Introduction to Sanger Land Content

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Sanger_B37 and Sanger_B38

In order to improve their utility, the Sanger Cancer Genome Project has embarked on a systematic characterization of the genetics and genomics of large numbers of cancer cell lines.

Data Source

Data source: Data source: COSMIC

Land Version Genome Build Gene Model
Sanger_B37 Human.B37.3 OmicsoftGene20130723
Sanger_B38 Human.B38 OmicsoftGenCode_V24

Data Types

  • CNV
  • DNA-Seq Mutation (Exome)
  • Expression Intensity Probes (Affymetrix)
  • Methylation450 Bead Chip

Laboratory Methods

  • Affymetrix Expression Array

Processing Methods

Expression Data: Omicsoft Affymetrix Microarray Preprocessing

Key Meta Data Columns

  • Primary Site: The body site where the cell line sample is derived from.
  • Histology: Histological types of cancer, such as carcinoma, glioma and sarcoma.
  • Land Tissue: The tissue from which the cell line was derived, using OmicSoft's curation Controlled Vocabulary
  • Land Sample Type: A detailed description of the cell type from which the cell line was derived, using OmicSoft's curation Controlled Vocabulary
  • TCGA Cancer Type: Descriptions of cancer types, matching "Disease" in TCGA
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Primary Grouping

Primary Site

Sample Distribution by Primary Site

Primary site Sanger.png

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Key Views

Gene Expression

One of the most common ways to visualize gene expression data is a per-sample Scatter plot (Expression View), with each sample grouped by Primary Site on the Y-axis, and expression level plotted on the X-axis:

BrafExpressionSanger.png

Expression profile of BRAF.

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Mutation Site Distribution

Exome Sequencing mutation data can be queried and grouped by metadata columns. For example, it is clear from this graph that BRAF is highly mutated in skin cancers:

Mutation Sanger.png

Note: in this view, all alleles will be plotted in separate charts (arrow indicates there are 62 alleles of BRAF found in this land). The mutation distribution view will show a summary of ALL mutations in the gene(s) queried.

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