mapping 250k sty2 snp array  (Thermo Fisher)

Journal: Cancers

Article Title: Bioinformatics Screen Reveals Gli-Mediated Hedgehog Signaling as an Associated Pathway to Poor Immune Infiltration of Dedifferentiated Liposarcoma

doi: 10.3390/cancers15133360

Figure Lengend Snippet: Gli2 has higher expression than Gli1 in DDLPS tumors but not as a result of Gli1 amplification. Gli1 and Gli2 mRNA expressions were evaluated in two separate cohorts (TCGA-SARC n = 58) ( A ) and GSE21124 ( n = 50) of DDLPS tumors ( B ). Gli1 mRNA expression was compared to Gli1 genomic status in the respective cohorts ( C , D ), as was Gli2 mRNA expression ( E , F ). Pearson correlation analysis was performed to evaluate the strength of the relationship between Gli1 and Gli2 expression in DDLPS tumors in both cohorts ( G , H ). Statistical evaluation was performed following Rout’s outlier test with subsequent Student’s t -test or one-way ANOVA when appropriate. Outliers were removed as follows: 3B, Gli1 n = 6; 3C, Diploid n = 7, Gain n = 2, Amp. n = 1; 3D, Diploid, n = 1. Paired values from patient tumors were removed following outlier removal. (ns: not significant, ** p < 0.01, *** p < 0.001, **** p < 0.0001).

Article Snippet: Genomics array profiling was collected using the Affymetrix Mapping 250K Sty2 SNP Array (GSE21124 [ ]).

Techniques: Expressing, Amplification

Journal: Cancers

Article Title: Bioinformatics Screen Reveals Gli-Mediated Hedgehog Signaling as an Associated Pathway to Poor Immune Infiltration of Dedifferentiated Liposarcoma

doi: 10.3390/cancers15133360

Figure Lengend Snippet: Datasets used and accession locations.

Article Snippet: Genomics array profiling was collected using the Affymetrix Mapping 250K Sty2 SNP Array (GSE21124 [ ]).

Techniques: Expressing, Cell Differentiation, Sequencing, RNA Sequencing Assay

Journal: Genome Biology

Article Title: GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

doi: 10.1186/gb-2011-12-4-r41

Figure Lengend Snippet: Comparison of RegBounder to MCR and leave-1-out procedures applied to primary lung adenocarcinomas . The advantages of RegBounder over previous peak-finding procedures are illustrated for two well-described oncogene peaks identified in GISTIC analysis of 371 lung adenocarcinoma samples characterized on the Affymetrix 250K StyI SNP array (as published in ). (a) A well-described amplification peak is identified on chromosome 12p12.1 with MCR (red dotted lines) near to but not containing the known lung cancer oncogene KRAS . Because there are more than two apparent passenger events in this region, the leave-1-out peak (blue dotted lines) also does not contain KRAS . However, RegBounder (green dotted lines) produces a wider peak that captures KRAS . (b) An amplification peak on chromosome 5p15.33 contains hTERT , the catalytic subunit of the human telomerase holoenzyme, within the MCR (red dotted lines). In this case, RegBounder (green dotted lines) produces a narrower peak region than the corresponding leave-1-out peak (blue dotted lines), demonstrating the ability of RegBounder to achieve a greater balance between peak region size and accuracy. In both (a) and (b), the y-axis depicts the amplification G-score and the x-axis denotes position along the corresponding chromosome.

Article Snippet: We made use of a large collection of 3,131 cancer samples run on the Affymetrix 250K StyI SNP Array [ ] plus several hundred additional samples run on the Affymetrix SNP6.0 Array (data not shown).

Techniques: Amplification