华盛顿大学医学院Bevan Tendon 医生关于基因检测的观点，希望对大家有用。
With ngs, the issue is that the test produces lots of information but you need a good physician with clinical experience and understanding to figure out the significance in clinical terms what the sequence variants mean for the patient and their disease.
Bevan
I don't know too much about Chinese lab. certainly there are others here in us, but washU is world leader for cancer sequencing. The first human cancer genome was fully sequenced at this institution for a patient with acute myeloid leukemia and GPS division here has experience processing approx 2000 cases for clinical ngs and cancer testing. It will test 49 genes with potential established therapeutic targets in the literature. Some companies here like foundation clinical medicine offer up to 250 genes but many other genes do not have clear cut clinical significance
Rate of identification of cancer specific therapeutic target is less than 50%. Probably lower. In lung cancer most common targets are egfr or alk mutations which have specific drugs. Stomach and liver cancer I will have to check. Everyone here is very excited about this technology. However, it is important to have realistic expectations about the potential yield. I will let you know liver and stomach cancer ngs let me research a little
Majority of patients I review are colon, lung, head and neck cancer
Also ngs testing can be done for all cancer types not just blood cancer leukemia
Other gene testing is prohibitively expensive to test multiple genes at same time. Conventional single gene sequencing prior to ngs was Sanger Sequencing and can cost up to several thousand dollars for just 1 gene. Clinical ngs is revolutionizing personalized medicine. If there can be a pipeline of patients from China and I had a lab of my own this could be very good business. Trust could be built up in first phase by sending to washU where I will have my name on the reports because I am generating the clinical report.
Will
what is the difference of next generation sequencing and other gene test?
Bevan
Hello, next generation sequencing is a major part of my job currently. I interpret the data and generate the report. The laboratory takes the patient material and extracts the DNA and runs it through the sequencer. The patients in China should have access to their ffpe blocks and slides. After surgery for either excision or other biopsy the tissue is usually processed and made into the blocks which are then cut very thin and sections are mounted into a glass slide and reviewed under microscope by a pathologist. Hope that answers your questions.
We would need his formalin fixed paraffin block biopsy from his cancer. The patient should be able to obtain this material and have it shipped over.
We get testing requests for therapeutic target identification using next generation sequencing from international patients. Last month one of the doctors brother who lives in Germany had his brain biopsy material sent over and I interpreted his testing and we identified an antitumor target for his brain cancer
http://gps.wustl.edu/cancer
????,????????????,?????22?,they went to mayo clinic in US in December this year ,conclusion is it can not be treated,they want to try targeting antitumor drugs,and all other possible treatment, any suggestion?
Bevan
Precise data for frequency of mutations that are clinically relevant is difficult to get from companies because they will always inflate the number for marketing purposes. Even at washU my experience had been only 10 percent of ngs cases yield useful clinical information
With ngs the issue is that the test produces lots of information but you need a good physician with clinical experience and understanding to figure out the significance in clinical terms what the sequence variants mean for the patient and their disease.
Will
this is the brochure from BGI , the major chinese player.i did a little research, there are many small agencies doing gene tests too, mostly for parent children identification, prenatal screening, also child talent gene tests, etc. serious testing are BGI and one lab from souel univ. korea. BGI says i will tests 508 genes.
Here in America company called clinical foundation medicine does over 200 genes. WashU does 151 but only 49 have been determined to be best for clinical report. Many genes lack clinical associations in specific diseases and for personalized medicine the number of genes for drug targets is still low overall. There are multiple technologies for gene sequencing but hybrid capture for targeted panel analysis is probably what bgi is doing for 500 genes
For marketing people might think more is better but when you generate data for genes that lack clear clinical association it becomes frustrating because then you don't know what conclusion to make
Also when you do more focused testing not only does that streamline interpretation to focus on genes that may have clinical association there is another major benefit
You can perform more sequencing where you sequence the same gene hundreds or thousands of times (you increase the "coverage depth"). This enhances sensitivity significantly and improves rate of detection for potential disease related mutations in the targeted genes
I don't know what coverage depth is in the bgi panel targeting 500 genes but that would be an important point of difference. There is very precise data available to demonstrate mutation detection rate based on sequencing experiments on known gold standard specimens. WashU has approximately 99% sensitivity and specificity for the clinically reported genes which is a very important point to consider when comparing platforms and different tests
In general when you widen The target capture space and increase number of genes then the coverage depth is reduced for each individual gene
But that is rule of thumb
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