Genome based studies
Recently, the spread of next generation sequencing (NGS) technology has led to active research on tumor genomes. In addition to the results of The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), a number of genomic data have been produced outside the country, and new attempts have been made in precision medicine based on the results. There are various genome studies such as whole genome sequencing (WGS), whole exome sequencing (WES), whole transcriptome sequencing (WTS), panel sequencing, and epigenome sequencing. There are also various types of equipment used for dielectric analysis, each of which has advantages and disadvantages.
[Benchtop Sequencers] [Production-Scale Sequencers]
To plan genome research, it is important to first clarify the purpose of the genome research and to choose the appropriate method. In addition, it is difficult to extract meaningful research results merely by listing the results of the genome analysis, and since it is necessary to verify the meaning of the genome analysis results by other methods, consideration of the subsequent verification method should be also provided.
Currently, NGS-based panel tests are proceeding in Korea, but pancreato-biliary cancer and liver cancer are not included in the permission items. In order to prove the clinical usefulness of genetic testing, several studies should be supported.

Human-derived tumor sample
Tumors, especially solid tumors, are composed of various cells. Tumor heterogeneity is well-established, and inter-tumor, intra-tumor, sequential, and spatial tumor heterogeneity are interesting and clinically significant in terms of research. However, these problems have a great impact on the interpretation of genome analysis results. Particularly, when the fraction of the tumor carcass in the cell component constituting the tumor mass is very small, much care is required in interpreting the genome results. In this case, it is most important to confirm the fraction of the tumor in the sample before the genome analysis.
In addition, in order to obtain a human-derived tumor sample and conduct research, the IRB approval should be preceded and appropriate procedures should be followed. Patient consent, sample collection and storage, collection and management of data and processing of samples after research should be considered before research.
Sample collection for genome research
Genomic studies include DNA sequencing, genomic analysis, and analysis of various RNA, gene expression and regulation, and detection of progeny gene mutations. The scope of the study is determined by the type of sample, the target substance to be analyzed, and the method of stabilizing and storing the sample for genome testing. The collection, handling and preparation of biological samples is an important step in the research process because the quality and quantity of the sample can affect the reliability and accuracy of the data to be generated. This can affect the interpretation and integration of the data and lead to unreliable results.
Nucleic acid is extracted from tissue-specific nucleic acids (eg, cell-free DNA, circulating tumor cells) extracted from a variety of clinical sample types and matrices (eg, blood cells, tissues, oral mucosa, saliva, bone marrow aspirate, urine, A separate separation method may be required. Some specimens may be used for both DNA and RNA testing, but some specimens may not be suitable for RNA analysis due to unstable types and substrates. Special care should be taken if the sample of the test subject, such as oral epithelial cells or saliva, is at risk of contamination by the DNA or RNA of the microorganism.
The tissue is also fixed for long-term storage sometimes. Parameters to be considered when fixing the tissue include fixation type, fixation time, humidity, and temperature. The type and size of specimen tissue may affect the optimal fixation period and should be considered. The quantity and quality of the extracted nucleic acids are, among other things, influenced by the quality of the initial sample. If you extract both DNA and RNA from the same sample, you should determine if extraction is optimal at the same time or if tissue samples should be split at the time of collection.
Due to the unstable nature of RNA compared to DNA, additional precautions are needed for RNA isolation. Repeated freezing and thawing of the sample prior to nucleic acid extraction may impair the original state of the sample, so if possible, such repeated freezing and thawing should be avoided and, if unavoidable, the effects thereof assessed. Appropriate quality control methods should be applied according to the substance to be evaluated in order to evaluate whether the quality and quantity of the extracted nucleic acid is appropriate for the subsequent genetic test.
PDX (Patient-Derived Xenograft) model 을 이용한 연구
Recently, PDX has been used in research for cancer-specific medical care such as screening of anticancer drugs using PDX. PDX, which transplants the cancer tissue of a patient into a mouse, preserves the blood vessels and substrates contained in the cancer tissue, and reflects the inherent heterogeneity of the cancer tissue of the patient. Therefore, it is expected that the cancer microenvironment implemented in PDX will enable more accurate evaluation of pharmacokinetics and further provide information to predict the clinical environment of the patient. There is also a service that provides such a PDX model, and a researcher himself can make a PDX model and utilize it for research. Since it is relatively expensive and there is a lot of possibility of technical errors in the experiment, it is necessary to examine the process of manufacturing the model. In particular, the problems of tissue change, problems due to tumor diversity, and the generation of lymphoma should be considered.