Release date: 2017-01-05
Genetic testing includes: PCR, FISH, chip technology, gene sequencing. Gene sequencing technology is a type of genetic testing. Gene sequencing currently has one generation of sequencing (Sanger sequencing), second generation sequencing (illumina/Life Tech), and third generation sequencing (single molecule sequencing). PCR, FISH and chip technology, mainly through the known sequence to investigate the presence or absence of a specific sequence or site, focusing on the "detection", while the gene sequencing technology is to nucleotide the gene sequence one by one. Tested out, the focus is on "measurement." The most widely used is the second generation sequencing, namely NGS.
Although there are many opinions in the industry, due to the highest accuracy of gene sequencing, as the cost of gene sequencing declines, the final sequencing technology will replace PCR, FISH and chip technology. But we believe that this view is one-sided. First of all, FISH technology, due to the specificity of the cells in situ, combined with the pathological morphology of cells, has its irreplaceable role. Second, the presence of tumor heterogeneity, many tumor-driven genes, is based on copy number changes, or combined gene mutations and rearrangements. The copy number binding mutation rearrangement changes not only require full exon or even whole genome for deep sequencing. However, there are some clear point mutations and rearrangement and copy number changes. At present, there are many mature technologies that can be easily dealt with. The use of all in one is to look at the application of new technologies in clinical practice. Just like a high-speed rail, there is no need for express trains. And freight trains, with such huge weapons of destruction as nuclear weapons, are as naive as conventional weapons.
Classification of sequencing applications
(1) Non-human genome applications include: scientific research, agricultural applications, environmental pollution monitoring, etc.
(2) Applications related to the human genome and health diseases mainly include: judicial identification, consumer application, and medical application.
At present, medical-grade applications include: reproductive health (NIPT, preimplantation embryo genetic diagnosis), hereditary disease testing, cardiovascular disease, infectious diseases, pharmacogenomics and new drug development, physical examination and disease screening, medical foundation Research, gut microbiota, tumor diagnosis and treatment. Gene sequencing technology for medical grade applications is an important component of precision medicine and a hotspot for the application of gene sequencing technology.
Application status of tumor NGS
According to market estimates, in all of these applications, gene sequencing for humans' largest killer disease, tumors, will account for the highest proportion and market demand. Regarding the size of the domestic tumor sequencing market, a simple calculation can be made. Currently, about 3 million new cancer patients are added each year, and the incidence rate is on the rise. The cost of diagnosis and treatment for each patient is about 100,000, and the total market size is about 300 billion. According to the proportion of medicines, examinations, and clinics in the medical process, the market for gene diagnosis of tumors can reach 10 billion.
The tumor itself is a kind of genetic disease. The genes of tumor cells are constantly changing, the tumor tissues are dynamically changing, and the genomes detected in each period may have changed. At present, relevant knowledge and data are in the process of exploration and During the accumulation phase, continuous clinical practice and research input are still needed.
There are two main types of NGS gene detection for tumors, one is the genomic panel sequencing of solid tumors, and the other is liquid biopsy of peripheral blood and urine. ctDNA is part of a liquid biopsy that also includes detection of CTCs and exosomes.
At present, the top three hospitals in China, such as the Department of Pathology of Union Hospital and the Cancer Hospital of the Academy of Medical Sciences, have been able to independently develop NGS panels for solid tumors or hematological tumors based on their clinical needs and relying on the strong technical strength of their own medical molecular laboratories. And provide professional sequencing testing and professional data interpretation pathology report for clinical treatment.
But as Professor Ying Jianming of the Cancer Hospital of the Chinese Academy of Medical Sciences pointed out, the solid tumor NGS panel is only a measure of the state of a solid tumor at a certain moment. This is very timely and necessary for the medication guidance of newly diagnosed patients. However, if the patient is in the process of initial diagnosis and guidance to track the progress of tumor resistance, the state of the tumor in the body will change over time. In addition, considering some cancer patients who have already metastasized at the time of discovery, if only a certain part of the cancer tissue is taken, it does not reflect the overall condition of the patient; and some postoperative patients who have already implemented a tumor burden reduction, again sample the tissue puncture Not good operation. Therefore, NGS-based liquid biopsy and FISH-based CTC post-testing also have strong clinical needs.
The challenge of tumor NGS
In fact, gene sequencing services are not just what you usually understand, just sequencing. This is just one step. The whole process actually includes: sample processing (extraction, database construction and capture), sequencing on the machine, architecture algorithm and data processing, medical annotation corresponding interpretation and problem solving. In these four steps, in addition to the sequencing of the machine only need to buy lifel technology, illumina and other companies' sequencing instruments directly, there is no professional barrier, the other three steps for medical and computer bioinformatics and genetics professional level requirements Large, more able to show the professional level of a clinical pathology diagnostic laboratory.
In terms of architecture algorithms, although traditional open source algorithms can be imitated, these algorithms are mainly used in scientific research fields, and there is still much room for improvement in accuracy. Therefore, professional bioinformatics teams are required to optimize and improve. The raw data obtained by sequencing from the sequencer needs to be subjected to multiple steps such as genomic alignment and data filtering and screening to obtain variability information on the genome, thereby providing reference for the diagnosis and treatment of the disease. Genetic data analysis and interpretation are also key aspects of gene sequencing services.
Finally, medical annotations and interpretations, and accurate patient genetics, need to be based on the latest clinical medical research progress, medical interpretation of the patient's genetic situation, which puts high demands on the medical interpretation team, need to understand the biological Informatics clinical medical graduate students come to work. Because the current understanding of cancer is still progressing, this part of the work is also somewhat exploratory. In addition to the knowledge of existing knowledge, it also needs some research and analysis ability to discover new mutations and Drug target.
In addition, the accumulation of specimen data, the construction of the database is also very important, which requires the collaboration of the bioinformatics team and the medical interpretation team to complete the hardware and software requirements. Some top-level top three hospitals have their own databases and are constantly collecting data, but clinical data between hospitals cannot be shared. The lack of clinical data, pathological diagnosis and post-sequence data of the gene database can not play the value of the application. We can only hope that the hospital's database can quickly realize the accumulation of genetic diseases data of the Chinese people and serve the Chinese people with the support of national policies and funds.
Source: Pathology Lancet (Micro Signal Patholancet)
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