Introduction to TARGET Land Content
From Array Suite Wiki
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.
|Land Version||Genome Build||Gene Model|
- DNA-Seq Somatic Mutation
- Expression Intensity Probes (Affymetrix)
- Methylation450 BeadChip
- 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)
- Illumina HiSeq
- Affimetrix Expression Arrays
- Complete Genomics platform
Expression Data: Omicsoft Affymetrix Microarray Preprocessing
Omicsoft does not reprocess other genomic data, but extracts data directly from original datasets.
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.
One of the most common ways to visualize expression data is to group the data by Tumor Type:
Copy Number Variation
Per-sample Copy Number Variation can be visualized and grouped by metadata categories to identify associations between variables.
|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.