Fig. 1

a Chromosome Analysis Suite (ChAS) graphic results of Affymetrix CytoScan HD analysis for the 1q region that presented duplication (DUP), triplication (TRP), or isoUPD in the patient. Detection of CGR and isoUPD were performed using an Affymetrix CytoScan HD CMA platform (Affymetrix), which provides 906,600 polymorphic (SNP) and 946,000 non-polymorphic (CNV) markers, according to the manufacturer’s recommendations. In addition, we used Chromosome Analysis Suite software (ChAS, Affymetrix) to process the raw data, and the output data were interpreted with the UCSC Genome Browser (http://genome.ucsc.edu; GRCh37/hg19 assembly). Top, copy number log2 ratio; bottom, allele peaks. CN, copy number. Possible genotype calls based on the allele dosage normalization algorithm are shown using A and B. The location of each BAC used for FISH analysis is shown. b Images of two-color FISH mapping using six BAC clones and the scheme of distal 1q CGR based on FISH data. Metaphase FISH images with high-magnification images of the distal 1q. BAC clones labeled with either FITC (green) or rhodamine (red) were hybridized to 4’,6-diamidino-2-phenylindole (DAPI)-stained chromosomes of the patient. The location and detailed information of each BAC are shown in Fig. 1a and Additional file 1: Table S1, respectively. In the scheme, arrows indicate the direction of chromosomal fragments I, II (II’, II”), and III, which presented duplication, triplication, and isoUPD, respectively, in CMA. Two junctions (jct 1 and jct2) between fragments II and II’ and between I and II” are also shown. c Color-matched sequence alignment of breakpoint junctions in rearrangements. Top, jct1 (breakpoint junction 1 between segments II and II’); bottom, jct2 (breakpoint junction 2 between segments I and II”) (see Fig. 1b). Microhomology at the junctions is represented by underlined letters. Frequent mismatch sequences were only observed near jct2 within long-range PCR products (data not shown). Thick arrows indicate the possible orientation of chromosomal fragments. Various types of repeat elements observed around junctions are shown