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Table 2 Number of Affymetrix SNP 6.0 microarray probe sets within 15q11.2q13.1 targeting distinct interchromosomal duplicons

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

No. of Probes Interchromosomal Duplicon Matches Chromosome Location
BP1 (chr15:18,980,000-20,385,000, NCBI 36)
1 1 13q13.2
3 1 2q24.3
1 1 3q29
2 3 22q12.2, 13q12.1
4 7 13q12.1, 18p11.21, 21q11.2, 2q21.1, 22q11.1, 14q11.1
2 14 18p11.2, 21q11.2, 2q21.1, 22q11.1, 14q11.1
1 1 17q11.2
1 1 2q14.1
4 1 14q11.2
1 1 12p13.31
5 2 16q24.2
2 4 1p36.23, Yq11.22
3 1 2p24.3
3 1 3p22.1
7 2 20q13.12
BP2 (chr15:20,700,000-21,356,000, NCBI 36)
8 2 13q31.3
3 1 16p13.12
3 1 16p13.12
BP3 (chr15:25,941,000-27,286,000, NCBI 36)
4 8 13q31.3, 16p11.2
  1. The probe distribution along 15q11.2 q13 using the Affymetrix SNP 6.0 microarray showed 75% (n = 40/53) of the probes (left column) in BP1 occur within distinct interchromosomal duplicon loci (middle column) in a given chromosome band (right column). Probes within intrachromosomal duplicons and repeat-masked sequences showed poor representation in this region. Of the 59 probe features targeting SNPs in BP2, 19% (n = 11/59) were homologous with interchromosomal duplicon intervals and would be expected to cross-hybridize. The remaining 81% (n = 48/59) of probe features targeted repeat-masked sequences in intrachromosomal duplicons. Similarly in BP3, the majority of probes occurred within the repeat-masked sequences (89%, n = 158/177), however the remaining probes (11%) in BP3 contained interchromosomal and intrachromosomal duplicon targets. Probes within BP2 and BP3 are underrepresented relative to adjacent single copy regions.