LDLR gene rearrangements in Czech FH patients likely arise from one mutational event

Table 6 Characteristics of repeats present at the breakpoint

Rearrangement	Classification and orientation of repeat 1 ^a	Classification and orientation of repeat 2 ^a	Repeats in the same orientation	Chimeric Alu formation ^b	Homology between the two repeats (%) ^c	Length of alignment ^d	Length of microhomology region (bps)
promoter_exon2del	< AluY	< AluY	yes	yes	89	306	42
exon2_6dup	< AluSx	< AluSx	yes	yes	77	305	23
exon3_12del	> AluY	> AluY	yes	yes	91	304	49
exon4_8dup	< AluSx	non-Alu (MER83)	no homology	no	35	99	2
exon5_10del	< AluJb	> AluSx	no	no	35	395	4
exon9_14del	< AluJb	< AluY	yes	yes	87	280	5
exon9_15del	< AluJb	< AluSx	yes	yes	70	142	32
exon16_18dup	> AluY	> AluSx	yes	yes	84	291	0

^a" > " denotes that the Alu element aligns to the consensus Alu sequence in a 5′➔3' orientation. " < " denotes reverse complementary orientation. Classification of repeats is based on an analysis with RepeatMasker, version open-4.0.9, cross_match mode
^bChimeric Alu formation – A chimeric Alu was formed if the break occurred at the same location in both repeats flanking the breakpoint (+-a few bps)
^cGlobal homology between the two repeats flanking the breakpoint was determined using the EMBOSS Needle tool [28]. (If the polyA tail was longer in one repeat than the other, the extra As were excluded for the sake of calculating the percent homology.)
^dLength of the alignment that was used to compute percent homology between two repeats

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