Pan-cancer analysis aims to examine the similarities and differences among the genomic and cellular alterations found across diverse

tumor A neoplasm () is a type of abnormal and excessive growth of tissue. The process that occurs to form or produce a neoplasm is called neoplasia. The growth of a neoplasm is uncoordinated with that of the normal surrounding tissue, and persists ...

types. International efforts have performed pan-cancer analysis on

exomes The exome is composed of all of the exons within the genome, the sequences which, when transcribed, remain within the mature RNA after introns are removed by RNA splicing. This includes untranslated regions of messenger RNA (mRNA), and coding ...

and the whole

genomes In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding gen ...

of cancers, the latter including their non-coding regions. In 2018,

The Cancer Genome Atlas ''The'' () is a grammatical article in English, denoting persons or things that are already or about to be mentioned, under discussion, implied or otherwise presumed familiar to listeners, readers, or speakers. It is the definite article in ...

(TCGA) Research Network used

exome The exome is composed of all of the exons within the genome, the sequences which, when transcribed, remain within the mature RNA after introns are removed by RNA splicing. This includes untranslated regions of messenger RNA (mRNA), and coding re ...

transcriptome The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The ...

, and DNA

methylome DNA methylation is a biological process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence. When located in a gene promoter, DNA methylation typically acts t ...

data to develop an integrated picture of commonalities, differences, and emergent themes across tumor types. In 2020, the

International Cancer Genome Consortium The International Cancer Genome Consortium (ICGC) is a voluntary scientific organization that provides a forum for collaboration among the world's leading cancer and genomic researchers. The ICGC was launched in 2008 to coordinate large-scale can ...

(ICGC)/TCGA Pan-Cancer Analysis of Whole Genomes project published a set of 24 papers analyzing whole cancer genomes and transcriptomic data from 38 tumor types. A comprehensive overview of the project is provided in its flagship paper. Another project, pan-cancer analysis of

RNA-binding proteins RNA-binding proteins (often abbreviated as RBPs) are proteins that bind to the double or single stranded RNA in cells and participate in forming ribonucleoprotein complexes. RBPs contain various structural motifs, such as RNA recognition motif (R ...

(RBPs) across human cancers, explored the expression, somatic copy number alteration, and mutation profiles of 1,542 RBPs in ∼7,000 clinical specimens across 15 cancer types. This study characterized the

oncogenic Carcinogenesis, also called oncogenesis or tumorigenesis, is the formation of a cancer, whereby normal cells are transformed into cancer cells. The process is characterized by changes at the cellular, genetic, and epigenetic levels and abno ...

properties of six RBPs— NSUN6, ZC3H13, BYSL,

ELAC1 Zinc phosphodiesterase ELAC protein 1 is an enzyme that in humans is encoded by the ''ELAC1'' gene. References Further reading

* * * * * * * {{gene-18-stub ...

RBMS3 RNA-binding motif, single-stranded-interacting protein 3 is a protein that in humans is encoded by the ''RBMS3'' gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of here ...

, and ZGPAT—in colorectal and liver cancer cell lines. Several studies have found a causal, predictable connection between genomic alterations ( single-nucleotide variants or large

copy number variants Copy number variation (CNV) is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals. Copy number variation is a type of structural variation: specifically, it is a type of ...

) and gene expression across all tumor types. This pan-cancer relationship between genomic status and transcriptomic quantitative data can predict a specific genomic alteration from gene expression profiles alone; it can also be used as the basis for

machine learning Machine learning (ML) is a field of inquiry devoted to understanding and building methods that 'learn', that is, methods that leverage data to improve performance on some set of tasks. It is seen as a part of artificial intelligence. Machine ...

approaches.

Pan-cancer studies

Pan-cancer studies aim to detect the genes whose mutation is conducive to oncogenesis, as well as recurrent genomic events or aberrations between different

tumors A neoplasm () is a type of abnormal and excessive growth of tissue. The process that occurs to form or produce a neoplasm is called neoplasia. The growth of a neoplasm is uncoordinated with that of the normal surrounding tissue, and persists ...

. For these studies, it is necessary to standardize the data between multiple platforms, establishing criteria between different researchers to work on the data and present the results.

Omics The branches of science known informally as omics are various disciplines in biology whose names end in the suffix ''-omics'', such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. Omics aims at the coll ...

data allow the rapid identification and quantification of thousands of molecules in a single experiment.

Genomics Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...

addresses the potential that certain genes will be expressed,

proteomics Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...

addresses what genes are in fact being expressed, and

metabolomics Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprin ...

addresses what has happened in the tissue being studied. The combination of all of them gives information about the biological system.

Resources and databases

The nearly 800 terabytes of data from the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes project have been made available through various portals and repositories, including those at the

Ontario Institute for Cancer Research The Ontario Institute for Cancer Research (OICR) is a not-for-profit organization based in Toronto, Ontario, Canada that focuses on the prevention, early detection, diagnosis and treatment of cancer. OICR intends to make Ontario more effective i ...

, the

European Molecular Biology Laboratory The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 27 member states, two prospect states, and one associate member state. EMBL was created in 1974 a ...

European Bioinformatics Institute The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the We ...

, and the

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. T ...

. All data obtained from the TCGA efforts are available at the US National Cancer Institute's TARGET Data Matrix and the web portal ProteinPaint.

StarBase The concepts of space stations and space habitats feature in science fiction. The difference between the two is that habitats are larger and more complex structures intended as permanent homes for substantial populations (though generation ship ...

pan-cancer resources were created for the networks of long noncoding RNAs,

microRNAs MicroRNA (miRNA) are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides. Found in plants, animals and some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression. miR ...

, competing endogenous RNAs and RBPs.

External links

Nature journals' landing page for the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes project publications

* ttp://starbase.sysu.edu.cn/panCancer.php StarBase ENCORI Pan-Cancer Analysis Platformbr>US National Cancer Institute's TARGET Data MatrixProteinPaint portal

References

{{reflist Cancer research