PMC5410019_01
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
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Fig1
A high-resolution CMA using the CytoScan HD array (Affymetrix, Santa Clara, CA) with Chromosome Analysis Suite software (ChAS, Affymetrix) to process the raw data detected a 9.2-Mb trisomy at 1q42.12-q42.2, a 6.7-Mb tetrasomy consisting of the duplication of two haplotypes, each of which probably derives from either the father or the mother, at 1q42.2-q43, and a 8.2-Mb segment with the absence of heterozygosity at 1q43-qter consistent with isoUPD (arr[hg19]1q42.12q42.2(225,101,799_234,324,222)x3,1q42.2q43(234,330,738_240,992,219)x4,1q43qter(240,993,835_249,224,684)x2 hmz, Fig. 1a). In the tetrasomic region (the triplicated segment), three allele peaks (AA, AB, and BB) with unusually large spaces between them were observed (Fig. 1a), suggesting the presence of AA/AA, AA/BB, and BB/BB tracks, which is only possible if each parent contributed equally with two alleles (either AA or BB).  Bio, Otsu, Japan) with the two step protocol according to the manufacturer instructions. The direct sequencing of PCR products defined sequences around two breakpoint junctions, jct1 and jct2 (Fig. 1c). Based on these results, the duplication and the triplication start around chr1:225,104,328 and 234,324,641, respectively, and the triplication stops around 240,990,090. Mb in proximal and distal duplications, respectively), indicating that our case is the first with a large proximal duplication (approximately 9.2 Mb) in this type of CGR. Microhomology (ATAT) was observed at the jct1 breakpoint interval, whereas a microhomologous sequence with some mismatch sequences including insertions, deletion, and point mutations was observed at the jct2 breakpoint interval (Fig. 1c). Mismatch sequences only near jct2 of CGR, which might occur during the same event as the de novo CGR/isoUPD formation, have previously been reported.