How can genetic testing help patients fight disease?

brief introduction ： High performance computing on the cloud EHPC Help Shengting medical to improve the efficiency of gene testing , Provide patients with more accurate medical solutions .

Why do other people still become thin after eating haisai , I get fat when I drink water ？

Why am I so unlucky , Illness will find me ？ If I had known, I would have stopped drinking .

Why is it the same disease , It is useful for others to take this medicine , It's useless for me to eat ？

 

From daily health management 、 Disease prevention , Even the most effective medical plan in case of severe illness , It's all about genes . In tracing the source of COVID-19 and drug research and development , Sequencing the whole genome of the virus , It also plays an important role .

 

However , It is a long and arduous journey for human beings to explore genes . Known as the field of life science “ Mission to the moon ” Of “ Human genome project ” On 1990 Launched in , Plan to determine the composition of the human chromosome 30 Billion base pairs . After six countries 2000 Many scientists worked hard , At a cost of 30 Billion dollars , Finally in the 2003 Complete the mapping of the human genome .

With the development of technology , The cost of gene sequencing is rapidly decreasing . With the second generation 、 The emergence of the third generation of high-throughput sequencing technology , The cost of human genome sequencing has gradually decreased from US $10 million to US $1000 in the past decade .

 

This makes many scholars in the field of life sciences see the possibility of applying gene sequencing technology to clinical practice , And hope to learn by yourself , Bring new hope to those who suffer from diseases .

 

Dr. tanhongcang is also a scholar with such a vision .

01 From birth to entry , Fight cancer with gene sequencing

go back to 2013 year , Dr. tanhongcang is at Harvard University - MIT bode Institute (The Broad Institute of Harvard and MIT) To serve . Bode Institute is the world's top team in biogenetics , By the head of genomics Eric S. Lander found .Lander Doctor is mentioned earlier “ Mission to the moon ” One of the initiators and main executors of .

 

In such a team , Every year there is no shortage of 《Nature》 and 《Cell》 And other top journals , It has been the dream of countless scholars . The only drawback is , Basic science mainly focuses on theoretical exploration , Few clinical demonstrations , Dr. Gu also hopes to do something for the development of human health , Thinking about turning to clinical research .

Dr. tanhongcang

 

It coincides with the following year , Zhejiang Tianyu Pharmaceutical Co., Ltd （ Stock code ：300702. SZ.） Tuyongjun, chairman of the board of directors of , I found Dr. Gu Hongcang , Dr. Gu is invited to join and lead the newly invested gene sequencing experimental company -- Zhejiang Shengting Biotechnology Co., Ltd . At the time , China's domestic gene sequencing industry is also surging , The pattern is beginning to form . genomics （BGI）、 Berry and Kang （BERRYGENOMICS）、 Anouda （ANNOROAD） And other enterprises in the field of non-invasive prenatal gene testing .

 

Face this choice , Gu Hongcang promised to serve as a consultant in Shengting for two years , At last, the chairman of Tu Yongjun's “ to call on sb. repeatedly ” after , Decided to go back to , As the founder and chief scientist of the holy court , Lead this laboratory . meanwhile , He is for himself , Also made a major decision for the holy court ： The transformation of .

 

At the beginning of its establishment, Shengting biology mainly served for basic scientific research , Provide sequencing services and technical guidance for scientific research institutes . After transformation , The holy court will face patients with tumors , Carry out accurate gene sequencing and professional interpretation of the results , Provide personalized treatment for cancer patients . Improve patients' quality of life and extend their life cycle , This is more in line with Dr. Gu's original intention , It is also more in line with his judgment on the industry .

 

You may wonder , How important is the significance of gene sequencing to patients ？

 

Even if you have the same kind of cancer , Different patients may have different driving gene mutations , The mutation is different , Will cause some drugs to be effective for a patient , It has no effect on other patients . The movie 《 I am the God of medicine 》 The targeted drug in is a typical example . How to find your own special medicine ？ Not through gene sequencing , Patients who need chemotherapy can only keep trying different drugs . Apple founder Steve Jobs spent 10 Million dollars for gene sequencing , Guide personalized therapy , in return 10 Life expectancy .

 

Shengting wants to extend this technology to more patients .

02 Rapid development after transformation , Facing the pressure of growth

2017 year , The holy chamber creature is changed to “ Holy court Medical ”, Start transforming .

 

Shengting medical Hangzhou laboratory

 

For clinical gene sequencing , American Committee of medical genetic experts (American Board of Medical Genetics and Genomics, ABMGG) Laboratory genetics and genomics （ Laboratory Genetics and Genomics） project , It standardizes the acquisition of samples from gene sequencing 、 Handle 、 testing 、 The whole process from analysis to report issuance , To train qualified clinical medical genetic laboratory directors . Only about... Students are admitted to this subject in the United States every year 50 people .“ Domestic genetics is still blank , until 2021 The establishment of a similar discipline began in ”.

 

In order to make the gene sequencing of Shengting reach the international leading level , Dr. Gu spent two years in the United States , Full time Full-time participated in this project , At the same time, we learn and train our colleagues in the holy court , Eventually led the holy court to win the American Society of pathologists （College of American Pathologists, CAP） Qualification , It means that the inspection report issued will be globally comparable and mutually recognized , It marks that the laboratory capacity has reached international standards .

 

Since then, Shengting medical has also ushered in a period of rapid development . The business consists of early tumor gene detection , It has developed into pathogen detection based on nanopore sequencing technology and gene examination of mental diseases and chronic diseases . The team changed from the original 20 Many people have developed 200 Many people , Gradually in Beijing 、 Hangzhou 、 Taizhou 、 Changsha 、 Guangzhou has set up medical testing centers and laboratories ; The number of samples contacted and business received are also growing rapidly .

 

A large number of patients have been suffering from illness for a long time , Finally through gene sequencing technology , Find out the gene mutation or pathogen causing the disease , Found the right medicine , The condition has been greatly relieved . such as , Shengting Cancer friend Li Ming ( alias ) Is a patient with advanced lung cancer , Complicated with bone metastasis 、 Lymphatic metastasis , The doctor once estimated that the survival time would be less than half a year . Start with the first targeted drug , It has been four years now , It is breaking through five years . And in the meantime , Li Ming has undergone four genetic tests in Shengting , Time and time again to find a cure , Get a new lease of life .

 

Under the right strategy and development strategy , The holy court has also helped more and more patients . However , The rapid development of Shengting has also encountered growing pains ： The development of infrastructure cannot keep up with the development of business .

 

High throughput gene sequencing goes through sample preparation 、 After sequencing on the computer , Will generate huge amounts of gene sequence data , And involves massive data storage 、 Computing and transmission , This has very high requirements for the underlying infrastructure . The original IDC Computer room , Has been unable to keep up with the rapid development of the holy court .

 

The holy court needs to change again .

（ Click on the picture to enlarge it ）

03 High performance computing on the cloud EHPC Improve sequencing efficiency

 

Massive amounts of data generated by gene sequencing , Basically, they don't leave the cloud . Once upon a time , Bode research institute where guhongcang is located , As early as 10 Years ago, there were data generated every day 20T, Ranked second in the United States , I chose cloud computing very early . And the holy court was the first one because of less data , Colleges and universities do not have strong requirements for timeliness , It also chose to build its own Internet data center according to the inertia of the industry （Internet Data Center,IDC） Computer room .

 

build by oneself IDC The computer room is not an easy task for scientists of bioscience , You have to be tough “ Self taught ”.

 

Holy court IT The experience of Huang Yun, the person in charge, seems to be a microcosm of the industry , To build the company's IDC Computer room ,“ Which decoration company to look for , How much power does the power system need , How many watts 、 The thickness of the wire 、UPS How much do you want , How to make sound insulation , Cluster architecture 、 Storage technology what storage technology , What does the cluster scheduling software use …… From decoration 、 Deploy 、 Implementation to operation and maintenance 、 Use , They are all self-taught . The industry has experienced this , Posts are not so segmented ”.

 

Huang Yun revealed , The life science industry has developed rapidly in recent years , Researchers have multiple roles , There are no special operation and maintenance personnel . This approach has not only the potential Data security risks , In case of fire in the machine room 、 Flood or disk damage means data loss , As the business grows , O & M costs The increase in the number of .

 

The business volume of Shengting has grown rapidly in recent years , As the amount of data increases , The number of servers needed is growing , Operation and maintenance costs are also rising . Gu Hongcang remembers ：“ be responsible for IT Students from the team , Go to Taizhou every week for maintenance . The monthly electricity bill is as high as tens of thousands ,2021 There was also a power shortage in .” He saw all this .

 

what's more , Computational efficiency affects the patient's experience . Laboratory test reports for cancer patients , General commitments 7 Heaven reports , It takes a lot of time to transport the samples , Time is running out . With the increase of business volume ,IDC The computing power of the computer room is difficult to meet the requirements , A large number of sequencing files need to be queued , Time puts a lot of pressure on sequencers , It can also affect the patient's experience .

 

The cancer detection business of Shengting , The laboratory is in Taizhou , Samples need to be tested in Taizhou , The analysts are in Hangzhou . After gene data calculation , It needs to be transferred from Taizhou to Hangzhou for analysis , Later, with Beijing 、 Laboratories in Guangzhou and other places have appeared , Data transmission efficiency and security risks are rising .

 

A family member and friend of the founding team of the holy court , It happens to be a cloud computing practitioner , I heard about the operation and maintenance faced by the holy court 、 Calculation 、 Storage 、 After a series of troubles such as transmission , Found that cloud computing can perfectly solve , They are recommended to use Alibaba cloud . The two sides can say that it was too late for each other , It is imperative for the holy court to raise the cloud .

 

2021 year , Shengting medical decided to move its business to Alibaba cloud .

 

After the cloud , Shengting uses Alibaba cloud elastic high-performance computing EHPC Make a genetic comparison , The efficiency of computing has been greatly improved . Huang Yun still remembers , At most one day recently 5 Batch data , If you don't go to Alibaba cloud , Using the self built computer room may take several days to analyze , It will take three days to queue up for the last batch of data .

 

But after the cloud , There is no need to worry about this problem , The elasticity of the cloud allows santing to directly adjust the data volume at any time “ eject ” Calculate the force , And can be based on at any time HPC The scheduling system creates the specifications of different queues , And make resource isolation , To flexibly meet the resource requirements and concurrency of different business scenarios . The original analysis of a batch of samples requires 10 Hours , After going to the cloud, you just need 3 Hours , Computing efficiency is improved 70%, Be able to report to patients quickly .

 

The cloud free operation and maintenance feature greatly reduces the operation and maintenance pressure of Shengting , Focus on the core business . Alibaba cloud's high-performance data center has professional operation and maintenance personnel , The trouble of high operation and maintenance cost of Shengting has been eliminated ; meanwhile , The data on Alibaba cloud always adopts the multi copy disaster recovery mechanism , Reliability up to 10 individual 9, Data security is guaranteed ; Alibaba cloud's data centers all over the country can also ensure data transmission efficiency , Facilitate efficient collaboration within the holy court .

 

Now , The light - packed holy court medical is also exploring more fields , Provide patients with more accurate medical solutions .

 

The three categories of Shengting based on patented technology IVD product " Human genome methylation test kit " It has entered the clinical trial stage . In the field of infection , Based on the two platforms of second generation sequencing and third generation nanopore sequencing “ Thinking can heal ” A series of precise infection diagnosis products , And successfully launched the first domestic product based on high-throughput sequencing technology for Mycobacterium identification and drug resistance gene detection .

 

Looking forward to the future , I hope that with the common development of cloud computing and life science industry , Human beings can constantly “ Decrypt ” gene , The prevention of 、 Cure or even eliminate diseases .

Click on here , See more industry practices in the field of Life Sciences .

Link to the original text ：https://developer.aliyun.com/article/976196?

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