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
A... 阅读全帖 |
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t*d
发帖数: 1290 | 2 http://www.genomeweb.com//node/980559?hq_e=el&hq_m=1103092&hq_l
----------------------------------------
A recent study by scientists at Yale University suggests that the actual
cost of sequencing may be much higher than some current estimates indicate
since those figures may not factor in the analysis costs that are necessary
for a successful sequencing project.
In the paper, published in Genome Biology last month, Yale's Mark Gerstein
and colleagues consider costs that weren’t taken into accou... 阅读全帖 |
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y***k
发帖数: 40 | 3 终于有人忍不住下手了，可是到哪里找业务去喂饱这个巨兽呢
=================================================
SAN DIEGO & SHANGHAI--(BUSINESS WIRE)--Mar. 10, 2014-- Illumina, Inc. (
NASDAQ:ILMN) and WuXi PharmaTech (Cayman) Inc. (NYSE:WX), a leading
pharmaceutical, biotechnology, and medical device R&D outsourcing company
with operations in China and the United States, today announced that the
WuXi Genome Center has purchased an Illumina HiSeq X Ten sequencing system.
This new investment will enable WuXi’s clinical genomic ser... 阅读全帖 |
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n*********4
发帖数: 99 | 4 Illumina Introduces the HiSeq 2500
Speed and Performance Enhancements Pave the Way to Future Clinical Use
Illumina ILMN +2.61% today introduced the HiSeq(R) 2500, a next-generation
sequencing system that will enable researchers and clinicians to sequence an
entire genome in approximately 24 hours, "Genome in a Day". The HiSeq 2500
leverages the continued technology advancements from both the HiSeq 2000 and
MiSeq(TM) platforms.
"The ability to sequence an entire genome in a day with the same high... 阅读全帖 |
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j**W
发帖数: 89 | 5 You are right about a couple of things.I switch field and learned biology (
not including molecular biology) in English.And I did not make the targeting
vector. I took over the project starting from agouti mouse. Please bear
with me if I could not be clearer. I am sorry about the confusion on the
primer used for sequencing. We did sequencing with both P1 and P2. One came
back with no good sequence at all. From the sequencing result of the other,
it seems to me like P1. The sequencing result cove... 阅读全帖 |
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R****n
发帖数: 708 | 6 Generally speaking adaptor and primer are all oligo nucleotide sequences.
The difference lies in their roles in a 2nd generation sequencing reaction.
Adaptor is used for ligating the primer to the target sequences(usually for
DNA,RNA,miRs).Certain sequences are more efficient for ligation reaction.
Sometimes there will be a barcode sequences between adaptor and primer to
identify each sample when multiple samples are sequenced.common primer pair
is used for amplify a huge pool of ligated sequenc... 阅读全帖 |
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u*********1
发帖数: 2518 | 7 不晓得大家有没有看这个文章：
http://www.cell.com/abstract/S0092-8674%2812%2900166-3
Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes
Michael Synder在14个月内各种genomics，transcriptome，proteomics，
metabolomics的数据叠加起来，最后准确的预测了他要得糖尿病
我觉得只要：
1.DNA测序技术本身质量足够高（比如更加准确，read更加长），价格足够低；那么需
求量会越来越大。你看几年前exome sequencing还是不多；而现在成百上千的exome
sequencing都满天飞了。DNA测序可以解决genomics和transcriptome这两样最重要的
omics
2.搞清楚这些sequences到底干啥的。coding protein到底什么作用；noncoding区域
regulatory function（比如ENCODE project），以及这些regulato... 阅读全帖 |
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m****n
发帖数: 1066 | 8 1.PCR product is about 200bp. PCR product was run on an agarose gel, cut off
from the gel and purified using a Qia quick gel extraction kit from Qiagen
. The elution buffer doesn’t have EDTA.
2.PCR primers were used as sequencing primers.
3.During the first try, some part of the sequence was readable. The
remaining was mixed with NNNN.
4.During the second try, I redid the PCR and gel-purification. All of the
sequences were NNN. The same sequencing contractor was used.
I like to make some change... 阅读全帖 |
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m*********D
发帖数: 1727 | 9 请教行家：Feng Zhang的genome-wide Screening（CRISPR)后面的deep sequencing
对这个很感兴趣。读了几篇相关的文章和screening,前面的library--infection--drug
screening--genomic DNA extraction都懂。后面的deep sequencing部分就糊涂了。
理论上讲，resistant的细胞一定是有基因改变了的，我一直以为挑单克隆，一个一个
去作整个genome测序。仔细读了文章，是药物筛选几天后，细胞pool一起，再作deep
sequence；对照没有drug筛选（Non-resistant)的组，找出那些被CRISPR改变了的gene
，再确认。
几个问题：
1。这个deep sequencing是测（整个）genomic DNA，还是测留下来的guide sequence
（在lentiviral vector上面）？
2。可以测mRNA/cDNA序列来代替genomic DNA吗？突变的基因总该表现在mRNA上（先不
考虑其他类型的RNA）。
3。因为是pool一起的，不... 阅读全帖 |
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l******g
发帖数: 2 | 10 Hello all. I have a question about the conditional sequence. Thanks.
flowsheets 1000s (sequence day1) flowsheets 2000s (sequence day2) flowsheets
3000s(sequence nigt)
Sequence ovsq intl calc day1 day2 nigt
in "calc" block, I will calculate powr and descide to execute sequnce (day1
day2) or (nigt) rather than all sequences.
How can I do?
Thanks a lot |
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l***e
发帖数: 303 | 11 You are given a grid of numbers. A snake sequence is made up of adjacent
numbers such that for each number, the number on the right or the number
below it is +1 or -1 its value. For example,
1 3 2 6 8
-9 7 1 -1 2
1 5 0 1 9
In this grid, (3, 2, 1, 0, 1) is a snake sequence.
Given a grid, find the longest snake sequences and their lengths (so there
can be multiple snake sequences with the maximum length).
用dfs的话不太好算最长的sequences 用DP没思路 |
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l********s
发帖数: 395 | 12 Located on the beautiful sea shore of Honolulu, Hawaii, overlooking the
Pacific Ocean, the University of Hawaii Cancer Center (UHCC) is argubly the
most beautiful Cancer Center among 66 Cancer Centers designated by the
National Cancer Institute
Projects available in the bioinformatics/genomics group, include but are not
limited to (1) Characterization and comparative genomics of long-intergenic
non-coding RNAs with next-generation sequencing data etc. (2) develop
efficient multi-dimensional data... 阅读全帖 |
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W*******a
发帖数: 1769 | 13 You need to understand how Illumina seq works. Two ends of the
library molecule anneal to two oligos on the slide, forming
a bridge, and a PCR is performed in situ to amplify this molecule
into a cluster. The efficiency and consistence of cluster forming
is limited by the size of the insert, you can't have very long
product (>1kb)
classical pair-ends are generated directly from short inserts
usually less than 1kb, so no special library preparation method is
required.
For mate-paired, the t... 阅读全帖 |
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g**********t
发帖数: 475 | 14 你想做教授还是进公司？如果对学术界兴趣不大，可接收第一个offer。以鄙人拙见，
在可见的未来next generation sequencing大有用武之地，而且在未来很有可能大规模
outsource到国内。如果想找教授位置可以考虑进一个用next generation sequencing
方法做生物学问题的lab，很多相关文章的一作都是bioinformatician。大规模用next
generation sequencing的project一般都能发到比较好的杂志上。
总感觉Graph theory做结构发展缓慢，找教职估计比做next generation sequencing难
（当然你不能只做支持）。
sequencing |
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l**********1
发帖数: 5204 | 15 cited from OX dot ac dot uk
6 gene sequencing test for cancer patients on the NHS
Health
Science 25 Mar 13
The first multi-gene test that can help predict cancer patients' responses
to treatment using the latest DNA sequencing techniques has been launched in
the NHS, thanks to a partnership between scientists at the University of
Oxford and Oxford University Hospitals NHS Trust.
The test detects mutations across 46 genes in cancer cells, mutations which
may be driving the growth of the cancer in... 阅读全帖 |
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l**********1
发帖数: 5204 | 16 Illumina won first round Competition before QE2 of 2013
Genomics Conference Illustrates that Illumina is Outpacing the Competition
Ivan Deryugin
March 15, 2013
On the evening of March 14, Illumina (ILMN) announced that a federal jury
found it guilty of infringing a patent held by Syntrix Biosystems relating
to the company’s BeadChip product line, fining Illumina $96 million based
on a 6% royalty on all BeadChip sales between 2005 and September 2012 (
Syntrix’s lawsuit was filed in November 2010)... 阅读全帖 |
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w********a
发帖数: 324 | 17 Sanger sequencing：现在用的Eurofins。太奇葩了。
出现了好几次，收到的sequencing results(high quality results!)跟我们送去的
sample完全irrelevant。要求
重新sequence之后，终于得到了我们想要的结果。
这一次更好笑了。又是出现这样的情况，我们发信说，是不是你们把我们的sample或者
我们的数据跟别人的混了。一个老印女的Technician胡搅蛮缠，要命不承认。那好吧，
重新测序。Guess what：这次发给我们的序列跟第一次测的序列完全一样，1000多个bp
连里面出现的“N"都丝毫不差，就连任何一个碱基的chromotograph都是一模一样的，
而且是整个order里面大概10个samples都是这样的！我们又发信问，是不是你们这次直
接把上次的数据改了一下日期发给我们了一份? 老印还在狡辩，说绝无可能，并且把两
次sequencing的时间发给我们。我真是太无语了。
这个公司倒是挺便宜，$5/sample, 还有免费的shipping label。看来真是便宜无好货
啊。
大家有其它的san... 阅读全帖 |
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b********w
发帖数: 334 | 18 直接面向个人
Tech Details:
- FDA approved Saliva collection kit.
- Agilent SureSelect V5 50MB chip
- 75x on target coverage (after mapping, filtering, and duplicate removal,
130-140x raw throughput)
- 99% Coverage > 1x
- 90% Coverage > 20x
- CLIA certified Illumina sequencing.
Deliverable
- Ownership of your genome
- VCF file (Beta 期间你要原始数据 BAM，我们也可以提供。)
- CLINVAR, CGD summary about your variants
- Traits
- Beta 期间你要原始数据，我们也可以提供。
Public exposure
Genomeweb:
https://www.genomeweb.com/molecular-diagnost... 阅读全帖 |
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c******5
发帖数: 84 | 19 Detecting Cycles
Description:
Given a sequence, write a program to detect cycles within it.
Input sample:
A file containing a sequence of numbers (space delimited). The file can have
multiple such lines. e.g
2 0 6 3 1 6 3 1 6 3 1
Ensure to account for numbers that have more than one digit eg. 12. If there
is no sequence, ignore that line.
Output sample:
Print to stdout the first sequence you find in each line. Ensure that there
are no trailing empty spaces on each line you print. e.g.
6 3 1
Any... 阅读全帖 |
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g****r
发帖数: 14 | 20 Kozak
Sequence for
Mammalian
Expression
If you will be recombining your entry clone with a
destination vector for mammalian expression, your insert
should contain a Kozak consensus sequence with an ATG
initiation codon for proper initiation of translation (Kozak,
1987; Kozak, 1991; Kozak, 1990). An example of a Kozak
consensus sequence is provided below. Other sequences are
possible, but the G or A at position -3 and the G at position
+4 are the most critical for function (shown in bold). The
AT |
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k***x
发帖数: 34 | 21 看了Nature上那篇Inuk的原始人genome的paper，整个genome sequence出来之后，也只找到几个特征性的SNP，比如眼睛的颜色，earwax，门牙什么的。
是不是可以找很多种特征基因，只是这篇paper没专注这方面？还是特征性SNP就是不好找？
读了一下full genome sequencing的wiki，现在有这么多家公司都在开发，而且眼看成本就要到$1000以下了。 即使不提sequence出来的depth和false positive rate，就是质量极高的sequence，如果不知道怎么解释data，还是没有什么意义吧。有没有朋友了解的给介绍一下，谢谢了。 |
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L******e
发帖数: 679 | 23 I believe that the data analysis play a very important role in the next-
generation sequencer. As i mentioned that a pathologist do not want to waste
time in reading sequence results. I am thinking if hundreds of thousands of
sequence results were automatically analysed before they go to a
pathologist. Pathologist only need to pick up the final mutant results and
screen the one related to targeted therapy.
That need somebody to put all the normal sequence, SNP and mutation
information into the d |
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X***n
发帖数: 366 | 24 Seed sequence is only about 6-nt, it's possible for it presents in mRNA
sequence by chance. Besides, seed sequence matching is not sufficient to
make a mRNA the target. You may try RNA22. You can loose the stringent by
allowing UN wooble and lower folding energy parameters. |
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m*********n
发帖数: 215 | 25 如果你要detect de nova mutation的话，可以用whole genome sequencing。其实平均
到每个base pair，whole genome sequencing比exonme sequencing便宜，而且可以
detect在3'utr, 5‘utr和non-coding sequencing上的信号。 |
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l*****g
发帖数: 263 | 26 Could you please recommend a program for below purpose? Thanks.
I have a short (20-30 residues) protein sequence and I would like to find
the best matches on a long protein sequence (2000 residues). Can anyone
recommend a good program to handle this? It will be better if I can have a
list of matches on the long sequence with scores.
Now a bit difficult, I have a pattern, say DdGLLeqHLGGrgG (where capital
letters mean more conserved). I need to find the best match for this pattern
. Could someone... 阅读全帖 |
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g*******8
发帖数: 6 | 27 Thanks so much for your reply!
But if so, why most time we still do core sequencing (directly use pcr
product and primer to do sequencing)? Could you please tell me when should
we do core sequencing and when should we do TOPO cloning and then sequencing
?
Thanks again! |
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t*d
发帖数: 1290 | 28 找到一点信息
The Ion Proton I Chip, which the firm said will be ideal for sequencing
exomes, will be available mid-2012. The Ion Proton II Chip, designed for
sequencing whole human genomes, will be available about six months later.
Lucier said that the cost of exome sequencing would be brought down to $500
with the new chip.
不知道这个是不是包括 chip 和 reagent 的价。是不是还包括了 exome capture 的
cost？现在 exome 的 cost 大概多少？
如果genome 比exome 大至少20倍吧，这样算，whole genome 需要 $10,000? |
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t*d
发帖数: 1290 | 29 嗯，你是对的。
你提供的链接里面有路边社消息：
Ion Torrent will sell the tabletop machine, called the Ion Proton Sequencer,
for $99,000 to $149,000, making it affordable for large medical practices
or clinics; existing sequencers cost up to $750,000. The computer chip and
biochemicals to sequence a genome will cost $1,000
当然路边社的消息只有这水平，说不清楚这个 proton I 还是 Proton II 的费用。
的。 |
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H*****e
发帖数: 120 | 30 Hi experts,
I need to sequence PI3K and PTEN in tumors for determine whether there is
mutation. But I do not know much about sequencing mutations since I only
work kinase for years. So I have a few basic questions, wish to get answers
here:
1.RNA or DNA, The tumor sample will be provided by a colleague in Hospital.
I can get both DNA and RNA purified. Should I sequence DNA or RNA after I
PCR them out?
2.If only 1 copy has mutation and the other copy is wt, can routine sequence
in core lab det... 阅读全帖 |
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l**********1
发帖数: 5204 | 31 GC contents of that P2 to AscI site if >65% DMSO 5% to buffer or try
Clontech GC rich kit
Cycle time 35 that is no problem
pls refer
GC-rich PCR concerns DNA templates with high GC content, which is defined as
the percentage of guanine-cytosine base pairs. When amplifying templates
with >60% GC content (i.e 5' ends of most mammalian cDNAs), the three
hydrogen bonds shared by GC pairs lead to enhanced thermostability, which is
problematic for un-optimized Taq polymerase systems.
http://www.clon... 阅读全帖 |
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s*****g
发帖数: 87 | 32 谢谢回复！
我们可以算是一个独立实验室，主要需要做exome sequencing 和 RNA sequencing, 不
需要做de novo human genome sequencing，加上预算有限，所以准备买一台这个试试
看。 Miseq似乎不能满足exome sequencing 的要求。 |
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p*******e
发帖数: 3 | 33 Scientist / Senior Scientist, Next Generation Sequencing
OncoDiagnostics Technologies - San Francisco, CA
Job ID: 00001
Who We Are
OncoDiagnostics Technologies is a Silicon Valley-based biotech start-up
company focusing on precision diagnostics and medicine in cancer and other
serious illnesses. We aim to provide innovative non-invasive diagnostic
tests to enable precision medicine. At OncoDiagnostics, we believe that
people are our most vital assets and we are dedicated to creating a great
plac... 阅读全帖 |
|
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w**a
发帖数: 1024 | 35 a cauchy sequence defined in matric space (X,d)
we know any cauchy sequence is bounded.
But this sequence also has infinite number of elements?
infinite bounded sequence can have NO accumulation point? Thanks. |
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f*********m
发帖数: 726 | 36 谢谢。
Permutation Sequence
The set [1,2,3,…,n] contains a total of n! unique permutations.
By listing and labeling all of the permutations in order,
We get the following sequence (ie, for n = 3):
"123"
"132"
"213"
"231"
"312"
"321"
Given n and k, return the kth permutation sequence.
Note: Given n will be between 1 and 9 inclusive. |
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e******6
发帖数: 6 | 37 Job Description
Cooperation Introduction
GenScript is a contract research organization (CRO) specialized in
biological research and drug discovery services. Ever since its inception in
2002, GenScript has experienced rapid, constant, and organic growth. Now
GenScript has become a leading biology contract research organization (CRO)
in the world, with a global operating team of over 900 dedicated scientists,
staffs.
Headquartered in Piscataway, New Jersey, GenScript has become a leading
Biology C... 阅读全帖 |
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g******1
发帖数: 295 | 38 email resume to arthurbuffet At hotmail dot com if interested
https://boards.greenhouse.io/guardanthealth/jobs/525188#.WEjjvrIrLIU
About the Role
We are looking for a Research Associate team member who will partner with
the successful delivery of world-class in vitro diagnostic (IVD) quality
products for Guardant Health as we undergo an explosive growth phase. You
will work closely with the R&D teams to perform laboratory experiments
including sample preparation, nucleic acid extraction, PCR... 阅读全帖 |
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G****a
发帖数: 10208 | 39 A child has been born in the US after physicians and scientists used next-
generation sequencing to select an embryo for in vitro fertilization.
This birth marks the first time that sequencing has been used to screen
embryos for IVF, a process that generally sees only around 30 percent of the
embryos that are selected actually successfully implant, likely due to
chromosomal or genetic defects.
Although other genetic tests screening methods have already been introduced
to identify candidate embry... 阅读全帖 |
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h****8
发帖数: 599 | 40 The WeighTrainer
Making A Strength/Size Routine Part II: Exercise Sequence
by Casey Butt
There are some simple, generally accepted rules of how to properly sequence
exercises in resistance training workouts. While, no doubt, many of you will
already know these things, many may not. And because it is such a crucial
part of routine design, no series of this sort would be complete without
addressing exercise sequence.
Ground Rules
Unless under special circumstances, the free-weight compound exercis |
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y****m
发帖数: 1322 | 41 简意:人家就是按这个顺序排的没有tricky的东西.好吧,我想不出来只好接受她的解释,
THIS IS HER EXPLATION,
I am not sure if my explanation is correct or others may have a better
explanation.
the question asked "choose the answer that best CONTINUES the sequence". a
showed up in first part of the original sequence. if the sequence continues
with the same order, it could be
ΔΟΟΟ ΔΟΔΟ ΔΟΔΔ ΔΟΟΟ ΔΟΔΟ ΔΟΔΔ.
so a is ok. b and c both do not fit. |
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s*******y
发帖数: 558 | 42 Let G=(V, E) be a simple undirected graph with degree sequence d_1 >=
d_2 >= ... >= d_n, where n >= 1.
Let d_1+a_1, d_2+a_2, ..., d_n+a_n be another graphic sequence (which
is realizable). Here
0 <= a_i <= n-1-d_i , i=1, ..., n.
问题是： 如果对图G进行修改， 要求只加边不减边， 加的边是原图没有的。
有没有可能构造出一个新的简单图， 使得其degree sequence是 d_1+a_1, ..., d_n+a
_n.
当什么情况下是可能的， 什么情况下是不可能的？
谢谢 |
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b**********g
发帖数: 806 | 43 我又有个问题要打扰大家了
my mapping file is like this
person_id_sequence
然后在UI上删除一个record的时候,发现sequence不连着了,比如0,1,3,4这样子,这是为
什么? |
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m******t
发帖数: 2416 | 44
No... trust me, you really don't want that to happen. 8-)
A sequence is only responsible for _generating_ a sequence of numbers. Once
they are generated, the sequence no longer keep tracks of them. |
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M***7
发帖数: 2420 | 45 Hi there.
I was trying to collect some HIV whole genome sequences as many as possible.
The only thing I found is this HIV database http://www.hiv.lanl.gov/content/index. However, I did not get any useful HIV whole genome sequence from NCBI.
Dose anyone know is there any other public HIV whole genome sequences
available?
Thanks |
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d****t
发帖数: 139 | 46 For regular sequencing----
Been in different labs and all uses different sequencing companies. Want to
know which one you guys are using. Is it good regarding to the quality (
sequence length), time (fast or not) and cost? Thanks! |
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f*****4
发帖数: 83 | 47 顶，好文。这个行业发展很快，对于普通的医生或研究人员来说，数据分析和解读是个
很大的CHALLENGE.
我看好PACBIO，拭目以待十个仪器的结果，如果好的话，可能会DOMINATE THE MARKET
替代ILLUMINA。其实COMPLETE GENOMICS 不能算THIRD GEN SEQUENCING，只能算SECOND
GEN，因为有AMPLIFICATION, 不知道实际的结果怎么样，但是从设计上来说是简单化
的SOLID，没有COLOR CODE，不是很IMPRESSIVE，错误率可能不会低，成本低主要是
LIBRARY PREP 简单。ILLUMINA 的成功主要在于它的USER FRIENDLY. 喜欢SOLID的设计
，没有用过，SEQUENCE ALIGNMENT 比较依赖REFERENCE，否则错一个，整个SEQUENCE就
错了。 |
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D****g
发帖数: 275 | 48 我们怀疑一个基因的突变可能是某种疾病的致病原因。现在我们有病人的DNA,如何能快
速的sequencing这个基因的genome 序列？我们知道怎样sequencing 质粒，但是
sequencing 一个基因却从没做过。有没有人有standard protocol? 谢谢。 |
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W*******a
发帖数: 1769 | 49 yes, because when Illumina first developed the seq platform, the
default is to sequence from just one end of the molecule with one
primer. They soon came up with the pair end module, allowing two
seq rxns to be performed sequentially and get sequences from both ends.
PE is backward compatible with single end seq, so nowadays most kits use
PE primers, and you have the option to sequence just one end of it.
I think mate-paired gets its name because you 'mated' the two
ends together, so in the... 阅读全帖 |
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c*******3
发帖数: 80 | 50 你可以上一些miRNA的database比对你的miRNA sequence。比如现今比较常用的miRNA
sequence database有
miRBase：http://www.mirbase.org/ 将你得到的sequence 与其中的进行比对。hsa-mir-1-1 不一定对应 hsa-mir-
1, 因为hsa－mir－1 还包括 hsa－mir－1－2。 |
|
