA). Subsequent analyses of deletion and duplication breakpoints were performed using long-range PCR, PCR, and DNA sequencing.

Results: In set of 1441 unrelated FH patients, large genomic rearrangements were found in 37 probands. Eight different types of rearrangements were detected, from them 6 types were novel, not described so far. In all rearrangements, we characterized their exact extent and breakpoint sequences.

Conclusions: Sequence analysis of deletion and duplication breakpoints indicates that intrachromatid non-allelic homologous recombination (NAHR) between Alu elements is involved in 6 events, while a non-homologous end joining (NHEJ) is implicated in 2 rearrangements. Our study thus describes for the first time NHEJ as a mechanism involved in genomic rearrangements in the LDLR gene.

Figure 1

Schematic illustration of rearrangements in the LDLR gene including DNA sequence of breakpoints. A: promoter_exon2del, B: exon2_6dup, C: exon3_12del and D: exon4_8dup. Consensus Alu sequences are depicted as red and blue boxes, their monomer subunits are given in dark and light tones. Sense orientation is marked by a darker tone of the first monomer of the Alu consensus sequence, the opposite order marks antisense orientation. MER83 repeat is depicted as a green box. Grey boxes represent sequence overlaps between 5'end and 3' end of the reference sequence.

Figure 2

Schematic illustration of rearrangements in the LDLR gene including DNA sequence of breakpoints. A: exon5_10del, B: exon9_14del, C: exon9_15del and D: exon16_18dup. Consensus Alu sequences are depicted as red and blue boxes, their monomer subunits are given in dark and light tones. Sense orientation is marked by a darker tone of the first monomer of the Alu consensus sequence, the opposite order marks antisense orientation. Grey boxes represent sequence overlaps between 5' end and 3' end of the reference sequence.