Context-based FISH localization of genomic rearrangements within chromosome 15q11.2q13 duplicons

Table 1 Number of Agilent 244 K microarray oligonucleotide probe sets within 15q11.2q13.1 targeting distinct interchromosomal duplicons

No. of Probes	Interchromosomal Duplicon Matches	Chromosome Location
BP1 (chr15:18,980,000-20,385,000, NCBI 36; hg18)
4	1	13q13.2
2	1	2q24.3
13	29	13q11, 18p11.21, 21q11.2, 2q21.1, 22q11.1, 14q11.1
3	3	17q11.2
1	1	2q14.1
11	1	14q11.2
6	1	14q32.33
1	1	Yp11.32
2	1	16q24.2
1	4	16p11.2, 13q31.3
2	1	3p22.1
1	1	20q13.12
BP2 (chr15:20,700,000-21,356,000, NCBI 36; hg18)
3	1	16p13.12
1	1	13q31.3
1	1	16q12.2
BP3 (chr15:25,941,000-27,286,000, NCBI 36; hg18)
3	4	16p11.2, 13q31.3
1	1	3p22.3
1	1	5p15.31

The track features from the UCSC genome browser (hg18) of the Agilent SurePrint G3 Human CGH Microarray were analyzed. The Galaxy metaserver was used to extract probe sequences coincident with the non-repeat-masked regions within BP1, BP2 and BP3. Interchromosomal duplicons with complete overlap to the Agilent probe sets were enumerated. In BP1, approximately 73% (n = 47/64) of the probes (left column) targeted distinct interchromosomal duplicon loci (middle column) in a chromosome band (right column). Probe targets in intrachromosomal duplicons and repeat-masked sequences were poorly represented in this region (27%). In BP2, approximately 74% (n = 14/19) of the Agilent 244 K probe sets targeted repeat-masked sequences or intrachromosomal duplicons; however their paralogs were distal to the BP3 region common to AS/PWS deletions. The remaining 26% (n = 5) of the probe sets targeted interchromosomal loci. Probe coverage in BP3 constituted 94% (n = 74/79) of both repeat-masked and intrachromosomal duplicon sequences. The remaining probe coverage (6%) in BP3 contained targets to both interchromosomal and intrachromosomal duplicon loci that are coincident with BP2.

ISSN: 1755-8166