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?Epigenome association study

genomics
By shengliu, Section Biology
Posted on Fri Apr 30th, 2010 at 04:15:43 PM PST
In the process of disease initiation, there are bunch of genes been inactivated through

epigenetic approach, such as DNA methylation or histone modification. The example

include MLH1 methylaiton in colorectal cancer. This idea is to find genes inactivated in the

epigenome through populations, The approach is the same as normal Genome wide

association study (GWAS), the difference is the target.

Detail:

  1. Get patient sample and normal sample from some tissue, like colon.
  2. Get DNAs from the sample and treat with bisulfite.
  3. Bisulfite chip (if there is*)
  4. analysis of the data from patient and normal.
*  Bisulfite Chip, (maybe also a new idea:). the company should make this product, their

CpG island Chip is not accurate enough to locate genes. and it is doable as what they need

to do is just bisulfite convert the sequence they usually attach to the chip)

 

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Epigenome association study | 5 comments (1 topical, 4 editorial)
[new] bisulfite chip (none / 0) (#1)
by kjs86 on Fri Apr 30th, 2010 at 11:38:39 AM PST
(User Info)

A bisulfite ChIP experiment does seem like a good idea! It would make a ChIP experiment more specific, would it not?



Bisulphite ChIP none (#2)
by SarahLepage on Fri Apr 30th, 2010 at 02:18:56 PM PST
(User Info)

Bisulphite ChIP is a tried and true method, called MeDIP (methylation-dependent immunoprecipitation).
http://www.epigenome-noe.net/researchtools/protocol.php?protid=33

I like the idea, however I think you will have a very hard time telling when the difference in methylation status between test and control is meaningful. Do you plan on also doing an expression analysis afterwards?



expression analysis none (#3)
by fishes on Fri Apr 30th, 2010 at 06:06:53 PM PST
(User Info)

I think it is important to do expression analysis. Maybe the same epigenetic modification has the opposite effect in 2 individuals. It is important to know whether your modification is silencing or activating gene expression. Epigenetics is such a new field that in order for a study such as the one proposed here to have meaning in the future, expression data here is key.

[ Parent ]


Bisulfite Chip and eQTL none (#4)
by shengliu on Fri Apr 30th, 2010 at 06:08:29 PM PST
(User Info)

First, what I said is Bisulfite "Chip", not ChIP, the idea is to hybridize with bisulfite converted DNA.
Then, the idea for doing an expression array is an good complement, as firstly it could confirm the result, what's more, it is also an data for eQTL, expression quantitive trait, which could be used to build a data base on observed association.


[ Parent ]


Bisulphite Chip none (#5)
by SarahLepage on Fri Apr 30th, 2010 at 07:06:18 PM PST
(User Info)

Oh, sorry Sheng! I've got ChIP on the brain...bisulphite microarrays would be VERY interesting!

[ Parent ]


Epigenome association study | 5 comments (1 topical, 4 editorial)
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