Table 2.
Number of Affymetrix SNP 6.0 microarray 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) | ||
| 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 |
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.