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OncoMap in tumor analysis refers to what, in response to this question, this article details the corresponding analysis and solution, hoping to help more small partners who want to solve this problem find a simpler and easier way.

When browsing the data in CCLE, I saw the following mutation detection result file

What exactly is Oncomap here? After querying a lot of results, OncoMap is actually a tumor somatic mutation detection platform, which was first developed by Laura E. MacConaill et al. proposed that the related article title is as follows

Profiling Critical Cancer Gene Mutations in Clinical

Tumor Samples

The article links to the following

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774511/pdf/PCD63A109.pdf

At that time, NGS technology had not been applied to the field of mutation detection on a large scale, and there were no mature somatic mutation detection algorithms, basically identifying and analyzing somatic mutations on a certain gene. In order to better carry out the study of somatic mutation in tumor cells, the author proposes a method to detect mutation profile of tumor samples. The schematic diagram is as follows

It is divided into the following steps

DNA was extracted from fresh frozen or paraffin-embedded tumor tissue and mass spectra were obtained by mass spectrometry

Based on the mass spectrum, the algorithm automatically identifies the typing results of mutation sites

Manual calibration to obtain highly reliable mutation spectrum

At its core, the chip was designed based on known mutation sites. In the original version, the v1 version, it contained 460 mutation sites from 33 tumor genes. This technology was called oncomap. It was a high-throughput typing technology at that time. Many articles used this technology to study mutations in tumors, such as the following article.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5266405/

OncoMap has been continuously improved since its invention. It has been upgraded to v4 version. The typing results in CCCLE database are based on v3. The contents of CCLE_Oncomap3_Assays_2012-04-09.csv file are as follows

There are many columns, only part of them are truncated here, each row represents a mutation site, the direction of the second column represents the direction of the chip detection site and the mutation site, F represents the same direction of the two sites, located on the same strand, R represents the opposite direction of the two sites, located on the reverse complementary strand, and other columns record the gene, transcript, protein and other information corresponding to the mutation site. Oncomap can be thought of as a panel designed for known mutation sites, similar to chips.

About OncoMap in tumor analysis refers to what the answer to the question is shared here, I hope the above content can be of some help to everyone, if you still have a lot of doubts not solved, you can pay attention to the industry information channel to learn more related knowledge.

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