custom-designed 16q24.1 region-specific 4 × 180k microarray  (Agilent technologies)

Journal: BMC Medical Genetics

Article Title: Molecular and clinical analyses of 16q24.1 duplications involving FOXF1 identify an evolutionarily unstable large minisatellite

doi: 10.1186/s12881-014-0128-z

Figure Lengend Snippet: Results of aCGH and DNA sequence analyses in patient 1. (a) aCGH plot with the custom-designed NimbleGen 720K microarray showing duplication on chromosome 16q24.1. (b) Chromatogram of the DNA sequence of the junction fragment showing the 8 bp microhomology GTGGTCAG. (c) Schematic representation of the strategy used to amplify the duplication breakpoint junction fragment. The wildtype band is not amplified using this approach with the outward facing primers.

Article Snippet: Fine duplication mapping was performed in patient 1 using aCGH with a custom-designed 16q24.1-specific 720K microarray covering 2-Mb regions flanking FOXF1 [Roche-NimbleGen (Madison, WI, USA)] as described [ ], and in patients 2 and 4 using a custom-designed 16q24.1 region-specific 4 × 180K microarray (Agilent Technology), as described [ ].

Techniques: Sequencing, Microarray, Amplification

Journal: BMC Medical Genetics

Article Title: Molecular and clinical analyses of 16q24.1 duplications involving FOXF1 identify an evolutionarily unstable large minisatellite

doi: 10.1186/s12881-014-0128-z

Figure Lengend Snippet: Results of aCGH and DNA sequence analyses in patients 2 and 3. (a) aCGH plot obtained using 4x180K microarray (Agilent) in patient 2 shows three duplicated regions in 16q23.3, 16q24.1, and 16q24.2. (b) aCGH plot from Illumina SNP-Array (Infinium® CytoSNP-850K showing duplication on chromosome 16q24.1 in patient 3’s daughter. (c) Duplication junction fragment visualized on 1% agarose gel in the proband (P) and her daughter (D), but absent in the control DNA (C). (d) Chromatogram of the DNA sequence of the junction fragment showing the 3 bp AGA microhomology.

Article Snippet: Fine duplication mapping was performed in patient 1 using aCGH with a custom-designed 16q24.1-specific 720K microarray covering 2-Mb regions flanking FOXF1 [Roche-NimbleGen (Madison, WI, USA)] as described [ ], and in patients 2 and 4 using a custom-designed 16q24.1 region-specific 4 × 180K microarray (Agilent Technology), as described [ ].

Techniques: Sequencing, Microarray, Agarose Gel Electrophoresis

Journal: BMC Medical Genetics

Article Title: Molecular and clinical analyses of 16q24.1 duplications involving FOXF1 identify an evolutionarily unstable large minisatellite

doi: 10.1186/s12881-014-0128-z

Figure Lengend Snippet: Results of aCGH and DNA sequence analyses in patient 4. (a, b) aCGH plot (4x180k Agilent microarray) showing the duplicated region in patient 3 in chromosome 16q24.1. (c) Result of FISH analysis showing the 16q24.1 duplication in the proband. (d) Duplication junction fragment visualized on 1% agarose gel in the proband (P), but absent in father (F), mother (M), and control DNA (C). (e) A proposed model of duplication formation mediated by the adjacent unstable minisatellite: 1, 2, and 3 represent template switches with 8 bp insertion (1) and microhomologies (2 and 3). Asterix (*) represents the initial DNA replication slippage event that might have triggered the formation of the described complex genomic rearrangement. Red boxes represent the MLT1D ERVL-MaLR repeat sequences flanking the minisatellite. Green and yellow boxes represent triplicated sequences.

Article Snippet: Fine duplication mapping was performed in patient 1 using aCGH with a custom-designed 16q24.1-specific 720K microarray covering 2-Mb regions flanking FOXF1 [Roche-NimbleGen (Madison, WI, USA)] as described [ ], and in patients 2 and 4 using a custom-designed 16q24.1 region-specific 4 × 180K microarray (Agilent Technology), as described [ ].

Techniques: Sequencing, Microarray, Agarose Gel Electrophoresis

Journal: BMC Medical Genetics

Article Title: Molecular and clinical analyses of 16q24.1 duplications involving FOXF1 identify an evolutionarily unstable large minisatellite

doi: 10.1186/s12881-014-0128-z

Figure Lengend Snippet: High-resolution custom-designed region-specific Agilent CGH microarray analyses of the studied minisatellite in 16q24.1. aCGH plot for patient 4 and 6 non-duplicated control samples run on 4x180k 16q24.1-specific Agilent microarray. Due to the repetitive nature of the minisatellite, contraction or expansion of the minisatellite shows decrease or increase in log ratios for all oligo probes in this region.

Article Snippet: Fine duplication mapping was performed in patient 1 using aCGH with a custom-designed 16q24.1-specific 720K microarray covering 2-Mb regions flanking FOXF1 [Roche-NimbleGen (Madison, WI, USA)] as described [ ], and in patients 2 and 4 using a custom-designed 16q24.1 region-specific 4 × 180K microarray (Agilent Technology), as described [ ].

Techniques: Microarray