s****l
发帖数: 10462 | 1 NIH最近又房顶了八个小组，大家看看哪一个最有可能成功？
The new grants are awarded (pending available funds) to:
University of California Santa Cruz, $2.29 million over three years
Principal Investigator: Mark Akeson, Ph.D.
Investigators plan to sequence single DNA molecules by using a nanopore
device comprised of a sensor that touches, examines and identifies each
nucleotide, or DNA building block, in a DNA strand as an enzyme motor moves
it through the pore. The scientists will focus on DNA “resequencing” —
examining the DNA nucleotides over and over — because of the difficulty in
accurately reading each strand initially.
Illumina, Inc., San Diego, $592,000 over two years
Principal Investigator: Boyan Boyanov, Ph.D.
Dr. Boyanov and his team aim to create a hybrid protein solid-state nanopore
array system that can enable scientists to sequence DNA on a large scale.
Their goal is to improve the robustness of nanopore platforms by combining
computer chip fabrication methods with biological nanopores to enable high-
throughput sequencing. The latter refers to a very high rate of sequencing
DNA by sequencing large numbers of DNA samples in parallel.
University of Pennsylvania, Philadelphia, $880,000 over two years
Principal Investigator: Marija Drndic, Ph.D.
Investigators plan to develop a synthetic nanopore from graphene — an
extremely conductive material consisting of a lattice of atoms, one atom
thick — that will enable the detection of individual DNA bases without the
need to slow down the DNA molecule as it passes through a pore. Researchers
hope to directly identify DNA bases by measuring unique differences in
current flowing through the graphene.
Caerus Molecular Diagnostics, Inc., Mountain View, California, $701,000 over
three years
Principal Investigator: Javier Farinas, Ph.D.
Researchers commonly use a system to identify DNA bases that entails making
many copies of DNA and detecting a light signal from the DNA. Dr. Farinas
and his co-workers plan to test a technology that uses an engineered enzyme
switch to convert the product of a single molecule DNA sequencing reaction
into many copies of a reporter molecule that are easily detected. The method
promises to more accurately identify DNA bases.
The Scripps Research Institute, La Jolla, California, $4.4 million over four
years
Principal Investigator: M. Reza Ghadiri, Ph.D.
Investigators plan to produce protein nanopore arrays in order to sequence
tens of thousands of DNA molecules in parallel, with the eventual goal of
sequencing a human genome in as little as 10 minutes. They will explore
three separate approaches, including arrays of lipid bilayers containing
nanopores, protein pores individually embedded in synthetic films, and
nanopores made of DNA that are distributed on DNA scaffolds.
Eve Biomedical, Inc., Mountain View, California, $500,000 over two years
Principal Investigator: Theofilos Kotseroglou, Ph.D.
Researchers will study a system to sequence DNA using an enzyme (polymerase)
on a carbon nanotube, in an array format. Carbon nanotubes are long, thin
cylindrical tubes that are highly conductive. When an enzyme is anchored on
a tube, the enzyme’s motion — while interacting with a DNA sample —
changes the conductivity on the nanotube, and enables bases of the sample
DNA to be identified.
University of Washington, Seattle, $1.7 million over three years
Principal Investigator: Jay Shendure, M.D., Ph.D.
Dr. Shendure and his colleagues plan to develop new molecular biology
techniques to efficiently and cost-effectively stitch together genomes
across long distances. They hope this will help improve the quality of
genomes that are generated by new DNA sequencing technologies.
University of California, San Diego, $3.7 million over four years
Principal Investigators: Kun Zhang, Ph.D. and Xiaohua Huang, Ph.D.
This team plans to develop a system using microfluidics that will enable
accurate genome sequencing of a single mammalian cell. Investigators will
separate and sequence single chromosomal DNA strands, and then with the help
of novel technology to make many copies of genomes, they will create DNA
sequence libraries for DNA sequencing of single cells. | s******s
发帖数: 13035 | 2 听到nanopore和graphene，我high了
moves
in
【在 s****l 的大作中提到】
: NIH最近又房顶了八个小组，大家看看哪一个最有可能成功？
: The new grants are awarded (pending available funds) to:
: University of California Santa Cruz, $2.29 million over three years
: Principal Investigator: Mark Akeson, Ph.D.
: Investigators plan to sequence single DNA molecules by using a nanopore
: device comprised of a sensor that touches, examines and identifies each
: nucleotide, or DNA building block, in a DNA strand as an enzyme motor moves
: it through the pore. The scientists will focus on DNA “resequencing” —
: examining the DNA nucleotides over and over — because of the difficulty in
: accurately reading each strand initially.
| s****l
发帖数: 10462 | 3 why?
【在 s******s 的大作中提到】
: 听到nanopore和graphene，我high了
:
: moves
: in
| f*******e
发帖数: 628 | 4 有点儿意思。
看来各种 nanopore 横行。可是最先的 oxford nanopore 现在算成功了么？
moves
in
【在 s****l 的大作中提到】
: NIH最近又房顶了八个小组，大家看看哪一个最有可能成功？
: The new grants are awarded (pending available funds) to:
: University of California Santa Cruz, $2.29 million over three years
: Principal Investigator: Mark Akeson, Ph.D.
: Investigators plan to sequence single DNA molecules by using a nanopore
: device comprised of a sensor that touches, examines and identifies each
: nucleotide, or DNA building block, in a DNA strand as an enzyme motor moves
: it through the pore. The scientists will focus on DNA “resequencing” —
: examining the DNA nucleotides over and over — because of the difficulty in
: accurately reading each strand initially.
| y*****3
发帖数: 961 | 5 还没把。
测试的结果良莠不齐。
【在 f*******e 的大作中提到】
: 有点儿意思。
: 看来各种 nanopore 横行。可是最先的 oxford nanopore 现在算成功了么？
:
: moves
: in
| s****l
发帖数: 10462 | 6 NIH最近又房顶了八个小组，大家看看哪一个最有可能成功？
The new grants are awarded (pending available funds) to:
University of California Santa Cruz, $2.29 million over three years
Principal Investigator: Mark Akeson, Ph.D.
Investigators plan to sequence single DNA molecules by using a nanopore
device comprised of a sensor that touches, examines and identifies each
nucleotide, or DNA building block, in a DNA strand as an enzyme motor moves
it through the pore. The scientists will focus on DNA “resequencing” —
examining the DNA nucleotides over and over — because of the difficulty in
accurately reading each strand initially.
Illumina, Inc., San Diego, $592,000 over two years
Principal Investigator: Boyan Boyanov, Ph.D.
Dr. Boyanov and his team aim to create a hybrid protein solid-state nanopore
array system that can enable scientists to sequence DNA on a large scale.
Their goal is to improve the robustness of nanopore platforms by combining
computer chip fabrication methods with biological nanopores to enable high-
throughput sequencing. The latter refers to a very high rate of sequencing
DNA by sequencing large numbers of DNA samples in parallel.
University of Pennsylvania, Philadelphia, $880,000 over two years
Principal Investigator: Marija Drndic, Ph.D.
Investigators plan to develop a synthetic nanopore from graphene — an
extremely conductive material consisting of a lattice of atoms, one atom
thick — that will enable the detection of individual DNA bases without the
need to slow down the DNA molecule as it passes through a pore. Researchers
hope to directly identify DNA bases by measuring unique differences in
current flowing through the graphene.
Caerus Molecular Diagnostics, Inc., Mountain View, California, $701,000 over
three years
Principal Investigator: Javier Farinas, Ph.D.
Researchers commonly use a system to identify DNA bases that entails making
many copies of DNA and detecting a light signal from the DNA. Dr. Farinas
and his co-workers plan to test a technology that uses an engineered enzyme
switch to convert the product of a single molecule DNA sequencing reaction
into many copies of a reporter molecule that are easily detected. The method
promises to more accurately identify DNA bases.
The Scripps Research Institute, La Jolla, California, $4.4 million over four
years
Principal Investigator: M. Reza Ghadiri, Ph.D.
Investigators plan to produce protein nanopore arrays in order to sequence
tens of thousands of DNA molecules in parallel, with the eventual goal of
sequencing a human genome in as little as 10 minutes. They will explore
three separate approaches, including arrays of lipid bilayers containing
nanopores, protein pores individually embedded in synthetic films, and
nanopores made of DNA that are distributed on DNA scaffolds.
Eve Biomedical, Inc., Mountain View, California, $500,000 over two years
Principal Investigator: Theofilos Kotseroglou, Ph.D.
Researchers will study a system to sequence DNA using an enzyme (polymerase)
on a carbon nanotube, in an array format. Carbon nanotubes are long, thin
cylindrical tubes that are highly conductive. When an enzyme is anchored on
a tube, the enzyme’s motion — while interacting with a DNA sample —
changes the conductivity on the nanotube, and enables bases of the sample
DNA to be identified.
University of Washington, Seattle, $1.7 million over three years
Principal Investigator: Jay Shendure, M.D., Ph.D.
Dr. Shendure and his colleagues plan to develop new molecular biology
techniques to efficiently and cost-effectively stitch together genomes
across long distances. They hope this will help improve the quality of
genomes that are generated by new DNA sequencing technologies.
University of California, San Diego, $3.7 million over four years
Principal Investigators: Kun Zhang, Ph.D. and Xiaohua Huang, Ph.D.
This team plans to develop a system using microfluidics that will enable
accurate genome sequencing of a single mammalian cell. Investigators will
separate and sequence single chromosomal DNA strands, and then with the help
of novel technology to make many copies of genomes, they will create DNA
sequence libraries for DNA sequencing of single cells. | s******s
发帖数: 13035 | 7 听到nanopore和graphene，我high了
moves
in
【在 s****l 的大作中提到】
: NIH最近又房顶了八个小组，大家看看哪一个最有可能成功？
: The new grants are awarded (pending available funds) to:
: University of California Santa Cruz, $2.29 million over three years
: Principal Investigator: Mark Akeson, Ph.D.
: Investigators plan to sequence single DNA molecules by using a nanopore
: device comprised of a sensor that touches, examines and identifies each
: nucleotide, or DNA building block, in a DNA strand as an enzyme motor moves
: it through the pore. The scientists will focus on DNA “resequencing” —
: examining the DNA nucleotides over and over — because of the difficulty in
: accurately reading each strand initially.
| s****l
发帖数: 10462 | 8 why?
【在 s******s 的大作中提到】
: 听到nanopore和graphene，我high了
:
: moves
: in
| f*******e
发帖数: 628 | 9 有点儿意思。
看来各种 nanopore 横行。可是最先的 oxford nanopore 现在算成功了么？
moves
in
【在 s****l 的大作中提到】
: NIH最近又房顶了八个小组，大家看看哪一个最有可能成功？
: The new grants are awarded (pending available funds) to:
: University of California Santa Cruz, $2.29 million over three years
: Principal Investigator: Mark Akeson, Ph.D.
: Investigators plan to sequence single DNA molecules by using a nanopore
: device comprised of a sensor that touches, examines and identifies each
: nucleotide, or DNA building block, in a DNA strand as an enzyme motor moves
: it through the pore. The scientists will focus on DNA “resequencing” —
: examining the DNA nucleotides over and over — because of the difficulty in
: accurately reading each strand initially.
| y*****3
发帖数: 961 | 10 还没把。
测试的结果良莠不齐。
【在 f*******e 的大作中提到】
: 有点儿意思。
: 看来各种 nanopore 横行。可是最先的 oxford nanopore 现在算成功了么？
:
: moves
: in
| | | b****r
发帖数: 17995 | 11 单分子技术已经做得这么多了，DNA这么大一分子 ，全世界的这么砸钱，应该用不了多
久就会做出来的。到时候就有意思了。要革命了！
【在 f*******e 的大作中提到】
: 有点儿意思。
: 看来各种 nanopore 横行。可是最先的 oxford nanopore 现在算成功了么？
:
: moves
: in
| n******7
发帖数: 12463 | 12 这两天研究了一下MinIon
目前基本是垃圾
通量超低，错误率1/3左右，一个run要1000刀
唯一的亮点是读长
【在 f*******e 的大作中提到】
: 有点儿意思。
: 看来各种 nanopore 横行。可是最先的 oxford nanopore 现在算成功了么？
:
: moves
: in
| C***H
发帖数: 508 | 13 1/3的错误率是最开始的时候了吧，现在好象小于15%乐
对了，pacbio一个run多少钱？
【在 n******7 的大作中提到】
: 这两天研究了一下MinIon
: 目前基本是垃圾
: 通量超低，错误率1/3左右，一个run要1000刀
: 唯一的亮点是读长
| n******7
发帖数: 12463 | 14 你自己看最近的publication。pacbio的东西多年没关注了，这个nano pore应该是他们
最直接的竞争者。
http://biorxiv.org/content/early/2015/01/06/013490
We describe software developed to make use of these data as existing
packages were incapable of assembling long reads at such high error rate (~
35% error).
Some runs have produced upwards of 490 Mb of sequencing data per flow cell
over a 48 hour period. All together, we generated a total of 120x coverage
of the genome with an average read length of 5473bp but with a long tail
extending to a maximum read length of 146,992bp
Of the 267,768 reads produced by our 30 sequencing runs, 64,849 reads (24%)
aligned to the reference yeast genome, and 31,013 (11%) aligned to the known
spike-in sequence used for calibrating the instruments. The remaining 65%
of reads did not show significant similarity to the W303 genome or spike-in
sequence, presumably because of insufficient read quality (Supplemental note
4). Supplemental Figure S5A shows that the mean identity to the reference
of “1D” reads was 64% while “2D” reads produced many reads exceeding 75%
identity.
The results of this study indicate the Oxford Nanopore sequence data
currently have substantial errors (~25% to 40% error) and a high proportion
of reads that completely fail to align (~65%). This is likely due to the
challenges of the signal processing the ionic current measurements13 as well
as the challenges inherent in any type of single molecule sequencing.
Oxford Nanopore has indicated that the pores are more than a single base in
height so that the ionic signal measurements are not of individual
nucleotides but of approximately 5 nucleotides at a time. Consequently the
base calling must individually recognize at least 45=1024 possible states of
ionic current for each possible 5-mer. We also observed the potential for
some bias in the signal processing and basecaller, particularly for
homopolymers. Despite the limitations of this early phase device, there has
been notable improvement over the course of this program, and well
performing flowcells of the current iteration (R7 at the time this
publication was written) can generate upwards of 400Mb on a single run and
we remain optimistic to see yields improve with future generations of the
technology.
【在 C***H 的大作中提到】
: 1/3的错误率是最开始的时候了吧，现在好象小于15%乐
: 对了，pacbio一个run多少钱？
| s******r
发帖数: 1245 | 15 1k刀很便宜啊
能读多长？通量多大？
【在 n******7 的大作中提到】
: 这两天研究了一下MinIon
: 目前基本是垃圾
: 通量超低，错误率1/3左右，一个run要1000刀
: 唯一的亮点是读长
| n******7
发帖数: 12463 | 16 1k要看得到啥
1k做个30x的WGS那是不错
这个是MinION啊
最近一个文章就测了3个gene，coverage倒是有1000左右
最长reads我上面贴的那个是146,992bp
这个技术现阶段的亮点也就是读长，用来做scaffold 还凑合
【在 s******r 的大作中提到】
: 1k刀很便宜啊
: 能读多长？通量多大？
| y*****3
发帖数: 961 | 17 几百刀的样子。
【在 C***H 的大作中提到】
: 1/3的错误率是最开始的时候了吧，现在好象小于15%乐
: 对了，pacbio一个run多少钱？
| s****l
发帖数: 10462 | 18 MinIon的数据已经出来了一些了。
大概看了下，总体上讲，还有很远的路要走。能不能真正进入市场还很难说。
single read accuracy只有60～70%，相当坑爹，但是可以长达好几千甚至好几万个碱
基。大部分有效的在几千的水平吧。
有的人说error is biased，也就是说很多reads都会在同一区域出错，这样一来，high
depth coverage也不太能帮上忙。但是也有的说，error is not biased，那么多测若
干遍也就能提高consensus accuracy了。
最大的好处就是便携和便宜了
【在 s******r 的大作中提到】
: 1k刀很便宜啊
: 能读多长？通量多大？
| n******7
发帖数: 12463 | 19 好处是可以做scaffold
我感觉对isoform 或者SV 分析会很有用，这对准确率要求不高
但是目前的通量也太低了
还在玩票阶段
high
【在 s****l 的大作中提到】
: MinIon的数据已经出来了一些了。
: 大概看了下，总体上讲，还有很远的路要走。能不能真正进入市场还很难说。
: single read accuracy只有60～70%，相当坑爹，但是可以长达好几千甚至好几万个碱
: 基。大部分有效的在几千的水平吧。
: 有的人说error is biased，也就是说很多reads都会在同一区域出错，这样一来，high
: depth coverage也不太能帮上忙。但是也有的说，error is not biased，那么多测若
: 干遍也就能提高consensus accuracy了。
: 最大的好处就是便携和便宜了
| C***H
发帖数: 508 | 20 http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.32
这个刚出来的结果算是比较新的，看样子正确率还不错85%，通量比较差，总的来
说好像比较正面？
high
【在 s****l 的大作中提到】
: MinIon的数据已经出来了一些了。
: 大概看了下，总体上讲，还有很远的路要走。能不能真正进入市场还很难说。
: single read accuracy只有60～70%，相当坑爹，但是可以长达好几千甚至好几万个碱
: 基。大部分有效的在几千的水平吧。
: 有的人说error is biased，也就是说很多reads都会在同一区域出错，这样一来，high
: depth coverage也不太能帮上忙。但是也有的说，error is not biased，那么多测若
: 干遍也就能提高consensus accuracy了。
: 最大的好处就是便携和便宜了
| | | s****l
发帖数: 10462 | 21 那你得看看这是那个lab发的文章
要是MA的文章都不正面，那这技术还搞个球
【在 C***H 的大作中提到】
: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.32
: 这个刚出来的结果算是比较新的，看样子正确率还不错85%，通量比较差，总的来
: 说好像比较正面？
:
: high
| s******s
发帖数: 13035 | 22 如果没有bias，肯定没问题。这玩意儿这么长，根本没有multimapping的问题，
多测就行了。不过想一想这技术，多半是有bias的，当然，如果原厂的algorithm
多调整，也许能解决。
high
【在 s****l 的大作中提到】
: MinIon的数据已经出来了一些了。
: 大概看了下，总体上讲，还有很远的路要走。能不能真正进入市场还很难说。
: single read accuracy只有60～70%，相当坑爹，但是可以长达好几千甚至好几万个碱
: 基。大部分有效的在几千的水平吧。
: 有的人说error is biased，也就是说很多reads都会在同一区域出错，这样一来，high
: depth coverage也不太能帮上忙。但是也有的说，error is not biased，那么多测若
: 干遍也就能提高consensus accuracy了。
: 最大的好处就是便携和便宜了
| C***H
发帖数: 508 | 23 又出新文章了：
http://biorxiv.org/content/early/2015/02/20/015552
29X coverage, de novo bacterial genome, nanopore only, 98.4%
最近nanopore文章不断阿
【在 s******s 的大作中提到】
: 如果没有bias，肯定没问题。这玩意儿这么长，根本没有multimapping的问题，
: 多测就行了。不过想一想这技术，多半是有bias的，当然，如果原厂的algorithm
: 多调整，也许能解决。
:
: high
| s****l
发帖数: 10462 | 24 能达到98.4%的话，还是很不错的，我觉得。这样准确度要求第一点，但是要求快速和
方便的应用就可以用了。
【在 C***H 的大作中提到】
: 又出新文章了：
: http://biorxiv.org/content/early/2015/02/20/015552
: 29X coverage, de novo bacterial genome, nanopore only, 98.4%
: 最近nanopore文章不断阿
|
|
