How does genetic testing help patients fight disease?

Introduction: High-performance computing EHPC on the cloud helps Shengting Medical to improve the efficiency of genetic testing and provide more precise medical solutions for patients.

Why do other people still lose weight when they eat Haisai, and I get fat when I drink water?

Why am I so unfortunate that disease finds me? I knew I wouldn't drink alcohol.

Why is it the same disease, other people take this medicine and it works, but it doesn't work for me?

From day-to-day health management, disease prevention, and even the most effective medical plan for severe illness, it is all related to genes. In the traceability and drug development of the new crown epidemic, the sequencing of the whole virus genome also plays an important role.

However, the human exploration of genes is a long and arduous journey. The "Human Genome Project", known as the "Moonshot Project" in the field of life sciences, was launched in 1990 and planned to determine the 3 billion base pairs that make up the human chromosome. After the efforts of more than 2,000 scientists from six countries and a cost of 3 billion US dollars, the map of the human genome was finally drawn in 2003.

With the development of technology, the cost of gene sequencing is falling rapidly. With the emergence of second- and third-generation high-throughput sequencing technologies, the cost of human whole genome sequencing has gradually decreased from US$10 million to US$1,000 in the past decade or so.

This has made many scholars in the field of life sciences see the possibility of applying gene sequencing technology to the clinic, and hope to bring new hope to people suffering from diseases with what they have learned.

Dr. Gu Hongcang is also a scholar with such a vision .

01 From birth to WTO entry, fighting cancer with gene sequencing

Back in 2013, Dr. Gu Hongcang was working at The Broad Institute of Harvard and MIT. The Broad Institute is the world's top team in biogenetics, founded by genomics leader Eric S. Lander. Dr. Lander is one of the initiators and main executors of the "Moon Landing Program" mentioned above.

Being in such a team, there is no shortage of opportunities to publish papers in top journals such as "Nature" and "Cell" every year, which is the dream of countless scholars. The only fly in the ointment is that basic science mainly focuses on theoretical exploration, with little clinical demonstration . Dr. Gu also hopes to do something for the development of human health, and thinks about turning to clinical research.

Dr. Gu Hongcang

Coinciding with the following year, Tu Yongjun, the chairman of Zhejiang Tianyu Pharmaceutical Co., Ltd. (stock code: 300702. SZ.), found Dr. Gu Hongcang and invited Dr. Gu to join and lead his newly invested and established gene sequencing experimental company--Zhejiang Shengting Biotechnology Co., Ltd. At that time, China's domestic gene sequencing industry was also surging, and the pattern was beginning to take shape. Companies such as BGI, BERRYGENOMICS, and ANNOROAD are racing to the field of non-invasive prenatal genetic testing.

Faced with this choice, Gu Hongcang agreed to serve as a consultant for Shengting for two years, and finally decided to return to China after Chairman Tu Yongjun’s “three visits” to lead the laboratory as the founder and chief scientist of Shengting. At the same time, he made a major decision for himself and for the Holy Court: transformation.

At the beginning of its establishment, Shengting Bio mainly served basic scientific research and provided sequencing services and technical guidance for scientific research institutes. After the transformation, Sanctuary will target tumor patients, perform precise gene sequencing and professional interpretation of results, and provide personalized treatment for cancer patients. Improving the quality of life of patients and prolonging their life cycle is more in line with Dr. Gu's original intention and his judgment on the industry .

You may be wondering, how important is genetic sequencing to patients?

Even with the same type of cancer, different patients may have different driver gene mutations, and different mutations may cause some drugs to be effective in some patients but not in other patients. The targeted drug in the movie "I am the God of Medicine" is a typical example. How to find your own special medicine? Without genetic sequencing, patients in need of chemotherapy would have to keep trying different drugs. Apple founder Steve Jobs spent $100,000 on genetic sequencing to guide personalized treatment in exchange for 10 years of life.

The Holy Court wants to bring this technology to more patients .

02 Rapid development after transformation, facing the pressure of growth

In 2017, Shengtian Bio was changed to "Shengyuan Medical" and began to transform.

Shengting Medical Hangzhou Laboratory

For clinical gene sequencing, the American Board of Medical Genetics and Genomics (ABMGG) has set up the Laboratory Genetics and Genomics project, which regulates gene sequencing from sample acquisition, processing, The whole process from detection, analysis to report issuance, in order to train qualified clinical medical genetic laboratory directors. Only about 50 students are admitted to the subject each year in the United States. "The domestic genetics is still blank, and similar disciplines will not be established until 2021."

In order to make Sun Court’s gene sequencing at an international leading level, Dr. Gu spent two years in the United States, participating in this project full-time, while training colleagues from Sun Court, and eventually led Sun Court to obtain the American Pathology Program. The College of American Pathologists (CAP) accreditation means that the inspection reports issued will have global comparability and mutual recognition, marking that the laboratory capacity has reached international standards.

Since then, Shengdi Medical has also ushered in a period of rapid development. The business has developed from early tumor gene detection to pathogen detection based on nanopore sequencing technology and genetic examination of mental and chronic diseases. The team has grown from more than 20 people to more than 200 people, and gradually opened medical testing centers and laboratories in Beijing, Hangzhou, Taizhou, Changsha, and Guangzhou; the number of samples exposed and the volume of business received are also growing rapidly.

A large number of patients have been tortured by the disease for a long time. Finally, through gene sequencing technology, the disease-causing gene mutation or pathogen has been identified, and the symptomatic drug has been found, and the condition has been greatly relieved . For example, Sheng court cancer friend Li Ming (pseudonym) is a patient with advanced lung cancer, complicated by bone metastasis and lymphatic metastasis. The doctor once estimated that the survival time is less than half a year. It has been four years since I took the first targeted drug, and it is breaking through five years. During this period, Li Ming went through four genetic tests in the Holy Court, found a way to cure him again and again, and gained a new life.

With the correct strategy and development strategy, the Holy Court has also helped more and more patients. However, the fast-growing Holy Court also encountered growing pains: the development of infrastructure could not keep up with the development of business.

After sample preparation and on-machine sequencing, high-throughput gene sequencing will generate huge gene sequence data and involve massive data storage, calculation and transmission, which has extremely high requirements on the underlying infrastructure . The original IDC computer room has been unable to keep up with the rapidly developing Holy Court.

The Holy Court needs to change again.

(Click the picture to enlarge it)

03 Cloud high-performance computing EHPC improves sequencing efficiency

The massive data generated by gene sequencing basically does not leave the cloud. In the past, the Broad Institute, where Gu Hongcang is located, generated 20T of data every day as early as 10 years ago, ranking second among institutions in the United States, and chose cloud computing very early. At the earliest, because of the lack of data and the lack of timeliness of colleges and universities, Shengting also chose to build a self-built Internet Data Center (IDC) computer room according to industry inertia.

Self-built IDC computer room is naturally not an easy task for bio-informatics scientists, and they can only bite the bullet and "self-taught".

The experience of Huang Yun, the head of Shengting IT, seems to be the epitome of the industry. In order to build the company's IDC computer room, "Which decoration company should I find, how much power does the power system need, how many watts, the thickness of the wires, how much UPS should be equipped, and how to make sound insulation? Cluster architecture, what storage technology is used for storage technology, and what is used for cluster scheduling software... From decoration, deployment, implementation to operation and maintenance, use, all are self-learning . This is what the industry has experienced, and the positions are not so subdivided."

Huang Yun revealed that the life science industry has developed rapidly in recent years, and researchers are all multi-taskers, and there are no dedicated operation and maintenance personnel. This method not only has potential data security risks , but once a fire, flood or disk damage occurs in the computer room, it means data loss. With the development of the business, the increase in operation and maintenance costs is also unsustainable.

In recent years, the business volume of Sun Court has grown rapidly. With the increase of data volume, the required servers are increasing day by day, and the operation and maintenance cost is also rising. Gu Hongcang recalled: "The students in charge of the IT team have to go to Taizhou for maintenance every week. The monthly electricity bill is as high as tens of thousands, and there will be a power shortage in 2021." He saw all these.

More importantly, computational efficiency affects the patient experience . The test report provided by the laboratory to cancer patients generally promises to issue the report within 7 days. The transportation of the sample takes a lot of time, and the time is urgent. With the increase of business volume, the computing power of the IDC computer room cannot meet the requirements, and a large number of sequencing files need to be queued, which brings a lot of pressure to the sequencing staff and affects the patient's experience.

Shengting's tumor detection business, the laboratory is in Taizhou, the samples need to be tested in Taizhou, and the analysts are in Hangzhou. After the genetic data is calculated, it needs to be transmitted from Taizhou to Hangzhou for analysis. Later, with the emergence of laboratories in Beijing, Guangzhou and other places, the data transmission efficiency and security risks have increased.

A relative of the founding team of Shengting, who happens to be a cloud computing practitioner, after hearing about a series of troubles faced by Shengting, such as operation and maintenance, computing, storage, transmission, etc., found that cloud computing can be perfectly solved, and recommended them to use it. Ali Cloud. It can be said that the two sides meet each other late, and it is imperative to go to the cloud in the holy court.

In 2021, Shengting Medical decided to fully move its business to Alibaba Cloud .

After going to the cloud, Shengting performed gene comparison through Alibaba Cloud Elastic High Performance Computing (EHPC), and the computing efficiency has been greatly improved . Huang Yun still remembers that at most 5 batches of data have been sent in one day recently. If you don't have access to Alibaba Cloud, it may take several days to analyze the data in the self-built computer room. The last batch of data will take three days to queue up.

But after going to the cloud, you don't need to worry about this problem. The elasticity of the cloud allows the Holy Court to "pop up" computing power at any time directly according to the amount of data , and can create different queues of computing power based on the HPC scheduling system at any time, and make Resource isolation to flexibly respond to resource requirements and concurrency in different business scenarios. Originally, it took 10 hours to analyze a batch of samples, but it only took 3 hours after going to the cloud. The computing efficiency was improved by 70% , and reports could be quickly issued to patients.

The feature of cloud free operation and maintenance has greatly reduced the pressure of operation and maintenance of Shengting, focusing on core business . Alibaba Cloud's high-performance data center is operated and maintained by professionals, which eliminates the trouble of high operation and maintenance costs of Sheng Court; at the same time, the data on Alibaba Cloud has always adopted the mechanism of multi-copy disaster recovery, with a reliability of up to 10 9s, ensuring data security. Guarantee; Alibaba Cloud's data centers across the country can also ensure the efficiency of data transmission and facilitate efficient collaboration within the Holy Court.

Today, Sundwell Medical, which is lightly loaded, is also exploring more fields to provide patients with more precision medical solutions.

The three types of IVD products "Human Genome Methylation Detection Kit" based on patented technology have entered the clinical trial stage. In the field of infection, based on the dual platform of second-generation sequencing and third-generation nanopore sequencing, the "Sikeyu" series of infection precision diagnosis products have been developed, and the first domestic high-throughput sequencing technology-based product specifically for the identification and resistance of mycobacteria has been successfully launched. Pharmacogenetic testing products.

Looking forward to the future, it is hoped that with the common development of cloud computing and the life science industry, human beings can continue to "decipher" genes to prevent, treat and even eliminate diseases.

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