Introduction to TARGET Land Content

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Contents

TARGET_B37

The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) project applies a comprehensive genomic approach to determine molecular changes that drive childhood cancers. TARGET initiated with two pilot projects on high-risk subtypes of acute lymphoblastic leukemia (ALL) and neuroblastoma (NBL). Later it expanded its efforts into additional childhood cancers. OmicSoft's TARGETLand provides samples featuring ALL, NBL, AML (Acute Myeloid Leukemia), and nine other tumor types.

Data Source

TARGET

Land Version Genome Build Gene Model
TARGET_B37 Human.B37.3 OmicsoftGene20130723
TARGET_B38 Human.B38 OmicsoftGenCode_V24

Data Types

  • CNV
  • DNA-Seq Somatic Mutation
  • Expression Intensity Probes (Affymetrix)
  • Methylation450 BeadChip
  • miRNA-Seq
  • RNA-Seq, including:
    • Single-end and Paired-end fusion calling
    • RNA-Seq somatic mutation, from matched tumor/normal pairs
    • RNA-Seq Mutation
    • Exon Junction and Exon Usage
    • Expression (Gene- and Transcript- level quantification)

Laboratory Methods

  • Illumina HiSeq
  • Affimetrix Expression Arrays
  • Complete Genomics platform

Processing Methods

Expression Data: Omicsoft Affymetrix Microarray Preprocessing

RNA-Seq data: OmicScript Pipeline and Building Land From RNA-Seq Data

Omicsoft does not reprocess other genomic data, but extracts data directly from original datasets.

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Key Meta Data Columns

  • Tumor Type: The types of tumor such as ALL (Acute Lymphoblastic Leukemia) and NBL (neuroblastoma)
  • Sample Type: The types of sample indicating where the sample is from. It includes information such as whether it is from normal or tumor tissue and whether it is primary, recurrent tumor, or from cell line etc.
  • Land Tissue: is curated by Omicsoft Land cutation team using Omicsoft's control vocabularies. Allow users to easily merge the data with other Lands.
  • Land Sample Type: is curated by Omicsoft Land cutation team using Omicsoft's control vocabularies. Allow users to easily merge the data with other Lands.
  • Tumor or Normal: indicates whether a sample is from tumor sample for normal sample.


Key Views

Gene Expression

One of the most common ways to visualize expression data is to group the data by Tumor Type:

Land TARGET ExpressionView.png

Copy Number Variation

Per-sample Copy Number Variation can be visualized and grouped by metadata categories to identify associations between variables.

Land TARGET CopyNumberView.png

Reduced copy number of CDKN2A is frequently observed in Acute Lymphoblastic Leukemia (ALL).
Forero-Castro, Maribel, et al. "Genome-Wide DNA Copy Number Analysis of Acute Lymphoblastic Leukemia Identifies
New Genetic Markers Associated with Clinical Outcome". PloS one 11.2 (2016): e0148972.


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