Fig. 6

Chromosomal rearrangement in patient 3 with 46,XX,t(7;15)(q21;q15),t(9;14)(q21;q11.2). a Ideograms showing translocation positions of patient 3. b Filtering out rearrangements shared with 33 controls produces 43 groups of reads with patient-only rearrangements. While there are 2 groups indicating chr9-chr14 reciprocal translocation, there are 8 groups involved in the chr7-chr15 translocation. cdnarrange-link with 5 additional groups involving chr14q11.2, 15 groups in total, which were linked to construct 5 derivative chromosomes. d Dotplot of reconstructed derivative chr9 and chr14 shows reciprocal balanced chromosomal translocation. Upper panel: horizontal dotted gray lines join the parts of each derivative chromosome. Asterisks indicate fragments. Lower panel: vertical dotted gray lines join fragments that come from adjacent parts of the reference genome, showing there is a 6-kb deletion on chr4. e Dotplot of joined fragments showing reciprocal chr7-chr15 translocation with complex rearrangements. Black arrow indicates inverted 129-kb region that caused misinterpretation of deletion size. Upper panel: horizontal gray lines join the parts of each derivative chromosome. Asterisks indicate fragments. An inset magnifies 4 tiny fragments. Lower panel: vertical gray lines join fragments that come from adjacent parts of the reference genome, showing loss of 677 kb and 4.7 Mb of chr7 and chr15, respectively. f Pie chart of patient-only rearrangements. g Processed pseudogene insertion in chr15 from exons of MFF on chr2, with nearby AluYa5 insertion