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Cheatography

lncRNA, Somatic Mutations & Gene Fusion in Cancer Cheat Sheet (DRAFT) by

This is a draft cheat sheet. It is a work in progress and is not finished yet.

lncRNA in Cancer

Key Facts on long non-coding RNA

Non-pr­otein coding RNA molecules >200nt in length
Can be oncogenic or tumor-­sup­pre­ssive by either inhibiting growth suppre­ssors or targeting growth promoters
Can be upregu­lated or downre­gulated in cancer - Majority are upregu­lated due to their low expression under normal conditions
Exhibit a high degree of tissue- and diseas­e-s­pec­ifi­city, making them an ideal candidate for cancer diagnosis and prognosis. Often expressed in a spatial, temporal, and tissue­-sp­ecific pattern

lncRNA Biomarkers

Important lncRNA Biomarkers in Cancer

Prostate Cancer:
PCA3, SChLAP1, PCGEM1, PCAT1, DLEU1, PCAT14
Breast Cancer:
HOTAIR, MALAT1, H19, XIST, NEAT1, ZFAS1, LINK-A
Lung Cancer:
MALAT1, NEAT1, UCA1, HOTAIR,

circRNA in Cancer

CircRNAs are a novel type of RNAs. Over 30,000 circRNAs have already been found. Owing to their unique structure, they are more stable than linear RNAs. CircRNAs play important roles in the carcin­oge­nesis of cancer. Similar as splice variants they can be detected with BaseScope.
 

Somatic Mutations

Identi­fic­ation of somatic mutati­ons in tumors is becoming increa­singly important for patient selection for targeted therapies.
High-t­hro­ughput sequencing (RNAseq) techno­logies allow for compre­hensive mutati­on-­pro­filing, however:
- Do not permit assessment of intr­atu­moral hetero­gen­eity or the associ­ation of genetic altera­tions with cellular morphology
- DNA mutational status does not predict expression of the mutant allele, which may provide inform­ation connecting genotype to phenotype
Solu­tion: Detection of point mutations by Basescope is currently available only through ACD’s pharma assay services.
Exam­ple: BRAF V600E data

Intert­umour and Intrat­umour hetero­geneity

Gene Fusions

Tradit­ion­ally, gene fusion events are detected by DNA fluore­scent in situ hybrid­ization (DNA FISH) methods. However, these can be laborious with complex workflows (2 days assay) and do not provide inform­ation on the transc­rip­tional activity of the fused genes.
BaseScope provides an altern­ative chromo­genic method for the detection of specific junc­tional sequen­ces created by gene fusions because it can provide single cell level detection of fusion transc­ripts with specific cell locali­zat­ion. Furthe­rmore, this assay can easily be performed in histology labs on routinely available FFPE samples, and results can be obtained rapidly since the assay can be performed in one day and reviewed under the light micros­cope.
Exam­ple: The CRTC­1-MAML2 fusion oncogene is typically associated with low-grade tumors and may signify a favorable prognosis in cases of mucoep­ide­rmoid carcinomas (MEC) - data available
   

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