Paper - Review

DOI: 10.5114/wo.2014.47136

Abstract

TCGA
→ a public funded project → which aims to (catalogues & discover) major cancer-causing genomic alterations
→ A major goal (← of the project) is to provide publicly available datasets → to help improve (diagnostic & treatment & prevent) cancer

New roads to conquer cancer

Cancer
→ the most complex disease (← which mankind has to face)
→ involves (dynamic changes) (← in the genome)
∴ The demand (← for better diagnosis & treatment & prevention of cancer) appeared

TCGA
→ a public funded project
→ aims to (catalogue & discover) major cancer-causing genome alterations (← in large cohorts)

⭐ Provide (a short description) & (major goal) of TCGA

The Cancer Genome Atlas Research Network

The structure of TCGA
→ is well-organised
→ involves (several cooperating centers) (← responsible for collection & sample processing)

Platforms and data types

TCGA applied high-throughput technologies (← which based on microarrays & NGS)

RNA sequencing

RNA sequencing (RNAseq)
→ is a high-throughput technology for transcriptome profiling → deriving strand information with high precision
→ is able to (identify & quantify) (rare & common) (transcripts & isoforms & novel transcripts & gene fusions & non-coding RNAs)

MicroRNA sequencing

MicroRNA sequencing (miRNAseq)
→ utilising material enriched in small RNAs (← which have the capacity to regulate genes)
→ defines (tissue-specific miRNA expression profiles & isoforms & connection with disease & discovery of un-reported miRNAs)

DNA sequencing

DNA sequencing (DNAseq)
→ determines the nucleotides within a DNA molecule
→ provides information about DNA alterations

SNP-based platforms

→ analyses genome-wide structural variation (← across multiple cancer genomes)
→ defines (SNP & CNV & loss of LOH) across multiple samples

Array-based DNA methylation sequencing

→ genome-wide analysis of DNA methylation profile → providing (information of epigenetic changes) in the genome
→ utilises DNA methylation assay mainly based on the Illumina platform

Reverse-phase protein array

Reverse-phase protein array (RPPA)
→ a highly (sensitive & reproducible & high-throughput & functional & quantitative) proteomic method
→ is an antibody-based technique allowing for many samples with up to 500 different antibodies at at time

Visualization and analysis of the genomic data

NGS & Array-based profiling methods
→ generate large amounts of diverse types of genomic data
Integrate multi-dimensional data visualization is an essential component (← of cancer genomic data analysis)

Pan-cancer project

Collected a broad range of genomic data (← of individual cancer types)
→ better understanding of the (biology & pathology) of each tumor
→ resulting in the development of specific treatment strategies

TCGA Pan-cancer project
→ aims to run new comprehensive integrated analysis (← of genomic data across multiple cancers)

Increasing (the number of tumor sample data) → enhanced statistical power
∴ Enhancing the ability to (detect & analyze) molecular defects in cancers

Common tumor-driving mutations & related mutation
→ were correlated with bad phenotypes across several cancer types

Future perspective

Systematic advances (← in cancer genomics) provided by TCGA → revealed a new comprehensive picture of the molecular biology of cancer

TCGA provided a huge amount of publicly available data (← which giving researchers around the world) a source of knowledge about (cancer genetic & epigenetic profiles)

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