Journal:

Article Title: A Novel Chromosome 19p13.12 Deletion in a Child with Multiple Congenital Anomalies

doi: 10.1002/ajmg.a.32691

Figure Lengend Snippet: Chromosome microarray data demonstrating 19p13.1 deletion. [A] Graphic representation. Each dot with vertical line deviating from the mean represents a value corresponding to loss or gain in copy number. In the combined column, data are average with gains to the right and losses to the left. Red circle indicates strong indication of a loss of the clone corresponding to the 19p13.1 region while the black circle indicates a loss of the clone corresponding to 3q29. The latter represents a commonly seen polymorphism. [B] Partial karyotype for chromosome 19 showing subtle differences on the short arm of chromosome 19 as indicated by the arrow. [C] The combined log ratio of −0.317 is significant by T statistics with p value at 0.004 suggesting a deletion in this region.

Article Snippet: A list of genes mapping to this interval is presented in . fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig. 6 caption a7 The loss on the chromosome 19 at band p13.12 is displayed from Test/Reference ratio data of this patient in a 244K microarray from Agilent.

Techniques: Microarray

Journal:

Article Title: A Novel Chromosome 19p13.12 Deletion in a Child with Multiple Congenital Anomalies

doi: 10.1002/ajmg.a.32691

Figure Lengend Snippet: The loss on the chromosome 19 at band p13.12 is displayed from Test/Reference ratio data of this patient in a 244K microarray from Agilent. The Agilent aberration detection algorithm detects intervals of consistent high or low log ratios within an ordered set of probes by measuring a set of genomic locations and considering their genomic order to make amplification or deletion calls. [A] ~2.52 mega base loss at 19p13.12 is observed. [B] High-resolution view of the deleted region of the patient as compared to her normal parents indicating this is a de novo event.

Article Snippet: A list of genes mapping to this interval is presented in . fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig. 6 caption a7 The loss on the chromosome 19 at band p13.12 is displayed from Test/Reference ratio data of this patient in a 244K microarray from Agilent.

Techniques: Microarray, Amplification

Journal: PLoS ONE

Article Title: Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic Levels

doi: 10.1371/journal.pone.0062982

Figure Lengend Snippet: Data are from (a) Agilent Human Genome CGH Microarray 244A (Memorial Sloan-Kettering Cancer Center), (b) Affymetrix Genome-Wide Human SNP Array 6.0 (Broad Institute of MIT and Harvard), (c) Illumina 550 K Infinium HumanHap550 SNP Chip (HudsonAlpha Institute for Biotechnology) platforms (chr 1–23). Green bars represent amplification and red bars represent deletion. The height of each bar represents the frequency of the alteration in the group. The differentially amplified genes are in chromosome 7 and differentially deleted genes are in chromosome 10.

Article Snippet: The samples from Agilent HG CGH 244 K data set cover all samples in Infinium HumanHap550 data set and 95% of the samples in SNP6 data set ( ).

Techniques: Microarray, Genome Wide, Amplification

Journal: Brain Pathology

Article Title: MIF Receptor CD 74 is Restricted to Microglia/Macrophages, Associated with a M 1‐Polarized Immune Milieu and Prolonged Patient Survival in Gliomas

doi: 10.1111/bpa.12194

Figure Lengend Snippet: CD74 mRNA and protein levels correlate with the content of glioma‐associated microglia/macrophages (GAMs). Hierarchical cluster analyses (A) of gene expression signatures of selected key factors of immune cells, glioblastoma cells as well as glioblastoma micromilieu of 424 primary glioblastomas and 11 normal brain samples deriving from the cancer genome atlas (TCGA) data portal using the Agilent 244K G4502A microarray to determine mRNA profiles. Hierarchical clustering of this data was performed using the Ward's minimum variance method. Dark red color indicates a perfect positive correlation (+1) gradually decreasing to a perfect negative correlation (−1) indicated in blue. Correlation analyses of the same data subset comparing CD74 with either (B) Iba1 (AIF1), (C) CD68 or (D) CD11b (ITGAM) are depicted. CD74 and Iba1 immunoblotting (E) of GAMs, glioblastoma cells (PC) and whole glioblastoma tissue (T) of three different patients with primary glioblastoma World Health Organization (WHO) grade IV showing a positive correlation of CD74 and Iba1 protein expression. Actin served as positive control.

Article Snippet: The cancer genome atlas ( TCGA ), the R epository of M olecular B rain N eoplasia D ata ( REMBRANDT ) and R 2: microarray analysis and visualization platform analyses To determine gene expression of the MIF‐CD74 system in gliomas, we additionally analyzed data from the TCGA using the Agilent 244K G4502A microarray to determine mRNA profiles ( http://tcga.cancer.gov/ ; accessed November 2011).

Techniques: Expressing, Microarray, Western Blot, Positive Control