s****l
发帖数: 10462 | 1 有人愿意讨论这里面提及的测序技术吗？优缺点，可行性，第一手经验等等
这里面谁现在是赢家很清楚，但是可见的将来和更远的将来谁会赢？
http://cen.acs.org/articles/92/i33/Next-Gen-Sequencing-Numbers-
全文拷贝如下
试试看图能不能贴上
/1407973177171.jpg
/1408028636124.jpg
OVER STORY
Next-Gen Sequencing Is A Numbers Game
As technical and cost barriers fall, instrument firms move their systems
into research and clinical markets
By Ann M. Thayer
Department: Business
Keywords: instrumentation, gene sequencing, diagnostics, genomics, cancer
[+]Enlarge
09233-cover-Openercxd_17647969-690
ADDS UP
Calculating the $1,000 human genome that Illumina claims can be achieved in
with its HiSeq X Ten system
Credit: Illumina
Sequencing the human genome the first time cost $3 billion and took 13 years
to complete. That was in 2003. Eleven years later, next-generation
sequencing technology has brought the single-genome price close to $1,000
and cut the time to days.
These advances have enabled new opportunities for genomic studies. For
example, Genomics England, set up by the U.K.’s Department of Health, plans
to sequence 100,000 human genomes by the end of 2017. The project will
focus on individuals with cancer and rare diseases in the hope of
transforming diagnosis and treatment.
Next-generation sequencing, or NGS, is moving quickly into research,
clinical, and diagnostic applications. As it does, users and regulators are
learning how to handle the technology and the resulting genetic information.
While researchers move up the learning curve, instrument developers are
close behind. Armed with a dizzying array of technologies, they are
competing with each other to introduce faster sequencing, higher accuracy,
and even lower costs.
[+]Enlarge
09233-cover-pie_17648723-700
DOMINATOR
Illumina rules the market for next-generation sequencers. SOURCES: Mizuho
Securities USA, Frost & Sullivan
So far, Illumina leads the race. In January, the San Diego-based firm
launched its HiSeq X Ten system with a price tag of $10 million. Consisting
of 10 ultra-high-throughput sequencers, each capable of generating up to 1.8
terabases of data in less than three days, the system can sequence about 18
,000 human genomes per year.
Illumina uses a sequencing-by-synthesis method. After DNA fragments are
amplified on a chip, sequencing occurs by synthesizing a DNA strand
complementary to the target strand by enzymatically attaching fluorescently
labeled nucleotides one at a time. When reactions occur, the labels are
optically imaged to identify what was attached, and the cycle is repeated.
Although Illumina says it has pushed the per-genome price under $1,000—
including instrument and operating costs, but not overhead and data handling
—the X Ten system is cost-effective only for large-volume users. The
company has already found at least 13 such customers, including the Boston-
based Broad Institute, the U.K.’s Wellcome Trust Sanger Institute,
Australia’s Garvan Institute of Medical Research, and the Sidra Medical &
Research Center in Qatar.
Even before the X Ten, Illumina commanded more than 70% of the $1.3 billion
NGS market, according to the research firm Frost & Sullivan. Two-thirds of
that money is spent on reagents and consumables and the rest on instruments
sold by Illumina, Thermo Fisher Scientific, Roche, and Pacific Biosciences,
usually for between $50,000 and $750,000.
“Newer instruments will generally fall into the category of low- to mid-
throughput, benchtop-sized sequencers for both the research and clinical
spaces,” says Christi Bird, life sciences senior industry analyst at Frost
& Sullivan. They will tend to sell for less than $100,000. Although she
expects some market share losses as new firms enter the business, the
erosion will largely be offset by expansion of the pie overall. Frost
expects the overall NGS market to grow about 16% per year through 2018.
You may have issues using the scroller below when using Internet Explorer.
Please try another browser, or view it as a PDF here.
Credit: Yang Ku / Ty Finocchiaro / C&EN
SEQUENCING GENEALOGIES
Trace the emergences, mergers, and milestones of the power players in gene
sequencing technology over the past 17 years. Companies’ techniques are
listed below their names.
Sales of X Ten systems no doubt look good on Illumina’s bottom line, but
the firm insists that selling a range of systems is important to its growth
strategy. It has developed a portfolio to target different markets,
applications, and throughput needs, explains Joel Fellis, senior manager for
systems and genomic services marketing. “We’re interested in making
sequencing much more widely accessible, easier to use, and focused on end-to
-end solutions.”
In January, for example, Illumina launched the NextSeq 500, a $250,000
benchtop machine priced between its small-scale MiSeq and workhorse HiSeq
2500 systems. In about a day, the NextSeq can run a whole 3 billion-base
genome, 20 prenatal test samples, 16 exomes, 48 gene-expression samples, or
96 targeted panels. “It really is expanding our customer base,” Fellis
explains.
Besides a core life sciences analysis market worth about $5 billion per year
, Illumina targets the $12 billion research and clinical oncology market,
the $2 billion reproductive and genetic health area, and about $1 billion in
emerging prospects, such as infectious disease and food. Clinical
sequencing will be a “turning point” as it drives the NGS business into
diagnostics, Frost’s Bird predicts.
In November 2013, Illumina became the first company to receive Food & Drug
Administration clearance for an NGS system used in diagnostics. The approval
covers its MiSeqDx instrument, reagents for isolating and copying genes,
and gene analysis software. As a result, labs will be able to use the system
to develop and validate tests that involve sequencing any part of a patient
’s genome. FDA also approved Illumina kits to detect cystic fibrosis-
related mutations.
With the new instrument, Illumina is testing the diagnostic waters for the
industry in a fast-changing regulatory climate. “Illumina’s recent
approval enhances marketing, increases the FDA’s comfort level, and stays
ahead of potential shifts in regulatory oversight,” Mizuho Securities USA
stock analyst Peter Lawson pointed out in a recent report to clients.
Not surprisingly, Illumina and other NGS companies plan to develop and
register more diagnostic systems, as do some leading diagnostic developers
that have bought NGS start-ups. The German diagnostics firm Qiagen acquired
U.S.-based Intelligent Bio-Systems in 2012. Similarly, in April, the U.S.
lab products and diagnostics supplier Bio-Rad Laboratories acquired GnuBio
of Cambridge, Mass.
Both the GnuBio and Qiagen NGS systems are being designed to go from sample
through DNA library preparation, sequencing, and data analysis. Bio-Rad isn
’t giving a timeline for selling a GnuBio system, but beta systems were
available in 2013. Qiagen anticipates launching its benchtop GeneReader
system for clinical applications in the second half of 2015.
Meanwhile, England-based QuantuMDx is developing what it says will be a low-
cost, simple-to-use device for 15-minute bedside diagnoses. It uses disease-
specific cartridges and sequencing on nanowire biosensors. It plans to
commercialize its handheld, chip-based device in 2015 for, it claims, “the
price of a smartphone.”
California-based GenapSys has a bread-loaf-sized device using what it calls
GENIUS, for Gene Electronic Nano-Integrated Ultra-Sensitive, technology. The
four-year-old company is aiming for a $50 genome and point-of-care
diagnostic use. According to analysts, performance data on the system could
appear this year, with commercialization targeted for 2015 at a cost of a
few thousand dollars.
Until these technologies are ready to compete, Illumina will enjoy the
earlymover advantage. Since it started selling sequencers in 2007, its sales
have nearly quadrupled, reaching $1.4 billion in 2013. Goldman Sachs stock
analyst Isaac Ro believes that Illumina will continue to dominate the NGS
market for the next few years.
[+]Enlarge
09233-cover-bargraph_17648010-690
BUYING POWER
Accuracy ranked highest in importance for users of next-generation
sequencing systems. NOTE: Based on a survey of 108 end users. SOURCE: Frost
& Sullivan
Thermo Fisher holds second place in the NGS market, with about 16% of sales.
Its Life Sciences Solutions business has a decades-long history in gene
sequencing and as a result offers several of the major technologies. Applied
Biosystems Inc., a predecessor company, supplied Sanger sequencing
instruments to decode the first human genome. In 2007, ABI launched its
first NGS system based on sequencing by oligonucleotide ligation and
detection, known as SOLiD.
Unlike highly accurate but less parallelizable Sanger methods, NGS systems
carry out massive numbers of reactions, or sequence reads, at one time. Like
Illumina’s approach, SOLiD uses sequencing by synthesis of amplified DNA
fragments on either a bead or chip. Instead of nucleotides, it uses
fluorescently labeled probes that are repeatedly ligated to the growing
strand, optically imaged, and cleaved off. How long these processes can be
kept going determines the “read length” that can be sequenced in a run.
The first lower-cost, nonoptical system appeared in 2010 after Life
Technologies—now part of Thermo Fisher and formed from the 2008 merger of
ABI and Invitrogen—acquired Ion Torrent for $725 million. Its systems use
sequencing by synthesis, but with unlabeled nucleotides on a semiconductor
chip. The chip electrically senses the release of hydrogen ions when bases
attach. The full sequence is read by sequentially adding bases and tracking
reactions across millions of microwells.
Today, Thermo Fisher continues to sell all the sequencing products, although
NGS is growing the fastest. “The applications really drive what is the
right choice of technology,” says Mark P. Stevenson, president of the Life
Sciences Solutions unit. Sanger sequencing, although saddled with lower
throughput and higher cost than NGS methods, is easy to use and offers long
read lengths. “Over the years we have updated Sanger sequencing with faster
reactions and newer software,” Stevenson adds.
“If you have just a few samples to run and want to know a small part of the
DNA very accurately, then Sanger sequencing is still the best method,”
Stevenson says. The industry considers it a “gold standard,” and the
method is widely used in clinical diagnostics and for DNA analysis in
forensics.
Thermo Fisher reports that it has sold more than 15,000 Sanger sequencers
and more than 2,500 Ion Torrent systems. In 2013, the Ion Torrent business
generated revenues of about $185 million, according to Goldman Sachs’s Ro.
He predicts the business will grow about 30% this year, 20% in 2015, and
then about 10% annually through 2018.
Since acquiring the Ion Torrent technology, Thermo Fisher has improved its
performance, but the method has “just begun to be optimized,” Stevenson
says. Although Thermo Fisher has looked at other technologies such as
nanopore detection and even made small investments, they have “some way to
go before having the same throughput or accuracy as the Ion Torrent,” he
maintains.
Similarly, Illumina remains focused on its core chemistry, according to Ro.
“While the company continues to research nanopore and single-molecule
technologies, it is not yet convinced that the quality of data can be as
high as sequencing by synthesis,” he says. This month, Illumina did receive
a $592,000 National Institutes of Health grant to create a sequencing
system around a hybrid protein and solid-state nanopore array.
The more gene sequencing technology is used, the more researchers are
finding out what it can—and can’t—do. For example, medical and research
centers are generating data on millions of genomic variants. Not only has
handling all those data become a challenge, but much of the data is not
understood. To overcome this, NIH is supporting a four-year, $25 million
Clinical Genome Resource program evaluating which variants play a role in
disease relevant to medical care.
Whole-genome and large population studies are expected to yield some of the
necessary associations. However, a recent Stanford School of Medicine study
found that even though NGS methods generally capture, or cover, most of the
genome, “depending on the sequencing platform, 10 to 19% of inherited
disease genes were not covered to accepted standards for single-nucleotide-
variant discovery” (J. Am. Med. Assoc. 2014, DOI: 10.1001/jama.2014.1717).
The problem is even bigger. “Variations in the genetic blueprint are not
just confined to single-base changes—the famous single-nucleotide
polymorphisms that people go after—but are present at all different size
scales,” explains Jonas Korlach, chief scientific officer at Pacific
Biosciences and a company founder. Thousands of bases can be involved in
structural variations such as insertions, deletions, inversions, and repeats
, many of which have connections to cancer, Huntington’s disease, and other
disorders.
For example, fragile X syndrome, the leading cause of heritable cognitive
impairment and autism, arises from the expansion of a nucleotide repeat
sequence in a specific gene. But sequencing the region has proven extremely
difficult, Korlach says. Sometimes such DNA simply can’t be amplified. “
Those pieces will often just fall out of the sample prep all together, and
they will never get to the sequencer,” he says.
Pacific Biosciences’ technology is designed to overcome problems that stem
from the gene sequencers themselves. If the region of interest is present
many times in the genome, the read length must be long enough to cover the
region and more. Otherwise, “it looks like a sky piece in the jigsaw puzzle
when you don’t have any tree branch to tell you where it might go,”
Korlach says. “The piece is scientifically useless because you won’t be
able to place it on the reference map of the human genome.”
Illumina and Ion Torrent technologies have read lengths up to a few hundred
base pairs, while Sanger sequencing covers several hundred. In contrast,
Pacific Biosciences’ technology has average reads of about 8,500 bases.
Some users have reached tens of thousands of bases. Its RS II system costs
about $700,000.
Pacific Biosciences’ single-molecule real-time sequencing is a sequencing-
by-synthesis approach that doesn’t use an amplified set of DNA fragments
and doesn’t require stopping and starting the reaction to add reagents and
image results. Reactions on individual DNA molecules are tracked in real
time across 150,000 nanoscale wells where isolated polymerases read the DNA
and incorporate fluorescently tagged nucleotides. Because detection occurs
only at the bottom of the wells, the background noise from the other
reactions is reduced.
Stability of the sequencing process depends in large part on the polymerase.
Pacific Biosciences has modified a simple bacteriophage enzyme, slowing it
down so that it incorporates about three bases per second and its detector
can keep up. To prevent inadvertent photo damage that could stop the process
, the company has put a protective scaffold on the enzyme.
Although fast and cheap sequencing will yield much useful knowledge, it has
come at a price because of the shorter read lengths, Korlach argues. Pacific
Biosciences “wanted to build a technology first and foremost that gives
the highest quality of sequence information,” he says.
The 10-year-old company launched its first sequencer in 2011 and has since
improved its chemistry, detection, and throughput. On target for 70% sales
growth this year, to about $47 million, Pacific Biosciences has installed
more than 100 systems and has a market share of a few percent. Its business
has seen “a nice boost as the platform continues to improve and be useful
in several niches,” Mizuho’s Lawson says.
Long reads and high accuracy are critical for de novo sequencing, or
deciphering a genome without comparison to an existing version. In February,
Pacific Biosciences published a de novo human reference genome, one of just
a few ever assembled. It is now focusing on providing nonhuman reference
genomes. For example, it is collaborating with Sanger Institute and Public
Health England to complete the sequences of 3,000 microbial strains.
To branch into the rapidly growing human diagnostics field, Pacific
Biosciences signed a deal in late 2013 with Roche worth up to $75 million.
The companies plan to develop a system for clinical use that Roche will sell
. Pacific Biosciences will get income from manufacturing the instrument,
software, and certain consumables.
In June, Pacific Biosciences also joined with the Dutch diagnostics firm
GenDx. The companies will offer products for full-length human leukocyte
antigen gene sequencing, which is gaining in clinical use. HLA sequencing is
difficult in part because of high levels of sequence homology, but it gives
clues to autoimmune and other diseases.
As new technologies such as Pacific Biosciences’ rise, others are falling
by the wayside. In late 2013, after an unsuccessful $6.8 billion attempt to
acquire Illumina, Roche decided to close down its 454 Life Sciences NGS
business and sunset its midrange sequencers by the end of 2016. The business
still accounts for about 10% of the NGS market. Roche acquired 454 Life
Sciences in 2007, two years after 454 launched the first NGS instrument
based on a sequencing-by-synthesis method. It is called pyrosequencing and
uses a luciferase to detect the release of pyrophosphate and emit light that
is detected by a camera.
[+]Enlarge
09233-cover-Nanoporecxd
HANDHELD
Oxford Nanopore Technologies’ MinION uses electronic sensing for single-
molecule sequencing.
Credit: Oxford Nanopore Technologies
In its favor, the 454 technology offered high accuracy and read lengths of
up to 1,000 bases. But “from a technological perspective, it had reached
its maturity point in being able to compete with some of the newer
technologies,” says Vinod Makhijani, vice president and project leader on
the business development team for Roche’s sequencing unit. “The throughput
of the instruments had pretty much reached its maximum, and we were unable
to significantly lower the cost, so the market started to move away from 454
.”
Just when it looked like Roche was out of the business, in June it agreed to
spend up to $350 million to acquire five-year-old Genia Technologies. The
California firm is developing single-molecule, semiconductor-based
sequencing. Nucleotides are identified through base-specific tags that are
cleaved and detected electrically as they go through protein nanopores.
Roche believes that Genia’s technology can reduce sequencing costs while
increasing speed and sensitivity.
Later in June, Roche signed a deal to invest up to $15 million in Seattle-
based Stratos Genomics. Its sequencing-by-expansion approach aims to convert
a DNA template into a larger surrogate molecule using a polymerase and
custom expandable nucleotides. The result, which the company calls an
Xpandomer, contains reporter molecules that mirror the DNA sequence and can
be read off when a single molecule passes through a nanopore. Stratos
believes the approach can overcome resolution and signal-to-noise problems
seen with other nanopore technologies.
Single-molecule, nanopore, and semiconductor technologies are considered a
step beyond current NGS methods. “We obviously wanted to go with platforms
that we consider disruptive,” Makhijani says. “All of these technologies
that we are looking at offer significant scalability.” Like other new
technologies, they will likely enter the research market first and have the
potential to evolve into clinical diagnostics.
Other small companies with intriguing but unproven technologies are close
behind. Quantum Biosystems, a Japanese start-up, released raw data in
February for its silicon-chip-based, direct electrical detection method.
About a year ago, England-based Base4 signed a deal with Japan’s Hitachi
High-Technologies to build a nanopore-based sequencer.
Most interest has been in the U.K.’s Oxford Nanopore Technologies as it
moves closer to launching a new sequencing device. Its MinION uses protein
nanopores held in a polymer membrane to sequence single-stranded DNA in real
time. Individual bases are identified through changes in electrical current
as a linear, single-stranded DNA molecule moves through a nanopore.
The nine-year-old company is conducting an early-access program for the
MinION. The disposable device, which is about the size of a USB memory stick
, is expected to sell for less than $900.
Still, interest in Oxford Nanopore’s device may have hit a lull. In a
survey of gene sequencing system users published in January, Mizuho’s
Lawson found that about 50% of respondents expect the firm to provide “the
next big leap in sequencing technology.” The number was down from 70% in
2012, “likely due to the delays and slow pace of commercialization,” he
says.
Full information on MinION’s performance will come when the access program
is complete. In February, analysts heard an early-user report that indicated
read lengths were averaging 5,000 bases, but errors were also popping up.
Despite such fits and starts, participants in the NGS field expect the move
toward faster, cheaper, and better tools to continue. “There still is a lot
of room for prices to drop,” Frost’s Bird says. Rapidly falling
sequencing costs don’t necessarily hurt the market, however, because they
drive sequencing throughput and make the technology accessible to more users.
In response to strong market growth and new opportunities, the number of
companies will expand threefold over the next five years, Bird predicts.
Unable to sustain such a large competitor base, the business will then enter
a new phase, she says. It will be marked by a mergers and acquisitions race
among top competitors and large-company entrants, along with many start-up
failures.
Chemical & Engineering News
ISSN 0009-2347
Copyright © 2014 American Chemical Society | i*******i
发帖数: 145 | 2 Future: Oxford Nanopore
Science: PacBio
Diagnosis: Illumina | s****l
发帖数: 10462 | 3 PacBio 在 Science/Research 能dominate? 除了长，在HLA/de novo测序上有些优势，
其他都不成气候，而且单独一个它自己的平台绝对不行
Oxford Nanopore好久都没有消息了。最后的消息是数据准确度不太行。你说future是
它家的，听上去你有些一手经验？
【在 i*******i 的大作中提到】
: Future: Oxford Nanopore
: Science: PacBio
: Diagnosis: Illumina
| h*****b
发帖数: 492 | 4 size matters including the length
【在 s****l 的大作中提到】
: PacBio 在 Science/Research 能dominate? 除了长，在HLA/de novo测序上有些优势，
: 其他都不成气候，而且单独一个它自己的平台绝对不行
: Oxford Nanopore好久都没有消息了。最后的消息是数据准确度不太行。你说future是
: 它家的，听上去你有些一手经验？
| i*******i
发帖数: 145 | 5 除了pacbio，没有一家的sequencing能在理论上达到perfect assembly。
pacbio只要有足够的coverage （现在很多大lab有钱，能达到100x以上的coverage），
是可以做perfect assembly的。所以做science的未来是pacbio的。
oxford有pacbio的优点，而且比illumina还要便宜。他们的问题并不是accuracy差，是
不stable。但是我相信这些都是engineering的问题。最终都会解决的。所以future是
oxford的 | g********6
发帖数: 86 | 6 做science的测序不只是assembly genome好不好，何来science的未来是pacbio的？
MinIon的data能不能用看看这篇paper就知道了
http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12324/abst
再看看这个Read，跟reference相似性为65%
http://nextgenseek.com/2014/06/behold-oxford-nanopore-reads-are
所以我觉得nanopore测序仪产品上市还得有一段时间
【在 i*******i 的大作中提到】
: 除了pacbio，没有一家的sequencing能在理论上达到perfect assembly。
: pacbio只要有足够的coverage （现在很多大lab有钱，能达到100x以上的coverage），
: 是可以做perfect assembly的。所以做science的未来是pacbio的。
: oxford有pacbio的优点，而且比illumina还要便宜。他们的问题并不是accuracy差，是
: 不stable。但是我相信这些都是engineering的问题。最终都会解决的。所以future是
: oxford的
| i*******i
发帖数: 145 | 7 assembly是sequencing中最难的问题（且不说重要性，这个见仁见智）。如果能解决
assembly，那么就可以解决任何问题。
我说的science的意思是，不计成本的情况下找到最准确的结果。有足够coverage的条
件下，pacbio完美解决一切sequencing的问题。准确度的问题可以通过多次测序取
consensus解决，理论上达到0 error rate。
对于oxford，我说了这个engineering的问题。这个问题迟早会解决。但是等一段时间
是肯定的（个人目测至少1年以上）。
【在 g********6 的大作中提到】
: 做science的测序不只是assembly genome好不好，何来science的未来是pacbio的？
: MinIon的data能不能用看看这篇paper就知道了
: http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12324/abst
: 再看看这个Read，跟reference相似性为65%
: http://nextgenseek.com/2014/06/behold-oxford-nanopore-reads-are
: 所以我觉得nanopore测序仪产品上市还得有一段时间
| s******s
发帖数: 13035 | 8
你这个毫无意义，技术上很美不等于应用上美。用最土的sanger sequencing
也能比illumina做de novo上强，没通量有人用么！
【在 i*******i 的大作中提到】
: assembly是sequencing中最难的问题（且不说重要性，这个见仁见智）。如果能解决
: assembly，那么就可以解决任何问题。
: 我说的science的意思是，不计成本的情况下找到最准确的结果。有足够coverage的条
: 件下，pacbio完美解决一切sequencing的问题。准确度的问题可以通过多次测序取
: consensus解决，理论上达到0 error rate。
: 对于oxford，我说了这个engineering的问题。这个问题迟早会解决。但是等一段时间
: 是肯定的（个人目测至少1年以上）。
|
| i*******i
发帖数: 145 | 9 这个不光是技术上的问题。
“Single Molecule, Real-Time (SMRT®) DNA sequencing achieves highly
accurate sequencing results, exceeding 99.999% (Q50) accuracy, regardless of
the DNA’s sequence context or GC content. - http://blog.pacificbiosciences.com/2013/01/a-closer-look-at-accuracy-in-pacbio.html”
首先这个说明pacbio的准确率足够绝大多数的分析。
“The stats are quite fascinating. They have 66 SMRT cells producing 32,559,
803,198 bases of post-filtered nucleotides. - http://www.homolog.us/blogs/blog/2013/10/22/pacbio-releases-library-covering-human-genome-10x/”
这是一台2013年pacbio的throughput，10天32G的data.
这已经是10X的human genome了。在这种长度和准确率下，10X的coverage已经能保证正
确的出大多数结论。很多structural variation用illumina测100X也测不出来。
你难道说测序测10天就没有应用了么？illumina本身技术上的缺陷就算通量再高又有什
么用？
【在 s******s 的大作中提到】
:
: 你这个毫无意义，技术上很美不等于应用上美。用最土的sanger sequencing
: 也能比illumina做de novo上强，没通量有人用么！
| s******s
发帖数: 13035 | 10 你是被忽悠了吧。第一个显然是公司自己的广告你也敢相信？
人准确率不到90%，要反复测序20x以上才可能，你的10x其实
只有0.5x的99.999% accuracy。另外，所谓的66个smrt cell
produce了32G的data，其实连0.5x都没，就是那66个smrt cell
那点序列。人家只是用来说明酶死掉之前还能用很久。
这玩意儿还是有用的，比如互补illumina一起使用，或者微生物
基因组，但是自己测人类基因组现在就是废柴一根。不是技术fancy
就是好技术，illumina那破技术第一个出来，人家就是能scale，
现在仍然是天下第一。
of
559,
【在 i*******i 的大作中提到】
: 这个不光是技术上的问题。
: “Single Molecule, Real-Time (SMRT®) DNA sequencing achieves highly
: accurate sequencing results, exceeding 99.999% (Q50) accuracy, regardless of
: the DNA’s sequence context or GC content. - http://blog.pacificbiosciences.com/2013/01/a-closer-look-at-accuracy-in-pacbio.html”
: 首先这个说明pacbio的准确率足够绝大多数的分析。
: “The stats are quite fascinating. They have 66 SMRT cells producing 32,559,
: 803,198 bases of post-filtered nucleotides. - http://www.homolog.us/blogs/blog/2013/10/22/pacbio-releases-library-covering-human-genome-10x/”
: 这是一台2013年pacbio的throughput，10天32G的data.
: 这已经是10X的human genome了。在这种长度和准确率下，10X的coverage已经能保证正
: 确的出大多数结论。很多structural variation用illumina测100X也测不出来。
| | | d*******e
发帖数: 1649 | 11 没有谁赢谁输的问题。几种技术会并存很长的时间。pacbio的想法很好，但是技术上迟
迟不能突破。illumina已经占领了大药厂和学术界，轻易不会被替代。我认为测序技术
需要有新的想法才会真正出现革命性的变革，在这之前基本是illumina的天下。留给
pacbio和nanopore的时间已经很短了。
【在 s****l 的大作中提到】
: 有人愿意讨论这里面提及的测序技术吗？优缺点，可行性，第一手经验等等
: 这里面谁现在是赢家很清楚，但是可见的将来和更远的将来谁会赢？
: http://cen.acs.org/articles/92/i33/Next-Gen-Sequencing-Numbers-
: 全文拷贝如下
: 试试看图能不能贴上
: /1407973177171.jpg
: /1408028636124.jpg
: OVER STORY
: Next-Gen Sequencing Is A Numbers Game
: As technical and cost barriers fall, instrument firms move their systems
| w**k
发帖数: 6722 | 12 我从另外一个角度征求一下大家的看法
几年前，我觉得LIFE 和 ILMN的技术比454好，所以买了这两家的股票。LIFE技术其实
不怎么样，从SOLiD到Ion，勉勉强强，最后公司被收购，百分之17%左右的premium，不
是很高，也还不错。ILMN这几年在测序市场上基本上可以说是舍我其谁独占鳌头的架势
，所以股票是翻了再翻。总之，两笔投资都还不错。
期间还做空了PACB，不过没赚到大头，再它狂泻的头一天怂了撤了。HLCS还没来得及想
怎么着，就倒闭了。
想知道从目前的技术竞争和发展来看，哪几家值得重点投资？
ILMN自然要继续持有
TMO，也就是LIFE/Ion，觉得好像还是不太行，accuracy是问题，通量也有些问题。不
知道应不应该重新找机会入场。
Roche，似乎是倒霉之星，买谁谁垮，投谁谁倒。
其他的新起的技术好像都没有上市，似乎也无从着手。
大家有什么看法？一起分享分享。 | s******r
发帖数: 1245 | 13 LIFE家大业大，sequencing在它家也就占一小部分，并入TMO后就更是九牛一毛了，因
为看好solid或者ion投资LIFE/TMO，简直是瞎猫碰死耗子
新技术没出来前就是ILMN最牛逼，反正也没什么其他可买的，要不你等华大上市吧
【在 w**k 的大作中提到】
: 我从另外一个角度征求一下大家的看法
: 几年前，我觉得LIFE 和 ILMN的技术比454好，所以买了这两家的股票。LIFE技术其实
: 不怎么样，从SOLiD到Ion，勉勉强强，最后公司被收购，百分之17%左右的premium，不
: 是很高，也还不错。ILMN这几年在测序市场上基本上可以说是舍我其谁独占鳌头的架势
: ，所以股票是翻了再翻。总之，两笔投资都还不错。
: 期间还做空了PACB，不过没赚到大头，再它狂泻的头一天怂了撤了。HLCS还没来得及想
: 怎么着，就倒闭了。
: 想知道从目前的技术竞争和发展来看，哪几家值得重点投资？
: ILMN自然要继续持有
: TMO，也就是LIFE/Ion，觉得好像还是不太行，accuracy是问题，通量也有些问题。不
| w**k
发帖数: 6722 | 14 谢谢指点。
LIFE当时确实是瞎猫碰到死耗子。当时主要觉得下一代测序肯定是技术发展方向，市场
会越来越大，而就三家技术，454份额是日渐式微，所以就决定ILMN和LIFE了。现在也
是，想到只投ILMN一家不是很保险，而且我相信市场绝对会变大翻倍。
【在 s******r 的大作中提到】
: LIFE家大业大，sequencing在它家也就占一小部分，并入TMO后就更是九牛一毛了，因
: 为看好solid或者ion投资LIFE/TMO，简直是瞎猫碰死耗子
: 新技术没出来前就是ILMN最牛逼，反正也没什么其他可买的，要不你等华大上市吧
| s****l
发帖数: 10462 | 15 Science也不是用钱就可以堆起来的
Pacbio如果Roche这一次没能扶持起来的话，估计就要挂了。这两年就见分晓。
Oxford不知道有什么进展。
【在 i*******i 的大作中提到】
: 除了pacbio，没有一家的sequencing能在理论上达到perfect assembly。
: pacbio只要有足够的coverage （现在很多大lab有钱，能达到100x以上的coverage），
: 是可以做perfect assembly的。所以做science的未来是pacbio的。
: oxford有pacbio的优点，而且比illumina还要便宜。他们的问题并不是accuracy差，是
: 不stable。但是我相信这些都是engineering的问题。最终都会解决的。所以future是
: oxford的
| s****l
发帖数: 10462 | 16 会不会illumina也会像ABI在Sanger测序时代统治十几年
【在 d*******e 的大作中提到】
: 没有谁赢谁输的问题。几种技术会并存很长的时间。pacbio的想法很好，但是技术上迟
: 迟不能突破。illumina已经占领了大药厂和学术界，轻易不会被替代。我认为测序技术
: 需要有新的想法才会真正出现革命性的变革，在这之前基本是illumina的天下。留给
: pacbio和nanopore的时间已经很短了。
| m***T
发帖数: 11058 | 17 这个现在看来很有可能。ilmn的技术最成熟，市场做得也最好，而且它也在发展自己的
nanopore。除了ont以外，还有多家在用nanopore发展的。pacbio因为成本问题机器很
难用于一线临床，只能在研究领域拼一拼。现在据说也在发展便携式的，具体到什么地
步了还不知道。solid已经停止发展了，所以基本上已经退出这块市场了，ion虽然
homopolymer的问题不大可能从现有技术上得到根本上的改善，但随着chemistry和更有
针对性的algorithm，现在的准确度还算不错。它的优势一是sample需要很低的起始量
，二是cancer hotspot panel等其它及个panel的效果在临床实验的观察来看feedback
比较positive，所以在临床论断市场还有些竞争力。如果它能彻底把tedious的epcr给
弃掉，会更有竞争力的。roche刚买了另一个以nanopore为技术的公司genia http://www.geniachip.com/，所以后面如何还不太清楚。genia的技术是在solid state上面不象目前的ont是engineering protein，所以更稳定，一是序列会更长也更准确，目前ont也在这个方向发展。另外需要提出的是qiagen，它最近一两年的在这方面的动作非常大，看看它收购的几个公司你就清楚了。
但不管怎么样，我的的感觉是近三五年内市场格局不会有太大的变化，应该还是ilmn一
家独大。
【在 s****l 的大作中提到】
: 会不会illumina也会像ABI在Sanger测序时代统治十几年
| s********n
发帖数: 2939 | 18 Genia还是用protein pore，不是solid state的；solid state nanopore是Stratos。
这两家都是Roche买/投资的。
feedback
【在 m***T 的大作中提到】
: 这个现在看来很有可能。ilmn的技术最成熟，市场做得也最好，而且它也在发展自己的
: nanopore。除了ont以外，还有多家在用nanopore发展的。pacbio因为成本问题机器很
: 难用于一线临床，只能在研究领域拼一拼。现在据说也在发展便携式的，具体到什么地
: 步了还不知道。solid已经停止发展了，所以基本上已经退出这块市场了，ion虽然
: homopolymer的问题不大可能从现有技术上得到根本上的改善，但随着chemistry和更有
: 针对性的algorithm，现在的准确度还算不错。它的优势一是sample需要很低的起始量
: ，二是cancer hotspot panel等其它及个panel的效果在临床实验的观察来看feedback
: 比较positive，所以在临床论断市场还有些竞争力。如果它能彻底把tedious的epcr给
: 弃掉，会更有竞争力的。roche刚买了另一个以nanopore为技术的公司genia http://www.geniachip.com/，所以后面如何还不太清楚。genia的技术是在solid state上面不象目前的ont是engineering protein，所以更稳定，一是序列会更长也更准确，目前ont也在这个方向发展。另外需要提出的是qiagen，它最近一两年的在这方面的动作非常大，看看它收购的几个公司你就清楚了。
: 但不管怎么样，我的的感觉是近三五年内市场格局不会有太大的变化，应该还是ilmn一
| p*****e
发帖数: 989 | 19 现在测序不是什么瓶颈了吧，就是个engineer的问题，和science都扯不上关系。给你
个perfect genome有什么用，人对自己那一万八千个protein coding基因的无知和十年
前没什么区别吧。NGS就是个新名词大家瞎追瞎吹，甚至对有的人来说NGS就是rna-seq
。真正内行的人知道read length越来越长，尼妈越来越像EST，时光仿佛回到了10年前
。 | s****l
发帖数: 10462 | 20 你夸张了
一个人的perfect genome是没什么用，一百万个人的就有用了，如果能加上完整的
phenotype的数据，简直就是宝藏了。很多事情还做不了，主要还是因为NGS还是太贵。
seq
【在 p*****e 的大作中提到】
: 现在测序不是什么瓶颈了吧，就是个engineer的问题，和science都扯不上关系。给你
: 个perfect genome有什么用，人对自己那一万八千个protein coding基因的无知和十年
: 前没什么区别吧。NGS就是个新名词大家瞎追瞎吹，甚至对有的人来说NGS就是rna-seq
: 。真正内行的人知道read length越来越长，尼妈越来越像EST，时光仿佛回到了10年前
: 。
| s****l
发帖数: 10462 | 21 比如说，如果从现在开始起，所有的三期临床都把所有的病人测一下序，就会有很多宝
贵的数据出来。每个病人多1000块的预算是测不出perfect genome的。
seq
【在 p*****e 的大作中提到】
: 现在测序不是什么瓶颈了吧，就是个engineer的问题，和science都扯不上关系。给你
: 个perfect genome有什么用，人对自己那一万八千个protein coding基因的无知和十年
: 前没什么区别吧。NGS就是个新名词大家瞎追瞎吹，甚至对有的人来说NGS就是rna-seq
: 。真正内行的人知道read length越来越长，尼妈越来越像EST，时光仿佛回到了10年前
: 。
|
|
