M**1
发帖数: 162 | 1 What's called somatic mutation? Thanks! |
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i*****i
发帖数: 154 | 2 老板想做有一个基因的mutation analysis，该基因编码区1.5kb。
大概有200个病人的DNA。
我想请教一下版上的牛人，目前比较认可，比较流行的方法是什么？
1. direct sanger sequencing 太贵了。
2. NGS做单一基因的分析有些太浪费了。
3. sequenom不知道是不是有一些out了？
谢谢 |
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f*******2
发帖数: 14 | 3 Using PacBio RS. PCR multiplex all sample. A single sequencing run could
have enough coverage for the mutation detection. more info:http://www.pacificbiosciences.com/applications/target/
I can work with you for your sequencing project. total price would be less
than 1000 |
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G***y
发帖数: 1082 | 4 How's PacBio's accuracy now? How much coverage would be needed for mutation
detection? |
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f*******2
发帖数: 14 | 5 Raw single pass error rate is about 10-15%. since the errors are random
distributed, they can be corrected by increasing the coverage. with 30X
coverage, accuracy can be Q30 with no systematic error or GC bias.
more info here:http://www.pacificbiosciences.com/applications/target/index.html#tab-2
If you need to run samples please let me know.
mutation |
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a****l
发帖数: 125 | 6 请问有人用TALEN 在细胞里做一个gene 的mutation (不是敲除）吗？有没有文章可以
科普一下。
多谢。 |
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e****e
发帖数: 3450 | 7 发现跟多cancer mutation都是用氨基酸来标注，什么BRAF V600E，怎么能快速找出对
应的genomic的location？或者反过来，用chromosome location找对应的AA change？
COSMIC database好像找起来不是很方便 |
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w*********d
发帖数: 82 | 8 谁有CRISPR mutation的经验可以分享？
先谢了！ |
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U**8
发帖数: 1921 | 9 想delete 32个氨基酸，不知道site directed mutation 可行吗？ |
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s********x
发帖数: 472 | 10 如果是连续的deletion，直接两个primer把vector pcr开在连回环状就可以了。delete
多大都可以。
如果是不连续的话可以试试multi mutation的试剂盒。 |
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n***i
发帖数: 1 | 11 找跟每一个疾病相关gene所有的missense mutations。不知道有没有现成的数据库？
看了一下OMIM，好像不是很全，而且数据要再提取。
谢谢！ |
|
s********r
发帖数: 312 | 12 如果用surveyor assay的话会不会很贵？PCR产物直接做，还是要用96-well
purification kit再过一遍？ 不同孔的DNA浓度怎么normalize？
另外好像以前听说过可以用Taqman做realtime PCR based point mutation detection,
这个有成熟的方法么？
谢谢！ |
|
x********e
发帖数: 35261 | 13 直接做genomic PCR啊
如果是random mutation的话我知道有人用realtime pcr去screen TALEN mutant
如果是有target的话，比如CRISPR，我身边也有人直接设计target site的primer，然后
普通pcr就筛出来了
听听其他有经验的同学怎么说 |
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r******g
发帖数: 600 | 14 楼主，问个naive question
你做point mutation 用什么办法select呢？
用的endonuclease来select吗？
成功率有多少？ |
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m*********D
发帖数: 1727 | 15 是。从single-replacement的“Wildtype"copy情况看，两个guide sequences都起了作
用。之所以加引号，是因为没有真正的wildtype，两个dsb上独有indels.
本意是让想用CRISPR作point-mutation的注意risk,没有筛选的情况下概率太小了一些
。我自己的概率是1 out of 1000左右呢。我看了biotechnique的那篇文章，也差不多
。所以，提醒一下。 |
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s********r
发帖数: 312 | 16 用loxp带抗性基因，放到mutation位点附近的intron里去不就可以了。 |
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m*********D
发帖数: 1727 | 17 我克隆到质粒里面的。一边一个1。2Kb的arm,中间是70bp的mutation region,正好两个
新的酶位点连接，作克隆用。 |
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i***9
发帖数: 106 | 18 好像CRISPR用来做knock-out在cell line里面还是比较straightforward的。
做mutation就看运气了。
不知道板上有谁有经验用CRISPR做knock-in的mouse。
难度是不是很大？
有什么好的参考文献?
谢谢大牛。 |
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g*****n
发帖数: 241 | 19 请问我给线虫做了EMS screen之后能否直接把若干个mutant line直接做WGS，然后看哪
些基因有重复出现的突变，以此作为causal mutation的candidate？请问这样的做法是
否可行，价格是否会很贵？
谢谢
PS: 我的突变体因为reporter的原因，做back cross太费时，如果用Hawaiian杂交然后
WGS/SNP的话也不好做。所以考虑用直接WGS省时间。如果大家有其他mapping的方法的
话也请告知。谢谢 |
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m*********D
发帖数: 1727 | 20 张峰应该找我，我昨天数了数，我有至少八个100￥sure不同的克隆，都是用了两个
Guide Sequences但不同的HDR template出来的，只要whole genome sequencing，大约
就知道答案了。：）。
我是用细胞作的CRISPR/HDR来create mutation,，和干细胞genetic校正后再放回病人
体内治病更相近一些。
:))). |
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d**********o
发帖数: 1321 | 21 第一个项目report
这时偶刚到CSAC工作不久，与小A同学还不熟，我用的还是latex。随着贴的作业越来越
多，应该是用有共同爱好的小伙伴更亲密些。这次贴latex，下次才再org-mode。
\documentclass[b5paper,11pt, abstraction, titlepage]{scrartcl}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{CJKutf8}
\usepackage{multirow}
\usepackage{multicol}
\usepackage{listings}
\usepackage{geometry}
\geometry{b5paper}
\usepackage{graphicx,floatrow}
\usepackage{graphicx,subfigure}
\newsavebox{\abstractbox}
\renewenvironment{abstract}
{\begin{lrbox}{0}\begin{minipage}{\t... 阅读全帖 |
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d**********o
发帖数: 1321 | 22 第一个项目report
这时偶刚到CSAC工作不久，与小A同学还不熟，我用的还是latex。随着贴的作业越来越
多，应该是用有共同爱好的小伙伴更亲密些。这次贴latex，下次才再org-mode。
\documentclass[b5paper,11pt, abstraction, titlepage]{scrartcl}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{CJKutf8}
\usepackage{multirow}
\usepackage{multicol}
\usepackage{listings}
\usepackage{geometry}
\geometry{b5paper}
\usepackage{graphicx,floatrow}
\usepackage{graphicx,subfigure}
\newsavebox{\abstractbox}
\renewenvironment{abstract}
{\begin{lrbox}{0}\begin{minipage}{\t... 阅读全帖 |
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a*******a
发帖数: 4233 | 23 http://www.cancer.gov/cancertopics/factsheet/Risk/BRCA
How do BRCA1 and BRCA2 gene mutations affect a person's risk of cancer?
Not all gene changes, or mutations, are deleterious (harmful). Some
mutations may be beneficial, whereas others may have no obvious effect (
neutral). Harmful mutations can increase a person’s risk of developing a
disease, such as cancer.
A woman’s lifetime risk of developing breast and/or ovarian cancer is
greatly increased if she inherits a harmful mutation in BRCA1 or... 阅读全帖 |
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g******t
发帖数: 230 | 24 http://www.nytimes.com/pages/health/research/index.html
Scientists Link Gene Mutation to Autism Risk
Kevin P. Casey for The New York Times
Teams of scientists working independently have for the first time identified
several gene mutations that they agree sharply increase the chances that a
child will develop autism. They have found further evidence that the risk
increases with the age of the parents, particularly in fathers over age 35.
The gene mutations are extremely rare and together account ... 阅读全帖 |
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r*****m
发帖数: 3619 | 25 Results: 46
Select item 25597018
1.
Exome-wide Sequencing Shows Low Mutation Rates and Identifies Novel Mutated
Genes in Seminomas.
Cutcutache I, Suzuki Y, Tan IB, Ramgopal S, Zhang S, Ramnarayanan K, Gan A,
Lee HH, Tay ST, Ooi A, Ong CK, Bolthouse JT, Lane BR, Anema JG, Kahnoski RJ,
Tan P, Teh BT, Rozen SG.
Eur Urol. 2015 Jan 14. pii: S0302-2838(14)01396-7. doi: 10.1016/j.eururo.
2014.12.040. [Epub ahead of print]
PMID: 25597018 [PubMed - as supplied by publisher] Free Article
Related citations... 阅读全帖 |
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d**********o
发帖数: 1321 | 26 第二次作业report
#+latex_class: cn-article
#+latex_header: \usepackage{CJKutf8}
#+latex_header: \begin{CJK}{UTF8}{gbsn}
#+latex_header: \lstset{language=c++,numbers=left,numberstyle=\tiny,
basicstyle=\ttfamily\small,tabsize=4,frame=none,escapeinside=``,
extendedchars=false,keywordstyle=\color{blue!70},commentstyle=\color{red!55!
green!55!blue!55!},rulesepcolor=\color{red!20!green!20!blue!20!}}
#+title: CS572 Project 2 Report
#+author: (me~~~)
#+begin_abstract
|---------------------------+------------... 阅读全帖 |
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d**********o
发帖数: 1321 | 27 第二次作业report
#+latex_class: cn-article
#+latex_header: \usepackage{CJKutf8}
#+latex_header: \begin{CJK}{UTF8}{gbsn}
#+latex_header: \lstset{language=c++,numbers=left,numberstyle=\tiny,
basicstyle=\ttfamily\small,tabsize=4,frame=none,escapeinside=``,
extendedchars=false,keywordstyle=\color{blue!70},commentstyle=\color{red!55!
green!55!blue!55!},rulesepcolor=\color{red!20!green!20!blue!20!}}
#+title: CS572 Project 2 Report
#+author: (me~~~)
#+begin_abstract
|---------------------------+------------... 阅读全帖 |
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发帖数: 1 | 28
Download pdf published by SfN (Chapter from 'The History of Neuroscience in
Autobiography, Volume 8' edited by Larry R. Squire)
Yuh-Nung Jan's CV
Lily Jan's CV
Yuh-Nung Jan and Lily Jan
Birth
Family History and Growing Up
National Taiwan University
The Hiking Trip to Shitou in the Spring of 1967
Graduate School Application
Graduate Study at Caltech (1968锟974)
Seymour Benzer Lab (1974锟977)
Steve Kuffler锟絪 Lab at H... 阅读全帖 |
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w*********r
发帖数: 3382 | 29 you are distorting words
i am not mutation expert but here is some of my humble opinion on this
subject
mutation can be spontaneous mutation, or induced mutation. what we are
talking about here is presumably spontaneous mutation that has been happening throughout the history of evolution
spontaneous mutation can be random, and the reason we think so is that so far scientists did not see a pattern of spontaneous mutation occurring, or any evidence that supports that spontaneous mutation happens i... 阅读全帖 |
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e******i
发帖数: 106 | 30 这是在career cup 上看到的题：
Given a hashmap M which is a mapping of characters to arrays of substitute
characters, and an input string S, return an array of all possible mutations
of S (where any character in S can be substituted with one of its
substitutes in M, if it exists).
What is the time complexity? What is the space complexity? Can you optimize
either?
Example input:
M = { f: [F, 4], b: [B, 8] }
S = fab
Expected output:
[fab, Fab, 4ab, faB, FaB, 4aB, fa8, Fa8, 4a8]
这是我的解法，用backtrack... 阅读全帖 |
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A********2
发帖数: 107 | 31 Thanks for the reference...I have read it through:
Evolution myths: Everything is an adaptation. Michael Le Page
This is an article for laymen I would say and the author's point is that not
every phenotype (or trait if you prefer) is fixed in population by positive
selection, with which I or other people working with evolution can't agree
more. Of course NOT all traits (mutations) fixed in population are neutral,
as a matter of fact, most spontaneous mutations would be either deleterious
or neut... 阅读全帖 |
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j*****g
发帖数: 8 | 32 Adjuvant systemic therapy in resectable non-small cell lung cancer
Author
Nasser Hanna, MD
Section Editors
Rogerio C Lilenbaum, MD, FACP
James R Jett, MD
Deputy Editor
Sadhna R Vora, MD
Contributor disclosures
All topics are updated as new evidence becomes available and our peer review
process is complete.
Literature review current through: May 2016. | This topic last updated: Nov
30, 2015.
MOLECULARLY TARGETED AGENTS — Despite the activity of tyrosine kinase
inhibitors in patients with metastat... 阅读全帖 |
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c******r
发帖数: 889 | 33 Yes, I believe complex cell cycle regulation is the result of evolution. You
just need to look at lower single cellular organisms, they have similar but
much simpler system. Complex systems are not created anew each time. They
are the result of gradual evolution.
Chromosomal translocation creates an abnormal fusion protein in AML (a form
of leukemia) that disrupts gene regulation and is the key cause of this type
of cancer. In some sense, this is a new gene.
It's a random event that has grave ou... 阅读全帖 |
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l**********t
发帖数: 5754 | 34
"you are distorting words. i am not mutation expert but here is some of my
humble opinion on this subject"
-- if you are not familiar with the subject, please don't start with an
allegtion about "distorting words", because I'm a biochem major so I know
what these terms mean in the context of biological science.
"mutation can be spontaneous mutation, or induced mutation. what we are
talking about here is presumably spontaneous mutation that has been
happening throughout the history of evolution"... 阅读全帖 |
|
发帖数: 1 | 35 她提出了一个观点就是control room, 核心思想是如果新冠是自然突变的，而且是这么
明显的突变，那么它会马上启动damage control自毁机制的，不会在自然界中存活长久
她还说美国科学家那篇说新冠是自然起源的文章是受美国政府指使的
https://www.dimsumdaily.hk/czech-molecular-biologist-dr-sona-pekova-explains
-in-layman-terms-that-covid-19-virus-originates-from-a-lab-in-u-s-and-not-
china/
30th March 2020 – (Prague) A Czech molecular biologist, Dr. Soňa Peková
explained in detail why she believed that the novel coronavirus originated
from the laboratory in the U.S. and not in China. She also tried to dis... 阅读全帖 |
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d**********2
发帖数: 831 | 36 Rate of de novo mutations and the importance of father’s age to disease
risk
Nature 488, 471–475 (23 August 2012)
Mutations generate sequence diversity and provide a substrate for selection.
The rate of de novo mutations is therefore of major importance to evolution
. Here we conduct a study of genome-wide mutation rates by sequencing the
entire genomes of 78 Icelandic parent–offspring trios at high coverage. We
show that in our samples, with an average father’s age of 29.7, the average
de novo ... 阅读全帖 |
|
d**********2
发帖数: 831 | 37 Rate of de novo mutations and the importance of father’s age to disease
risk
Nature 488, 471–475 (23 August 2012)
Mutations generate sequence diversity and provide a substrate for selection.
The rate of de novo mutations is therefore of major importance to evolution
. Here we conduct a study of genome-wide mutation rates by sequencing the
entire genomes of 78 Icelandic parent–offspring trios at high coverage. We
show that in our samples, with an average father’s age of 29.7, the average
de novo ... 阅读全帖 |
|
f******g
发帖数: 1003 | 38 A vaccine targeting mutant IDH1 induces antitumour immunity
Monoallelic point mutations of isocitrate dehydrogenase type 1 (IDH1) are an
early and defining event in the development of a subgroup of gliomas1, 2, 3
and other types of tumour4, 5, 6. They almost uniformly occur in the
critical arginine residue (Arg 132) in the catalytic pocket, resulting
in a neomorphic enzymatic function, production of the oncometabolite 2-
hydroxyglutarate (2-HG)7, 8, genomic hypermethylation9, 10, 11, genet... 阅读全帖 |
|
发帖数: 1 | 39 【 以下文字转载自 Military 讨论区 】
发信人: lubbock12 (非老非小将), 信区: Military
标 题: 捷克白妞女科学家新冠必须美国造原文
发信站: BBS 未名空间站 (Tue Mar 31 11:30:41 2020, 美东)
她提出了一个观点就是control room, 核心思想是如果新冠是自然突变的，而且是这么
明显的突变，那么它会马上启动damage control自毁机制的，不会在自然界中存活长久
她还说美国科学家那篇说新冠是自然起源的文章是受美国政府指使的
https://www.dimsumdaily.hk/czech-molecular-biologist-dr-sona-pekova-explains
-in-layman-terms-that-covid-19-virus-originates-from-a-lab-in-u-s-and-not-
china/
30th March 2020 – (Prague) A Czech molecular biologist, Dr. Soňa Peková
explained in d... 阅读全帖 |
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G****e
发帖数: 1912 | 40 https://www.theepochtimes.com/scientific-puzzles-surrounding-the-wuhan-novel
-coronavirus_3225405.html
Scientific Puzzles Surrounding the Wuhan Novel Coronavirus
BY YUHONG DONG February 3, 2020 Updated: February 6, 2020FONT BFONT SText
size Print
Analysis
The sudden outbreak of the Wuhan Novel Coronavirus (2019-nCoV) has resulted
in all of China’s Hubei Province and three major cities in Zhejiang
Province being subjected to quarantine. Other nations are anxiously trying
to get their people out o... 阅读全帖 |
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o********r
发帖数: 775 | 41 Review
Many different tumor types have polyclonal tumor origin: Evidence and
implications
Barbara L. ParsonsCorresponding Author Contact Information, a, E-mail The
Corresponding Author
aDivision of Genetic and Reproductive Toxicology, National Center for
Toxicological Research, HFT-120, 3900 NCTR Road, USFDA, Jefferson, AR 72079,
United States
Received 7 February 2008;
revised 14 May 2008;
accepted 15 May 2008.
Available online 31 May 2008.
Abstract
Few ideas have gained such strong acceptance i... 阅读全帖 |
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r***e
发帖数: 2539 | 42 Thank everyone for the discussion!
As pineseed pointed out, too many topics were discussed here.
But my personal interests are:
1. what is the cell origin of different type of lung cancers?
2. does cell origin or mutation decide tumor types?
3. how to model different type of lung cancer?
HGTPase, it seems you are working in this field (more lung development than
lung cancer?), and I hope you can give your opinions. We can also discuss in
private mails for technique details.
1. ... 阅读全帖 |
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A********2
发帖数: 107 | 43 很有意思的问题。如果从经典的mutation-selection分析，mutation可以分为
deleterious，neutral，和benefical，当然一个mutation会造成怎样的phenotype是取
决于环境的，deleteriou mutations被淘汰的可能性大，beneficial mutatons被选择
的可能性大，而neutral mutations能不能留下来就是随机了（genetic drift），但让
genetic drift也可以让deleterious mutations在种群中固定，去决议bottle neck的
大小和具体的fitness，楼主所说的问题我觉得实际上是由于Homo Sapiens这个species
的特殊性，有能力影响自身进化的fitness landscape，也就是说降低了那些
deleterious mutations的fitness cost，甚至使其面位neutral muations，实际上人
类对其他动物也做着同样地事情，比如各种各样cute的小狗，比如大熊猫，这些
mutants如果不人为保护早就挂了。对于人... 阅读全帖 |
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y**********n
发帖数: 478 | 44 看了下报告（Gene info - SLC25A13 on Dec 23, 2013.pdf），里面用的是HGMD数据库
（http://www.hgmd.org/）注释的SLC25A13基因，并没有给出宝宝的SLC25A13基因序列和突变信息。
下面是HGMD数据库的SLC25A13的注释信息：
Mutation type Number of mutations Mutation data by type (register or
log in)
Missense/nonsense 27
Splicing 10
Regulatory 0 No mutations
Small deletions 5
Small insertions 1
Small indels 0 No mutations
Gross deletions 2
Gross insertions/duplications 3
Complex rearrangements 0 No muta... 阅读全帖 |
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l****y
发帖数: 486 | 45 Assume your knock-in here refers to mutating a site at the endogenous locus
(thus over expression-type approach, such as making transgenic mouse from
Rosa26 locus, will not be applied here).
Then the question is: you expect your mutation is a gain-of-function
mutation or loss-of-function mutation.
If your mutation is GOF mutation, it is easy, see Kras V12 KI strategy--
basically insert stopper element LSL before Kras V12 Exon. Note that the
allele LSL Kras V12 (before crossing with Cre) is a nul... 阅读全帖 |
|
w******y
发帖数: 4871 | 46 NOVEL THERAPIES
Gene therapy — The identification of the gene responsible for the
dystrophinopathies led to initial excitement that transfer of a functioning
dystrophin protein (whether by transplanted myoblast or direct genetic
manipulation) may provide substantial benefit to or even "cure" affected
patients. Although myoblast transfer has been attempted in humans, the
results have thus far not been encouraging [47]. However, in one patient who
received a bone marrow transplant for severe combi... 阅读全帖 |
|
I***i
发帖数: 14557 | 47 http://news.discovery.com/animals/carnivores-taste-sweet-120312
WHY CATS, OTHER CARNIVORES DON'T TASTE SWEETS
With no need for carbohydrates, many carnivorous animals have lost the
ability to detect sweet flavors.
Lions and Asian otters don't care for sweets but raccoons and spectacled
bears will eat almost anything. Now a new study helps explain why.
Independently and fairly recently, genetic mutations have made various
carnivores unable to taste sweet foods.
Probably because these species were... 阅读全帖 |
|
发帖数: 1 | 48 转自Bloomberg：
https://www.bloomberg.com/amp/opinion/articles/2018-11-27/crispr-fears-
designer-baby-outrage-won-t-last-as-ethics-evolve
It’s too soon to know whether a Chinese researcher who claims to have
successfully edited the genomes of newly born twins is telling the truth.
But if he is, and if the girls turn out to be healthy and normal, it heralds
a significant change in the scientific and ethical status of human gene
editing. The outrage might not last long.
The consensus in the scientifi... 阅读全帖 |
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t*******d
发帖数: 2570 | 49 I am not a molecular genetics major, and I don't know what is the root cause
of mutation. It probably has something to do with thermophysics. But since
I don't have enough knowledge about it, I have no problem admitting that I
don't know the cause of the random mutations we observed. I can accept
random mutations happen due to a random cause or a directed cause, as long
as there is evidence to back up the claim.
However, not knowing the cause of the random mutations does not prevent me
from labe... 阅读全帖 |
|
E*****m
发帖数: 25615 | 50
你東施效顰得很差勁。
進化論的突變有很多種， spontaneous mutation 是其中一種。
Four classes of mutations are (1) spontaneous mutations (molecular decay), (
2) mutations due to error prone replication by-pass of naturally occurring
DNA damage (also called error prone translesion synthesis), (3) errors
introduced during DNA repair, and (4) induced mutations caused by mutagens.
你問題根本不是是非題， 你要是問『spontaneous mutation 會不會造成演化』，答案
是『會』
要是問『進化論的突變是不是只有 spontaneous mutation}』，答案是『不是』，因為
至少還有其他三種。
該你回答。 （嚴格來說，是看你怎樣繼續閃躲不回答） |
|
