human cpg island microarray kit, 244k  (Agilent technologies)

Journal: Breast Cancer Research : BCR

Article Title: Patient-derived breast tumor xenografts facilitating personalized cancer therapy

doi: 10.1186/bcr3355

Figure Lengend Snippet: Genomic and transcriptomic evaluation of breast tumor patient-derived xenografts

Article Snippet: Genomic , DNA copy number alterations: 14/18 pairs of tumors shared more than 56% copy number alterations, unsupervised hierarchical clustering showed 16/18 pairs segregated together. Recurrent changes between patient tumors and xenografts showed losses in 176 chromosomal regions and gains in 202 chromosomal regions , CGH array Agilent 244K human genome CGH microarrays. CGH results showed shared alterations between primary and xenograft tumors with more pronounced alterations in engrafted tumors, that is, TP53 patient 1 wild-type allele, xenograft LOH; ER+ tumor gained basal-like alterations , Paired-end sequencing to achieve deep coverage of patient blood, tumor, metastasis, and xenografted tumor Confirmed SNP coverage by Illumina 1M duo arrays. The PDX retained primary tumor mutations and showed enrichment of mutations similar to patient metastasis , Genome-wide SNPs with enhancement of existing aberrations , , .

Techniques: Sequencing, Genome Wide, Microarray, Expressing

Journal: PLoS ONE

Article Title: The Homeobox Gene MEIS1 Is Methylated in BRAF p.V600E Mutated Colon Tumors

doi: 10.1371/journal.pone.0079898

Figure Lengend Snippet: ( A ) The MEIS1 promoter is hypermethylated in colorectal tumors with a BRAF p.V600E mutation (black dots) when compared to wild type BRAF (white dots). The Y-axis represents the tumor vs. normal log 2 ratio for the median probe per CpG fragment. The horizontal dotted line at log 2 ratio 0 indicates an equal extent of MEIS1 methylation in tumor and normal samples. ( B ) Overview of the analyzed MEIS1 promoter, CpG islands within the promoter and the locus analyzed by MSP primers. Locations were based on the human genome browser (UCSC assembly March 2006, hg18). ( C ) MEIS1 -MSP data showing hypermethylation in BRAF p.V600E colorectal tumors when compared to BRAF wild types. T: tumor; N: normal tissue; M: methylated MEIS1 promoter (168 bp); Um: Unmethylated MEIS1 promoter (176 bp).

Article Snippet: DNA from the 19 colorectal tumors were hybridized on Agilent 244k human CpG island microarrays (Agilent Technologies, Santa Clara, CA, U.S.A.), as described previously [ ].

Techniques: Mutagenesis, Methylation