dna methylation maps  (Annoroad Gene Technology Co Ltd)

Journal: Cell systems

Article Title: Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons

doi: 10.1016/j.cels.2019.06.006

Figure Lengend Snippet: A) Overview of processing steps (rows) and data sets (columns). GDC legacy data and PanCancer Atlas data were derived from the TCGA quantification-level data. GDC harmonized data were regenerated from TCGA sequence data, using an updated version of the TCGA sequence data processing pipeline10. QC comparisons were done between legacy TCGA hg19 and GDC hg38 harmonized data. Library construction protocols: FT: the flow-through from poly(A) mRNA purification, and TR: Total RNA. Asterisks indicate that while the source data were generated using v16 miRBase annotations, names reported for stem-loops and 5p/3p mature strands, in TCGA publications, may be from a more recent miRBase version; in contrast to names, miRBase MI and MIMAT identifiers are stable. B-F) Results of QC comparisons for GDC miRNA-seq data. B) Distribution of rank correlation coefficients for hg19 vs. hg38 reads-per-million normalized abundance (RPMs) for stem-loops across all cancer types and miRNAs. C) Comparison of hg19 vs. hg38 median RPMs for stem-loops. The red circles highlight has-mir-21 and two hsa-mir-24 family members, see (D-F). D-F) RPM comparisons for mature strands. Dots represent samples, and are colored to indicate the sequencing instrument (GAII or HiSeq). Schematics below the RPM scatterplots show miRNA stem-loops and cytoband locations for hsa-mir-21, and for hsa-mir-24 family’s hsa-mir-24–1 and -2. Dashed lines highlight the 3p mature strand, MIMAT000080, whose reference sequence is identical in each family. G,H) Distributions of RPMs for legacy (GRCh37/hg19) and harmonized (GRCh38/hg38) mature strands and stem-loops, for primary tumours from the TCGA muscle-invasive bladder cancer (BLCA) cohort (n=409): G) has-mir-21, H) has-mir-24–1 and -2. P values are from Wilcoxon test. ‘SL’: stem-loop. See also Table S1.

Article Snippet: TCGA hg19 DNA methylation legacy gene mapping , Illumina , https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html.

Techniques: Derivative Assay, Sequencing, Purification, Generated, Comparison

Journal: Cell systems

Article Title: Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons

doi: 10.1016/j.cels.2019.06.006

Figure Lengend Snippet: A) Affy SNP array copy number pipeline: other than lifting probe loci over to hg38, the pipeline was identical for hg19 and hg38. Probesets used to create Level 3 hg19 and hg38 data were not identical in that 14811 (0.8%) probes that could not be uniquely mapped in hg38 were not used in segmentation. B) Genes sorted by number of cancer types in which each gene is “deviant” (as defined earlier). We observe a very small subset of genes that are deviant in more than a few cancer disease types. C) Distribution of SCNA disagreements for 20,616 genes between the hg19-aligned run and the hg38-aligned run for 33 TCGA tumor types ordered by increasing median fraction. Boxes are colored by median number of recurrent SCNAs (listed in parentheses) in each tumor type as determined by GISTIC2.0 with the hg19 reference build. See also Figure S1.

Article Snippet: TCGA hg19 DNA methylation legacy gene mapping , Illumina , https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html.

Techniques:

Journal: Cell systems

Article Title: Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons

doi: 10.1016/j.cels.2019.06.006

Figure Lengend Snippet: A) Summary of HM27/HM450 processing differences between legacy (hg19, GDCv1–3) and current (hg38, GDCv4–12) versions, and an upcoming version available for manual download in the GDC Community Tools repository (see supplement for details). B) Associating array features with genes in the hg19 and hg38 pipelines: hg19 used the RefSeq version 40 annotations from the Illumina HM450 manifest, and only associated probes within 1,500 bp upstream of a transcript start site (“TSS -1500”); hg38 used GENCODE 22 annotations, and includes distance from the nearest TSS, which can be used to associate probes both upstream or downstream from a TSS (“TSS +/−1500”). GENCODE 22 often includes additional alternative promoters for the same gene. C) Number of Strong Negative Correlations (SNCs) between DNA methylation beta value and RNA expression, using different associations: “Legacy -1500” used hg19 associations, “hg38 – 1500” used hg38 annotations but only upstream associations, and “hg38 +/−1500” used the same annotations but both upstream and downstream associations. The number of SNCs increased for all transcript types (only three shown here). D) Example of a new alternative promoter for PAX8 present in hg38 annotations but not hg19, which also coincided with an SNC identified in the hg38 but not hg19 version. E) Methylation vs. expression for this SNC (cg07772999-PAX8) across all TCGA-CHOL samples - about 50% of tumors are demethylated at this alternative promoter and overexpress PAX8. See also Figure S2, Tables S2–S5.

Article Snippet: TCGA hg19 DNA methylation legacy gene mapping , Illumina , https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html.

Techniques: DNA Methylation Assay, RNA Expression, Methylation, Expressing

Journal: Cell systems

Article Title: Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons

doi: 10.1016/j.cels.2019.06.006

Figure Lengend Snippet: (A) Outline of bioinformatic pipeline steps for TCGA Legacy (hg19) and current GDC (hg38) data. All aspects of sample processing differ including computational methods, the reference genome, reference transcriptome. (B) The distribution of sample rank correlation coefficients between matched samples of the two data versions from the BRCA cohort (n=1205). Correlation estimates arise from comparing gene level counts of the Legacy RSEM output to gene level counts from the Current htseq-count workflow. C) Comparison of log ratios between Legacy and Current for the BRCA basal versus non-basal comparison. Each point represents the log ratio of subtypes (basal / non-basal) from the Legacy (x-axis) or Current (y-axis) workflow. Genes exhibiting > 1.5-fold change in either direction are highlighted in red. Log ratio estimates were derived from upper quartile normalized gene level estimates for the Legacy workflow and FPKM transformed gene level estimates from the Current workflow. Log (base 2) ratios between subtypes demonstrate large changes across many genes, while changes between workflows are far fewer in both number and magnitude. See also Figure S3.

Article Snippet: TCGA hg19 DNA methylation legacy gene mapping , Illumina , https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html.

Techniques: Comparison, Derivative Assay, Transformation Assay

Journal: Cell systems

Article Title: Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons

doi: 10.1016/j.cels.2019.06.006

Figure Lengend Snippet: (A) Outline of pipeline steps for TCGA MC3 (hg19) and current (v12) GDC release (hg38). (B) Overlapping somatic mutation calls between GDC and MC3. Red and blue shaded regions represent the public somatic SNV calls unique in GDC and MC3 respectively. The lighter red and blue shaded regions represent the unrecoverable calls that were available in the public call of one group but were not found in neither public nor protected calls of the other group. (C) The overlap of somatic mutation call per sample in four different cancer types. The X and Y axes represent the proportion of shared calls over the total calls from GDC and MC3 respectively. Each dot represents a sample, and the dot size indicates the numbers of somatic SNVs called. A sample has more GDC-unique or MC3-unique calls is closer to the origin. The color indicates whether WGA sequencing was employed. See also Figure S4.

Article Snippet: TCGA hg19 DNA methylation legacy gene mapping , Illumina , https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html.

Techniques: Mutagenesis, Sequencing

Journal: Cell systems

Article Title: Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons

doi: 10.1016/j.cels.2019.06.006

Figure Lengend Snippet: Key Resources Table

Article Snippet: TCGA hg19 DNA methylation legacy gene mapping , Illumina , https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html.

Techniques: Expressing, DNA Methylation Assay, Mutagenesis, Software, Methylation

Journal: Molecular Biology and Evolution

Article Title: Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate–Vertebrate Boundary

doi: 10.1093/molbev/msv345

Figure Lengend Snippet: Distribution of DNA methylation in different TE classes of Ciona intestinalis . Only LINEs and SINEs have substantially methylated subsets.

Article Snippet: To directly analyze the patterns of DNA methylation, we used experimentally determined DNA methylation maps from four diverse chordates ( Homo sapiens , Gallus gallus , Danio rerio , and C . intestinalis ; data shown in ).

Techniques: DNA Methylation Assay, Methylation

Journal: Molecular Biology and Evolution

Article Title: Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate–Vertebrate Boundary

doi: 10.1093/molbev/msv345

Figure Lengend Snippet: ( A ) Distributions of promoter and gene body DNA methylation from whole-genome methylation maps in four species across the chordate phylogeny. Both promoters and gene bodies are composed of lowly (mean fractional methylation level < 0.3) and highly methylated (mean fractional methylation level > 0.5) subsets in these species, and show good correspondence with the CpG O/E values. ( B ) Using empirical cutoff values, the proportions of lowly and highly methylated promoters and gene bodies of the study species are depicted.

Article Snippet: To directly analyze the patterns of DNA methylation, we used experimentally determined DNA methylation maps from four diverse chordates ( Homo sapiens , Gallus gallus , Danio rerio , and C . intestinalis ; data shown in ).

Techniques: DNA Methylation Assay, Methylation

Journal: Molecular Biology and Evolution

Article Title: Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate–Vertebrate Boundary

doi: 10.1093/molbev/msv345

Figure Lengend Snippet: ( A ) Sea squirt ( Ciona intestinalis ) genes with low and high levels of DNA methylation in promoters and gene bodies. Figures drawn using values calculated from sliding windows that are 100 bases wide with a 10-base step size. Genes in this species can be classified into four groups, where promoter and gene bodies are lowly and highly methylated, respectively. The numbers of genes in each group are described in the main text. ( B ) Variation of gene expression levels of these four methylation categories.

Article Snippet: To directly analyze the patterns of DNA methylation, we used experimentally determined DNA methylation maps from four diverse chordates ( Homo sapiens , Gallus gallus , Danio rerio , and C . intestinalis ; data shown in ).

Techniques: DNA Methylation Assay, Methylation, Gene Expression