Hardware sequencing of genetic sequencing

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Editor’s note: This article comes from the “Interface News” technology channel, author Lin Teng, 36 氪 authorized to release.In 1986, an American biologist named Durbeco shocked the medical community.He published an article entitled “The Turning Point of Cancer Research – Full Sequence Analysis of the Human Genome”, which first proposed a new idea for studying cancer from a genetic perspective and conquering cancer.Around the 20th century, curious humans have carried out two major scientific projects on the road of exploring the unknown, one of which is called the “Manhattan Atomic Bomb Project” and the other is the well-known “Apollo Moon Landing Plan”.In the paper published in Durbeco for the past four years, the National Institutes of Health and the Department of Energy announced the third human science project: the Human Genome Project.This program will determine the nucleotide sequence contained in the human chromosomes, thereby mapping the human genome, and finally achieving the ultimate goal of deciphering human genetic information.Unlike the atomic bomb and the moon landing program, the Human Genome Project is a transnational science interdisciplinary project, because human races are diverse and global, and cannot be accomplished by the United States alone.Britain, Japan, France, Germany and other countries have joined.In the United States, a young man named Jay Flatly became a member of the Human Genome Project.Eight years later, he was recruited by a genetic company that had just been financed.Today, the company is already the world’s largest marketplace manufacturer of genetic sequencers.The company’s name is Illumina, and the executive chairman of the company’s board of directors is Flatley.Also in the 1990s, a Chinese researcher who was one year younger than Fletley jumped out of the Human Genome Project. Together with several Chinese scientists, he represented China in 1% of the Human Genome Project.Sequencing and analysis of approximately 30 cM regions on the short arm side of human chromosome 3.China has also become the sixth and final participating country of the Human Genome Project and the only developing country.The researcher is called Wang Jian. At the same time as Illumina, Wang Jian and others established the first genetic company in China, Huada Gene (hereinafter referred to as Huada Group) in 1999.In April 2016, Shenzhen Huada Zhizhi, a subsidiary of Huada’s sequencing equipment business, was established, and the latter has become a star company in the field of sequencers.Twenty years after the completion of the Human Genome Project, both Huada and Illumina stood on the top of the technology and business in the genetics field.One is considered to be “Tencent in the genetics world” in China, and the other is the hegemon of the genetic field for a long time.But Fletley and Wang Jian may have never thought that the two scientists who have joined forces to make a contribution to revealing the mystery of life will meet in a few years.In the three months of 2019, the two companies have had more than five confrontations in the patent war.From April to June, Illumina first filed a patent lawsuit against Huada Zhi in Germany and Denmark.In May, Huada Zhizao sued Illumina for patent infringement in the United States.Earlier, the two companies had already carried out intense “horse racing” in the field of genetic sequencers.In October 2018, Huada Zhizao released the self-developed ultra-high-throughput gene sequencer, “DNBSEQ-T7” (product name MGISEQ-T7 at the time of publication).This is a “super life computer” with a daily output of 6Tb, which is considered to be the most powerful genetic sequencer in the world.On the other hand, at the end of 2018, Illumina spent $1.2 billion to acquire PacBio. In addition, Illumina’s MiSeqTMDx gene sequencer was approved by the State Drug Administration.This is the first technical confrontation between the two companies in the field of genetic sequencing equipment.The champion and runner-up in the field of genetic sequencers is setting off one of the fiercest technical battles ever.The fifteen years of the sequencer’s past “get on the moon and cure cancer. Which one do you think is easier to achieve?” In a poll of the American media in the last century, most people who were asked this question would answer that cancer may be cured and boarded.The moon is impossible.However, to this day, the Apollo spacecraft has been on the moon for 50 years, and humans are still struggling to cure cancer.Today, one of the main consensuses of cancer in the biomedical community is that cancer is a type of genetic disease, and almost all cancers are caused by genetic changes (mutations).It can be said that the first step for humans to overcome cancer is to decipher the gene sequence.But at the beginning of this century, the first individual genome-wide sequencing took 13 years and cost $3 billion to be completed. This is also the main reason why genetic technology is difficult to break through and popularize.Cost, speed and quality are the three key points in the field of gene sequencing.By doing the above three things, it is possible to obtain enough genetic data to build a huge database and further explore the exact meaning of the variation of a certain gene.In other words, the secret of cancer, the secret of human life and death, the secret of the growth of all things are controlled by the genetic code of life – the genome, but to obtain these data with higher quality, faster and lower cost, to realize recognition of life.The core tool needed to know and control is the genetic sequencer.A medical researcher said that only the sequencer continues to iterate to drive down the cost of sequencing, and the entire genetic technology industry is likely to enter the public health field and have a business prospect.A researcher in the field of genetics told the interface journalist: Because the manufacture of sequencers requires the integration of many cutting-edge disciplines such as light, machine, electricity, liquid, biochemistry, chips, algorithms, etc., and needs long-term running-in.Therefore, the technical barriers of gene sequencers are extremely high.In the 15 years since the beginning of the Human Genome Project, a large number of companies have been involved in the manufacture of sequencers. In the process of technological and commercial changes, these companies have also experienced ups and downs, disappearances, and competition.The original market leader was Applied Biosystems (ABI), which designed the first automated flat panel fluorescence sequencer in the mid-1980s to help life sciences enter the era of automated sequencing.But not long after, its leading position was shaken.Another wave of sequencers emerged in 2005, and several companies that have driven the transformation of the industry and have been affected so far have begun to emerge.This year, the first high-throughput genetic sequencer was introduced by 454, the first high-throughput genome sequencing system based on pyrosequencing.Subsequently, Roche acquired 454 for $155 million and introduced the updated GS FLX sequencing system in 2006.Also in 2005, there was a company called Complete Genomics (CG), which has the ability to independently develop a sequencer and has a sequencer product.In the future, this company is of great significance to the development of China’s sequencer.In the second year, Solexa also launched its own sequencer system, the Genome Analyzer, or GA.In 2007, Illumina acquired Solexa for $600 million, which enabled the commercialization of GA and has since entered a period of rapid development.In 2008, ABI merged with Invitrogen to form Life Technologies.Ion PGM desktop sequencing was launched two years later, and in 2013, the company was acquired by Thermo Fisher.With the efforts of many Western companies, the cost of gene sequencing has also begun to decline.Through the iteration of sequencing equipment and technology, the cost of sequencing is significantly reduced and the market advantage is gained. It also becomes the logic behind many competitions and mergers and acquisitions in the field of gene sequencing.One figure is that in 2010, the cost of whole-genome sequencing has dropped from the cost of 100 million yuan to $5,000.In 2011, it dropped further to $4,000.For the Huada gene far away in China, for a long time in the past, its technology accumulation has been applied in genomics research and gene sequencing technology, rather than upstream sequencers.In 2000, Wang Jianhe and his team were first known by the public.When US President Bill Clinton and British Prime Minister Blair announced the completion of the mapping of the human genome work framework, they were especially grateful to Chinese scientists.Following the first large-scale project independently initiated and independently completed by Huada: Rice Genome.It is more than three years since Huada became more famous.In the SARS epidemic, the SARS virus sequence was measured in 30 hours, and the SARS detection reagent enzyme-linked immunoassay kit was made in 96 hours.In 2007, Huada was separated from the Chinese Academy of Sciences system and moved to Shenzhen in the south.In the same year, the high-throughput sequencer of the American company Illumina based on the side-synthesis sequencing method began to enter the market, the rapid breakthrough of gene technology and the increasingly fierce competition in international technology.Do upstream hardware or midstream and downstream applications?Choose a sequencer or a sequencing service?In the past five years, the companies that fought in the genetic field had already decided at the time.The eve of the sequencer war came to 2010.After more than ten years of development, Huada has formed a relatively mature business. The company’s main areas are concentrated in the middle and lower reaches of the industry, namely the sequencing business.But upstream sequencing equipment is almost in a blank space.Huada, which lacks a sequencer, faced a difficult situation at the time.The gene sequencing service business is on the rise. Due to the limited capacity of the sequencing platform, Huada has to purchase a large number of sequencers and re-arm the sequencing platform.One of the best sequencing instrument manufacturing companies in the world at the time was Illumina.Illumina’s instruments perform best, and the new sequencer retains both the side-by-side sequencing and optical and system design, which makes the founder of Huada, Wang Jian, quite heart-warming.In the end, in order to purchase Illumina instruments, Huada and Wang Jian took a step to shake the industry’s “risk chess.”At that time, Huada had limited funds and applied for a $1.5 billion credit to the China Development Bank, which spent $100 million to purchase 128 HiSeq2000 sequencers from Illumina, each with a market price of around $690,000.The price of a luxury sports car.Against the outside world, Huada has invested heavily in the purchase of Illumina instruments.One of the doubts about this move at the time was that the sequencing technology was changing rapidly, the price of the instrument would drop rapidly, and it was necessary to purchase so many such expensive sequencers. The second question is whether there is such a big market.Support the operation of these 128 sequencers.But in the end, from the results, Huada is right.After buying the equipment, 88 of them were deployed at the Huada Hong Kong Center, 20 were placed at the Shenzhen headquarters, and others were placed in laboratories around the world to serve customers around the world.In 2010, Huada’s revenue exceeded one billion.In 2009, this figure was only 343 million yuan.With these 128 sequencers, Huada has become the world’s largest genomics research institution.This collaboration also made Illumina a great harvest.One data is that Huada’s order is Illumina’s largest single transaction to date, accounting for 70% of Illumina’s total production in 2010.This may be the only short-lived honeymoon period between Huada and Illumina. It didn’t last long. In the following two years, the relationship between Huada and Illumina began to turn sharply.A management of Huada told the interface journalist that the price of the instrument that Illumina sold to Huada was twice as high as that of the North American market, but the subsequent sale to Huada’s reagents continued to raise prices every year.The increase was about 4%, and the arrival time was uncertain. The damaged instruments were not repaired in time, which seriously affected the cooperation and scientific research progress between Huada and downstream institutions.In addition, Illumina was negatively treated at the time when Huada was preparing to apply for the registration of genetic sequencing equipment from the national regulatory authorities based on the purchase of Illumina equipment.Some analysts in the genetic industry analyzed the interface journalists. The main reason for Illumina’s doing this is that Huada has already occupied a large share of the mid-stream and downstream sequencing services. Illumina, as an upstream company, hopes to “monopolize” through equipment and technical barriers.”The voice of the entire industry chain, and the negative treatment of this big customer, the core is to curb the rapid development of Huada.From 2011 to 2012, due to limited upstream equipment, Huada’s sequencing services business encountered unprecedented resistance.Suffering from the pain of the “card neck”, the development of the Chinese gene sequencer by pressing the “pause button” was started again.The domestic sequencer Shuguangchu is now in the chip field, and the upstream restricted “card neck” situation is commonplace.For example, the recent occurrence of Japan’s cessation of supplying raw materials to South Korea has also made South Korean companies quite passive.The same is true in the genetic field.Wang Jian and others clearly saw the threat posed by technical barriers, but the contradiction at the same time is that the path to solve this problem is difficult and narrow: either to start research from scratch or to an upstream manufacturer with technical property rights.Expand Cooperation.The independent research and development of instruments is the first consideration of Huada.However, because the manufacture of sequencers is a capital-intensive and technology-intensive area, it requires a long period of technical accumulation, and self-development is too difficult.Therefore, the second best, acquisition is the only feasible and realistic breakthrough path.But where is the target of the acquisition?At the time, apart from Illumina, there were not many companies in the sequencer industry chain, and Complete Genomics, Thermo Fisher, and Roche were counted as high-quality companies in the field of sequencers.Soon after, the opportunity came.In 2012, Huada received an invitation to acquire a company from Complete Genomics (hereinafter referred to as CG).This is a Silicon Valley company located in Mountain View, California, USA.Although Illumina is already a star company, CG is also a hard core in terms of technical strength.Founded in 2005, CG has the ability to independently develop a sequencer and has a sequencer product, but it only provides sequencing services and does not sell a sequencer.In the eyes of its founders, this can reduce the investment and time invested by researchers in equipment and spend more time on research itself.In 2009, Science published research results from researchers at CG, Harvard Medical School, and the University of Washington. They completely sequenced and analyzed the genome-wide sequences of three people, successfully ensuring the accuracy of their personal genomes.The cost of sequencing dropped to $1,726.The secret of this is the key technology of CG’s unique joint probe anchor polymerization, which can obtain 1000Gb of data per machine.Although the technology is advanced, the commercial operation of CG is not too smooth. As a Nasdaq-listed company, CG faces the dual pressure from investors and the industrial environment in product commercialization.In the case of a shortage of funds, CG announced in June of that year to seek strategic cooperation and purchase home.Outside of China University, Illumina and other manufacturers expressed their willingness to acquire.”CG is similar to Huada’s goal and complementary. Huada can obtain patented technology of sequencer, such as the key technology of joint probe anchor polymerization, and can get rid of Illumina’s development and get the initiative to reduce the cost of sequencing.”A senior person in the genetic industry told the interface journalist.According to Dr. Radoje Drmanac, founder of CG, Illumina mainly sells sequencing tools.In comparison, Huada is the perfect partner among dozens of organizations that express their willingness to buy.Not only will Huada continue to develop and develop CG’s unique sequencing technology, but it will also provide CG with a total solution from genome to proteomics. This is the development direction that CG wants.Dawning is beginning to appear, but even if you are willing to buy, the “germination” of China’s genetic sequencer needs to break through the “iron gate”.The $0.05 difference in the acquisition of “Hua Da is not 100% successful.” A person involved in the transaction said to the interface journalist.The acquisition of overseas Nasdaq-listed companies by Chinese private institutions has not been successful.Previously, Huawei, ZTE and CNOOC’s acquisition plans in the United States all failed because of various obstructions.Just before Huada announced the acquisition of CG, Sany Heavy Industry’s plan to invest in wind power plants in the United States was just rejected.This has also added new pressure to the acquisition of CG.The acquisition is risky, uncertain, and strong competitors.Among them, competitor Illumina is one of the biggest uncertainties.Illumina is a competitor of CG, and Illumina is the leader in the upstream of the genetic industry with its strong market share.Both sequencer manufacturers have their own unique core technologies. If Illumina owns CG, it may make CG technology disappear in the market in order to consolidate its technological status.On the eve of the merger, Illumina began to file a lawsuit against CG, infringing its patent rights.This “strategy” has once made China a dilemma – if this infringement is established, the key technology that Huada values ​​the combined probe anchor ligation reading will no longer be owned by CG, and the acquisition will become meaningless.At the same time, CG is at risk of bankruptcy at any time. Once CG is auctioned and declared bankrupt before the acquisition is completed, Huada will no longer have the possibility of acquisition.Faced with this risk, several people are waiting for the boots to land.The bidding requires participants to quote the price per share, whichever is higher.”This means that if the offer is much higher than the opponent, although it can make the opponent out, it will also increase the cost of the acquisition. If the offer is lower than the opponent, the exit is itself.” The person said.The financial team of Huada was estimated to give a suggested price of $3 per share, while Citi, the financial adviser to the acquisition, gave a price of $3.70 per share.Those who participated in the transaction recalled that Huada finally gave a price of $3.15. Wonderfully, this offer eventually defeated Illumina by $0.05.Huada and CG reached an acquisition agreement of $3.15 per share.On March 18, 2013, Huada completed the acquisition of CG for US$117 million.This full acquisition method not only preserves the integrity of CG, but also allows Huada to acquire the patented technology of CG, and quickly complete the technology and industrial upgrading, and to break through the layout in the field of upstream sequencing equipment in addition to sequencing services.Just having CG’s patents and early technology does not mean that it can directly convert a mass-produced and successful domestic genetic sequencer, otherwise the company will not choose the road to sell.At that time, the project team members felt that they had no idea when they got the prototype of CG’s genetic sequencer: the overall design of the equipment was precise, and the pursuit of hardware system was perfect, but it also created the price of two tons and the price of tens of millions of yuan.From the positioning and product form, it is like “super calculation”.In the view of Huada engineers, the original design of pursuing the limit is more suitable when the early sequencer is concentrated in a few players, but when the sequencer is gradually popularized to many corporate customers, universities and clinical hospitals, it is more cost-effective.A more flexible and equally accurate “desktop” or even a “notebook.”This has finally become a “road map” for the breakthrough of Chinese genetic sequencers.Three years after the acquisition of CG, in April 2016, Shenzhen Huada Zhizao Technology Co., Ltd. was established, which is a business unit independently set up by Huada Group for the upstream sequencer industry.According to Caixin’s report, in the patent dispute between Huada and Illumina, Huada’s sequencing signal amplification technology came from Radoje Drmanac, founder of CG Corporation of the United States.Over the past few years, Huada has made rapid development. According to its official data, the compound growth rate of revenue has exceeded 200% in the past three years, and the Chinese market has accounted for more than one-third.As of September 2019, Huada Zhizhi’s serializers exceeded 1200 units worldwide, with over 300 users in 24 countries and regions.Based on the cumulative output data of Huada’s sequencing platform, it has exceeded 28Pb and published over 500 high-level papers.The use of domestically-made sequencers to replace imported sequencers has also begun. Data show that from 2014 to 2016, Huada’s purchases from Illumina were 196 million yuan, 199 million yuan and 138 million yuan, respectively, which accounted for the purchase amount in the current year.Compared with 40.46%, 44.27% and 25.93%, in 2017, Huada’s purchases to Illumina decreased by 30.65%.The media report corresponding to this is that Huada said that in 2017, the company has “completely achieved independent replacement”.At present, only two countries and three companies in the world can mass produce clinical-grade high-throughput genetic sequencers, namely Illumina, Huada Zhizhi, and Thermo Fisher.The domestic genetic sequencer is in the environment of such an oligarchic struggle. At the beginning of the break, the war between technology and patents was launched.The journey has just begun. “Mr. Nixon, you can overcome cancer.” In 1969, the Lasker Medical Prize founder Mary Lasker spent $22,000 on the ad, a huge headline almost the New York Times.The entire layout.There is also a sentence below the title, “We will find the antidote soon, and we will only lack the determination, funds and overall plan to send people to the moon.” This sentence comes from Boston doctor Sydney, who is recognized as the godfather of cancer research.Sidney Farber.In the Human Genome Project, the United States is preparing to invest $200 million a year in the project, which is expected to be completed in 15 years.In December 1984, in a small conference room in Alta, Utah, the top genetic scientists gathered by the US Department of Energy were discussing how to explore the United States after the first atomic bomb was dropped in Hiroshima, Japan.The occurrence of genetic mutations in the population of the lower estuary.However, after a long discussion, the people did not come up with any feasible methods.Decades of genetic exploration, determination, funding, and planning, but human genes still do not get a perfect answer.“Humans’ understanding of themselves may be only 1%.” A genetic industry person told the interface journalist.People in the field of genetics understand that the most needed thing in the whole industry is to find ways to increase the throughput of sequencing data and lower prices. This is the only, core and necessary condition for genetic technology to finally reach the public.A new round of competition for sequencing costs has begun again, this time the “protagonist” replaced with the Chinese gene sequencer.The previously mentioned domestically delivered ultra-high-throughput sequencer DNBSEQ-T7 has reduced the cost of sequencing per Gb to approximately $5, which is currently the lowest sequencing cost in the world.The technology is constantly emerging, the sequencing time is constantly compressed, and the cost is decreasing year by year.There are no shortage of new players in this industry. Due to different technical routes, companies such as Oxford Nanopore are becoming market chasers, just like Illumina and Huada.In 2018 Tianjin Davos, Follley and Wang Jian met, they became a guest in a forum, expressing their opinions in a harmonious and free way, just like an old friend talking and laughing on the field.The psychology of both of them should be understood. In the 50 years of genetic exploration, the journey has only just begun..