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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.