s********n
发帖数: 2939 | 1 现在这种例子越来越多了
http://www.nytimes.com/2014/06/05/health/in-first-quick-dna-tes
In a First, Test of DNA Finds Root of Illness
Joshua Osborn, 14, lay in a coma at American Family Children’s Hospital in
Madison, Wis. For weeks his brain had been swelling with fluid, and a
battery of tests had failed to reveal the cause.
The doctors told his parents, Clark and Julie, that they wanted to run one
more test with an experimental new technology. Scientists would search
Joshua’s cerebrospinal fluid for pieces of DNA. Some of them might belong
to the pathogen causing his encephalitis.
The Osborns agreed, although they were skeptical that the test would succeed
where so many others had failed. But in the first procedure of its kind,
researchers at the University of California, San Francisco, managed to
pinpoint the cause of Joshua’s problem — within 48 hours. He had been
infected with an obscure species of bacteria. Once identified, it was
eradicated within days.
The case, reported on Wednesday in The New England Journal of Medicine,
signals an important advance in the science of diagnosis. For years,
scientists have been sequencing DNA to identify pathogens. But until now,
the process has been too cumbersome to yield useful information about an
individual patient in a life-threatening emergency.
“This is an absolutely great story — it’s a tremendous tour de force,”
said Tom Slezak, the leader of the pathogen informatics team at the Lawrence
Livermore National Laboratory, who was not involved in the study.
Mr. Slezak and other experts noted that it would take years of further
research before such a test might become approved for regular use. But it
could be immensely useful: Not only might it provide speedy diagnoses to
critically ill patients, they said, it could lead to more effective
treatments for maladies that can be hard to identify, such as Lyme disease.
Diagnosis is a crucial step in medicine, but it can also be the most
difficult. Doctors usually must guess the most likely causes of a medical
problem and then order individual tests to see which is the right diagnosis.
The guessing game can waste precious time. The causes of some conditions,
like encephalitis, can be so hard to diagnose that doctors often end up with
no answer at all.
“About 60 percent of the time, we never make a diagnosis” in encephalitis,
said Dr. Michael R. Wilson, a neurologist at the University of California,
San Francisco, and an author of the new paper. “It’s frustrating whenever
someone is doing poorly, but it’s especially frustrating when we can’t
even tell the parents what the hell is going on.”
For the last decade, researchers at the university have been working on
methods for identifying pathogens based on their DNA. In 2003 Dr. Joseph
DeRisi, a biochemist at the university, gained wide attention for using a
gene chip called a microarray to identify the coronavirus causing SARS.
The researchers’ latest method is called unbiased next-generation
sequencing. To identify a pathogen, the researchers extract every scrap of
DNA in a sample from a patient, which might be blood, cerebrospinal fluid or
stool. Then they sift the genetic fragments for those belonging to
pathogens.
The technique already has proved valuable for investigating mysterious
disease outbreaks, and a number of scientists have begun to hope it can be
adapted to the diagnosis of individual patients’ infections. Rather than
test for a suspected pathogen, a doctor could simply run a DNA test that
could identify the culprit no matter what it is — virus, bacterium, fungus
or parasite.
Continue reading the main storyContinue reading the main story
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“It could be one test to rule them all,” Dr. DeRisi said in an interview.
But such a test would be useful only if it were fast, and sorting through
millions of DNA fragments has been an intensive technological challenge.
Playing this match game can take weeks.
“The problem is that your critically ill patient will be dead by the time
you make a diagnosis,” said Dr. Charles Chiu, a pathologist at the
university who collaborates with Dr. DeRisi on diagnostic technologies.
Dr. Chiu and his colleagues have developed software that rapidly compares
DNA fragments with genetic sequences stored in online databases. They
describe their new strategy in a second paper published on Wednesday in the
journal Genome Research.
Last July, Dr. DeRisi and Dr. Chiu got a chance to put their methods to the
test when they received a call from a research collaborator, Dr. James Gern,
a pediatrician at the University of Wisconsin School of Medicine. He asked
them to help figure out what was wrong with Joshua Osborn.
Joshua had long been a patient of Dr. Gern’s, since doctors found that the
boy had an immune system disorder at two months old. In April 2013, he
developed severe headaches and a fever. He was admitted to the hospital and
tested for a long list of diseases, from West Nile virus to tuberculosis.
The tests all came back negative.
For the next two months, Joshua remained at home, his health wavering. When
his fever spiked again, he ended up back in the hospital. An M.R.I. revealed
that his brain was dangerously inflamed, but a spinal tap turned up no
pathogens. Even a biopsy of his brain tissue told the doctors nothing.
It was then that Dr. Gern called on Dr. DeRisi, who agreed to use the
experimental DNA technology to try to find what was causing the boy’s
ailments.
Dr. Gern’s team set about preparing samples of Joshua’s cerebrospinal
fluid and serum for testing. Dr. DeRisi’s team received the samples on Aug.
21, and by that evening, the lab’s sequencing machines were working on the
first batch of DNA.
Continue reading the main story
RECENT COMMENTS
Doug 2 days ago
Why is it that now, we are just deciding to look at "root causes" to
problems. I'd say it's pretty safe to say, at this point, that most...
Nick Landau 2 days ago
How does this test differ from the one offered by Diatherix? Diatherix uses
temPCR to detect dozens of pathogens simultaneously, including...
Charles Chiu MD/PhD 2 days ago
To address questions raised by readers:(1) Why was he not treated with
penicillin at the outset? Penicillin has efficacy only against a...
SEE ALL COMMENTS
Two days later, the machines had deciphered the sequences of three million
fragments of DNA present in Joshua’s samples. With Dr. Chiu’s software,
the team set aside the human DNA fragments and began grinding through DNA
databases to identify the other genes.
After only 96 minutes, the results appeared on a computer monitor. Joshua’s
cerebrospinal fluid contained DNA from a potentially lethal type of
bacteria called Leptospira. As dangerous as Leptospira can be, it is readily
treated with penicillin.
“It was a very exciting phone call to make to Wisconsin,” Dr. Wilson said.
“Not only was there an answer, but there was something they could
potentially do about it.”
That afternoon, Joshua started getting large doses of penicillin. The
swelling in his brain almost immediately started subsiding, and two weeks
after the first test results, Joshua was walking.
“I don’t have any headaches anymore,” Joshua said in an interview. “It’
s almost like a rebirth.”
Dr. Chiu is now leading a project to develop a DNA-based test for diagnosing
the causes of encephalitis and other life-threatening conditions. They also
hope to apply it more broadly, as a way to quickly diagnose any infection.
“It’s a demonstration that this technology has arrived,” Dr. DeRisi said.
“It can make a difference in real time.”
There are still many obstacles that scientists will have to overcome before
these tests can be a part of standard practice.
“Our bodies are full of microbes,” said Dr. Gregory Storch, a professor of
pediatrics at the Washington University School of Medicine in St. Louis.
DNA-based tests will turn up many of those species in any patient sample.
Often, it may be hard to figure out which are making someone ill.
“This technology allows us to see the world in a different way, and we have
to get used to that,” Dr. Storch said. | s******s
发帖数: 13035 | 2 这个显然是老土PCR。
这个肯定是方向，不过现在还早
in
【在 s********n 的大作中提到】
: 现在这种例子越来越多了
: http://www.nytimes.com/2014/06/05/health/in-first-quick-dna-tes
: In a First, Test of DNA Finds Root of Illness
: Joshua Osborn, 14, lay in a coma at American Family Children’s Hospital in
: Madison, Wis. For weeks his brain had been swelling with fluid, and a
: battery of tests had failed to reveal the cause.
: The doctors told his parents, Clark and Julie, that they wanted to run one
: more test with an experimental new technology. Scientists would search
: Joshua’s cerebrospinal fluid for pieces of DNA. Some of them might belong
: to the pathogen causing his encephalitis.
| s********n
发帖数: 2939 | 3 这个不是PCR，是直接提取DNA做测序。虽然还没到常规检测的阶段，但对于不少“疑难
杂症”的诊断很有效啊
【在 s******s 的大作中提到】
: 这个显然是老土PCR。
: 这个肯定是方向，不过现在还早
:
: in
| s******s
发帖数: 13035 | 4 my bad, 读了一遍，确实是ngs
【在 s********n 的大作中提到】
: 这个不是PCR，是直接提取DNA做测序。虽然还没到常规检测的阶段，但对于不少“疑难
: 杂症”的诊断很有效啊
| a***y
发帖数: 19743 | 5 个人认为ngs测病原体不是未来。
马上要上市的设备比这个牛逼多了，而且敏感度速度数据量等都有优势。
★ 发自iPhone App: ChineseWeb 8.7
【在 s******s 的大作中提到】
: my bad, 读了一遍，确实是ngs
| s********n
发帖数: 2939 | 6 马上要上市的设备是指？
【在 a***y 的大作中提到】
: 个人认为ngs测病原体不是未来。
: 马上要上市的设备比这个牛逼多了，而且敏感度速度数据量等都有优势。
:
: ★ 发自iPhone App: ChineseWeb 8.7
| a***y
发帖数: 19743 | 7 T2 Biosystems has developed the T2Dx instrument that is designed to
rapidly detect the bacterial and fungal pathogens that lead to sepsis in as
quickly as 3.5 hours and at limits of detection as low as 1 CFU/mL. Multiple
studies have shown that providing the appropriate antimicrobial therapy to
a patient within hours may reduce the mortality rate of bloodstream
infections by as much as 70%. The cost savings to the healthcare system in
the U.S. alone could be $12 billion per year from reduced hospital stays and
reduced use of unnecessary drugs.
【在 s********n 的大作中提到】
: 马上要上市的设备是指？
| s******s
发帖数: 13035 | 8 这个啥原理？我瞟了一眼，貌似有个核磁共振的测量方法？但是病原啥的还是靠ab?
as
Multiple
to
and
【在 a***y 的大作中提到】
: T2 Biosystems has developed the T2Dx instrument that is designed to
: rapidly detect the bacterial and fungal pathogens that lead to sepsis in as
: quickly as 3.5 hours and at limits of detection as low as 1 CFU/mL. Multiple
: studies have shown that providing the appropriate antimicrobial therapy to
: a patient within hours may reduce the mortality rate of bloodstream
: infections by as much as 70%. The cost savings to the healthcare system in
: the U.S. alone could be $12 billion per year from reduced hospital stays and
: reduced use of unnecessary drugs.
| a***y
发帖数: 19743 | 9 好像是ab上连得有nano beads，这些beads会给出一个NMR的信号
我觉得这个很牛。ngs测细菌相比起来就太原始了。
现在不是搞生物的来搞这个很厉害。上次在北京地铁里遇到一个墨西哥某大学的去参加
会议，他说他做的就是用nano material来检测食物里病原体，原理基本类似，就是
nano material bind到病原体上，就可以测到特殊的spectrum
【在 s******s 的大作中提到】
: 这个啥原理？我瞟了一眼，貌似有个核磁共振的测量方法？但是病原啥的还是靠ab?
:
: as
: Multiple
: to
: and
| s********z
发帖数: 5411 | 10 this is essentially a fast PCR, Right?
the problem is that you have to know what you are looking for and you can't
target many pathogens at the same time.
on ther other hand, NGS offers hypothesis free and precise targeting to
virtually any pathogen.
as
Multiple
to
and
【在 a***y 的大作中提到】
: T2 Biosystems has developed the T2Dx instrument that is designed to
: rapidly detect the bacterial and fungal pathogens that lead to sepsis in as
: quickly as 3.5 hours and at limits of detection as low as 1 CFU/mL. Multiple
: studies have shown that providing the appropriate antimicrobial therapy to
: a patient within hours may reduce the mortality rate of bloodstream
: infections by as much as 70%. The cost savings to the healthcare system in
: the U.S. alone could be $12 billion per year from reduced hospital stays and
: reduced use of unnecessary drugs.
| | | o*****a
发帖数: 2335 | 11 所以BME基本是化工,电子背景的来搞.生物的做苦力
【在 a***y 的大作中提到】
: 好像是ab上连得有nano beads，这些beads会给出一个NMR的信号
: 我觉得这个很牛。ngs测细菌相比起来就太原始了。
: 现在不是搞生物的来搞这个很厉害。上次在北京地铁里遇到一个墨西哥某大学的去参加
: 会议，他说他做的就是用nano material来检测食物里病原体，原理基本类似，就是
: nano material bind到病原体上，就可以测到特殊的spectrum
| s********n
发帖数: 2939 | 12 同意这个
问题是原文例子里，医生连是啥病原体都不知道，NGS才能解决问题
t
【在 s********z 的大作中提到】
: this is essentially a fast PCR, Right?
: the problem is that you have to know what you are looking for and you can't
: target many pathogens at the same time.
: on ther other hand, NGS offers hypothesis free and precise targeting to
: virtually any pathogen.
:
: as
: Multiple
: to
: and
| s********n
发帖数: 2939 | 13 你说的这个只能检测特定的病原体，不是针对广谱的，说ngs太原始有点搞笑吧？就效
果而言也未必比得上qPCR。
【在 a***y 的大作中提到】
: 好像是ab上连得有nano beads，这些beads会给出一个NMR的信号
: 我觉得这个很牛。ngs测细菌相比起来就太原始了。
: 现在不是搞生物的来搞这个很厉害。上次在北京地铁里遇到一个墨西哥某大学的去参加
: 会议，他说他做的就是用nano material来检测食物里病原体，原理基本类似，就是
: nano material bind到病原体上，就可以测到特殊的spectrum
| a***y
发帖数: 19743 | 14 it is not a PCR
it is not based on DNA
it is based on the presence of the bacteria: 1CFU/ml.
I am sure it can multiplex.
It is for clinical Dx not for research so it does not need "hypothesis free"
.
t
【在 s********z 的大作中提到】
: this is essentially a fast PCR, Right?
: the problem is that you have to know what you are looking for and you can't
: target many pathogens at the same time.
: on ther other hand, NGS offers hypothesis free and precise targeting to
: virtually any pathogen.
:
: as
: Multiple
: to
: and
| a***y
发帖数: 19743 | 15 临床监测就是快、准、灵敏、价格低、人力要求少。临床关注的病原菌就那么多种，又
不是做metagenomics。
NGS检测病原菌大概只适合研究。
【在 s********n 的大作中提到】
: 你说的这个只能检测特定的病原体，不是针对广谱的，说ngs太原始有点搞笑吧？就效
: 果而言也未必比得上qPCR。
| s******s
发帖数: 13035 | 16 是不是用抗体。
我看到使用核磁检测，不过核磁也看不到是啥玩意儿把，是不是
还是加抗体，用核磁检测的抗原抗体反应？
free"
【在 a***y 的大作中提到】
: it is not a PCR
: it is not based on DNA
: it is based on the presence of the bacteria: 1CFU/ml.
: I am sure it can multiplex.
: It is for clinical Dx not for research so it does not need "hypothesis free"
: .
:
: t
| a***y
发帖数: 19743 | 17 具体我也不清楚，可能是要用抗体。反正不同的病原菌最后给出的signature不一样。
是需要什么东西bind上去，只要bind了，就能读到相对应的signature。是否需要为每
种病原体设计不清楚，理想的是不需要，比如bind到某种细菌大分子上就好了。
NGS多快能出结果，需要多少sample处理步骤？NGS改良也可能可以做，不过我觉得这个
比较特别。不是测很多很多reads来大海捞针。
【在 s******s 的大作中提到】
: 是不是用抗体。
: 我看到使用核磁检测，不过核磁也看不到是啥玩意儿把，是不是
: 还是加抗体，用核磁检测的抗原抗体反应？
:
: free"
| s********z
发帖数: 5411 | 18 如果你都不知道什么原理，我看够呛。 怎么validate啊。
NGS的话，起码已经积攒了少database了。 这个新的还得build pathogen database吧
，如果mutate比较快的是不是也不好搞。
另外这个bind的东西是去bing整个genome吗？ 还是只是一小部分sequence,而且出来的
谱只反映一小部分sequence.
我本意是说结果跟pcr等效
【在 a***y 的大作中提到】
: 具体我也不清楚，可能是要用抗体。反正不同的病原菌最后给出的signature不一样。
: 是需要什么东西bind上去，只要bind了，就能读到相对应的signature。是否需要为每
: 种病原体设计不清楚，理想的是不需要，比如bind到某种细菌大分子上就好了。
: NGS多快能出结果，需要多少sample处理步骤？NGS改良也可能可以做，不过我觉得这个
: 比较特别。不是测很多很多reads来大海捞针。
| a***y
发帖数: 19743 | 19 你搞笑吗
别人都要商用了，不少医院应该都有订单了。前期的academic的research也做了。
又不是我开的公司我的技术，我为什么要把它家的原理搞得这么清楚？
bind的是surface。和DNA一点关系都没有。
【在 s********z 的大作中提到】
: 如果你都不知道什么原理，我看够呛。 怎么validate啊。
: NGS的话，起码已经积攒了少database了。 这个新的还得build pathogen database吧
: ，如果mutate比较快的是不是也不好搞。
: 另外这个bind的东西是去bing整个genome吗？ 还是只是一小部分sequence,而且出来的
: 谱只反映一小部分sequence.
: 我本意是说结果跟pcr等效
|
|
