acgh arrays (244k or 1m platform  (Agilent technologies)

Journal: Oncogene

Article Title: Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring V600E BRAF

doi: 10.1038/onc.2011.250

Figure Lengend Snippet: Landscape of copy-number alterations in V600EBRAF-mutant melanoma cell lines. (a) A total of 149 melanoma cell lines were characterized for mutations in BRAF and NRAS using mass spectrometric genotyping. (b) Segmented DNA copy-number data for 31 V600EBRAF cell lines characterized on one of two Agilent aCGH arrays (244K or 1M platform as shown) indicates highly altered profiles. Samples are sorted according to their chromosome 10q23 (encoding PTEN) copy-number status (heatmap; red indicates gain/amplification, blue indicates loss/deletion on scale shown at bottom; white is copy-number neutral). Chromosomes are indicated at left and are scaled genomically. Highlighted at right are focal amplifications of the 3p14.1 locus encoding MITF (top) and focal deletions affecting 9p21.3 encoding CDKN2A and CDKN2B (bottom). (c) Statistically significant genomic aberrations (red is amplification, blue is deletion) for the panel of 31 melanoma cell lines are shown (assessed by RAE; plotted are regions with FDR≤15%, autosomes indicated at center in genomic coordinates, centromeres in red, acrocentric arms in black).

Article Snippet: All mutations were confirmed by sequencing with an orthogonal platform ( Supplementary Figure 1 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 1 caption a7 Landscape of copy-number alterations in V600EBRAF-mutant melanoma cell lines. ( a ) A total of 149 melanoma cell lines were characterized for mutations in BRAF and NRAS using mass spectrometric genotyping. ( b ) Segmented DNA copy-number data for 31 V600EBRAF cell lines characterized on one of two Agilent aCGH arrays (244K or 1M platform as shown) indicates highly altered profiles.

Techniques: Mutagenesis, Amplification

Journal: Oncogene

Article Title: Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring V600E BRAF

doi: 10.1038/onc.2011.250

Figure Lengend Snippet: Characterization of PTEN status of V600EBRAF-mutant melanoma cell lines. (a) Nine V600EBRAF cell lines that expressed minimal to no PTEN protein and high levels of phosphorylated AKT (ser473 and thr308) were identified by immunoblot. Two of the nine V600EBRAF, PTEN-null cell lines, SKMEL-207 and A2058, were also RB1 null. (b) PTEN mRNA expression was detected by reverse transcription–PCR in six of the nine PTEN-null models. SKMEL-207 expresses a low level of PTEN mRNA. (c) Array CGH-based determination of DNA copy-number alterations identifies frequent single copy loss (light blue) of 10q encompassing PTEN with less common focal homozygous deletions (dark blue) with diverse breakpoints affecting the gene in the four cell lines indicated. (d) Probe level and segmentation data in SKMEL-178 from both Agilent 244K- and 1M-feature arrays (gray and blue/red, respectively). The higher resolution 1M platform (blue dots/red line) robustly identified a focal and intragenic micro-scale deletion encompassing exon 2 of PTEN that was not detected by the lower-resolution array.

Article Snippet: All mutations were confirmed by sequencing with an orthogonal platform ( Supplementary Figure 1 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 1 caption a7 Landscape of copy-number alterations in V600EBRAF-mutant melanoma cell lines. ( a ) A total of 149 melanoma cell lines were characterized for mutations in BRAF and NRAS using mass spectrometric genotyping. ( b ) Segmented DNA copy-number data for 31 V600EBRAF cell lines characterized on one of two Agilent aCGH arrays (244K or 1M platform as shown) indicates highly altered profiles.

Techniques: Mutagenesis, Western Blot, Expressing