Journal: JNCI Journal of the National Cancer Institute

Article Title: Differences in Genomic Profiles and Outcomes Between Thoracic and Adrenal Neuroblastoma

doi: 10.1093/jnci/djz027

Figure Lengend Snippet: Adrenal vs thoracic tumor copy number association analysis. A) Meta-analysis by nonoverlapping 1-Mb tiles. The y-axis reflects an inverse variance-weighted meta-analysis across four datasets—single nucleotide polymorphism (SNP) microarray, whole genome sequencing, whole exome sequencing, and gene panel sequencing cohorts—of average log-ratio (tumor normalized to normal) differences between adrenal vs thoracic cases divided by SD (z score). A positive z score (red) implies that the relative copy number is higher in adrenal vs thoracic cases and a negative z score (blue) implies the opposite. The inner dashed line illustrates the z score corresponding to a nominal P value cut point of .05, and the outer dotted line illustrates the z score corresponding to a multiple test-adjusted false discovery rate (FDR) cut point of 0.05. The 1-Mb bin containing MYCN is labeled, because it is the only focal copy number alteration to reach statistical significance. B) Meta-analysis by chromosome arm. “Avg Adrenal” and “Avg Thoracic” denote a weighted average copy number log-ratio for adrenal and thoracic cases, respectively. More positive/red values reflect regions of greater copy number gain and more negative/blue values reflect regions of greater copy number loss. From the difference of these values (Avg Difference), a z score and two-tailed P value were computed by inverse-variance meta-analysis. The FDR was controlled by the Benjamini-Hochberg method. Results with multiple test-adjusted statistical significance at FDR less than 0.05 are bolded.

Article Snippet: Functional Genomic Associations With Neuroblastoma Site of Origin To evaluate the relationship of primary site with functional subclasses of neuroblastoma, we performed unsupervised hierarchical clustering on adrenal (n = 143) and thoracic (n = 19) cases with RNA expression profiling obtained by HuEx microarray, as well as adrenal (n = 128) and thoracic (N = 15) cases with DNA methylation profiling by Infinium microarray.

Techniques: Microarray, Sequencing, Labeling, Two Tailed Test

Journal: JNCI Journal of the National Cancer Institute

Article Title: Differences in Genomic Profiles and Outcomes Between Thoracic and Adrenal Neuroblastoma

doi: 10.1093/jnci/djz027

Figure Lengend Snippet: Unbiased clustering analysis of functional genomic and DNA methylation data in the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) cohort. Heatmaps and hierarchical clustering for all adrenal and thoracic (A) HuEx RNA microarray samples and (B) DNA methylation microarray samples. Rows reflect independent patient profiles and columns reflect the 200 probesets with the highest variance after (A) log2 transformation of RNA probe intensity and (B) logit transformation of methylation beta values. Columns are mean-centered and normalized by SD (z score transformation) and illustrated on a blue-yellow scale. Additional colored boxes illustrate clinical annotations for each patient according to the legend (white = missing annotation).

Article Snippet: Functional Genomic Associations With Neuroblastoma Site of Origin To evaluate the relationship of primary site with functional subclasses of neuroblastoma, we performed unsupervised hierarchical clustering on adrenal (n = 143) and thoracic (n = 19) cases with RNA expression profiling obtained by HuEx microarray, as well as adrenal (n = 128) and thoracic (N = 15) cases with DNA methylation profiling by Infinium microarray.

Techniques: Functional Assay, DNA Methylation Assay, Microarray, Transformation Assay, Methylation

Journal: Orthopaedic Surgery

Article Title: Non‐coding RNA Identification in Osteonecrosis of the Femoral Head Using Competitive Endogenous RNA Network Analysis

doi: 10.1111/os.12834

Figure Lengend Snippet: Differentially expressed genes (DEGs) identification between osteonecrosis of the femoral head (ONFH) and normal samples. The DE‐lncRNAs and DE‐mRNAs between ONFH and normal samples were identified from GSE74089 by limma package in R based on the criteria of with the adjusted P value <0.05 and |log fold change (FC)| ≥2. DE‐miRNAs were identified from GSE89587 on the basis of adjusted P value <0.05. Volcano plots display the distribution of DE‐mRNAs (A), DE‐lncRNAs (C), and DE‐miRNAs (E). The vertical dotted lines in A and C represent |log FC| = 2 and the horizontal dotted lines represent adjusted P value = 0.05. Red spots represent up‐regulated genes and green spots represent down‐regulated genes in ONFH samples compared with normal samples. Hierarchical clustering demonstrates the top 10 DE‐mRNAs (B), DE‐lncRNAs (D), and DE‐miRNAs (F) in descending order by log FC.

Article Snippet: The microarray data of expression profile of GSE74089 (GPL13497) was obtained from the National Center for Biotechnology Information (NCBI) GEO database .

Techniques: