Computational protocol: Genomic characterization of five deletions in the LDL receptor gene in Danish Familial Hypercholesterolemic subjects

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Protocol publication

[…] Sequence traces were aligned to the genomic sequence of the LDLR gene using SeqScape version 2.5 (Applied Biosystems). The genomic sequence used as reference was taken from the May 2004 assembly in the Human Genome Browser [] using the LDLR reference sequence NM_00527.For each deletion breakpoint, the neighbouring 150 nucleotides (on each side of the breakpoint) were used to identify interspersed repeats using RepeatMasker [], and they were aligned to the consensus ALU sequence described by Deininger and colleagues []. The exact location of the breakpoints was defined using the BLAT function [] in the Human Genome Browser, by searching the May 2004 assembly using the sequences obtained from the amplification products harbouring the deletion of interest. Comparison of the LDLR sequence to a 15 bp insertion was performed using BLAST 2 sequences []. […]

Pipeline specifications

Software tools SeqScape, RepeatMasker, BLAT
Applications Sanger sequencing, Genome data visualization
Organisms Homo sapiens
Diseases Genetic Diseases, Inborn