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Patrick 09-05-2009 06:08 PM

Structural variation in human genome...
 
Can anybody briefly explain the general info about the structural variation in human genome?
Thanks a lot for sharing information :)

henry 09-07-2009 03:35 AM

Quote:

Originally Posted by Patrick (Post 8027)
Can anybody briefly explain the general info about the structural variation in human genome?
Thanks a lot for sharing information :)

There are mutation occuring in some segment of human genome. These mutation can be insertion, deletion and inversion of nucleotide sequences ranging from several bp to huandreds of bps.
There is a nature paper named " structural variation in the human genome" by Lars Feuk et al. You can read it, it definitely help you fully understand structural variation.
Hope these works for you.

Best

Jing

BENM 09-07-2009 07:11 AM

SVs concept come from CNV and CNP, you can find more details at DGV database: http://projects.tcag.ca/variation/
I had developed a kind of models to detect SVs by Paired-Ends mapping(PEM) before, which the results published with YH papers(Jun Wang, Wei Wang, Ruiqiang Li, et al. The diploid genome sequence of an Asian individual. Nature 2008; 456(7218): 60-5.). I am also glad to communicate with others who are insterested in SVs detection.

BENM 09-07-2009 07:19 AM

In 1000 Genomes Project there are 50% false positives in SV detection, so it is worth to pay more attentions to this field. Rather than use CNV BeadChip or PEM(alignment algorithm), maybe assembly is a better solution.

henry 09-07-2009 07:31 PM

Quote:

Originally Posted by BENM (Post 8067)
SVs concept come from CNV and CNP, you can find more details at DGV database: http://projects.tcag.ca/variation/
I had developed a kind of models to detect SVs by Paired-Ends mapping(PEM) before, which the results published with YH papers(Jun Wang, Wei Wang, Ruiqiang Li, et al. The diploid genome sequence of an Asian individual. Nature 2008; 456(7218): 60-5.). I am also glad to communicate with others who are insterested in SVs detection.

Hi, BENM
Thank you for sharing paper about structural variation. I'm reading it. I just jumped into next generation sequence research nearly one month ago.
To my knowledge, most majority of people use alignment tools and downstream analysis tools to perform analysis and identify SNP and structural variation. As for assembly, you mean denovo assembly? Could you give more information about the assembly you mentioned?

Best

Jing

Patrick 09-07-2009 07:53 PM

Hi, Henry.

Thanks for sharing.
Do you have the softcopy of the " structural variation in the human genome" paper?
I got try do download it from internet.
Unfortunately, I only can read the abstract of this paper but can't read the full article :(
Thanks a lot for your help again :)

Quote:

Originally Posted by henry (Post 8061)
There are mutation occuring in some segment of human genome. These mutation can be insertion, deletion and inversion of nucleotide sequences ranging from several bp to huandreds of bps.
There is a nature paper named " structural variation in the human genome" by Lars Feuk et al. You can read it, it definitely help you fully understand structural variation.
Hope these works for you.

Best

Jing


edge 09-07-2009 08:34 PM

Hi, BENM

Thanks for sharing the paper. It is fantastic and good research.
I got read this paper, sad to said that I not very understanding some of the findings inside these paper:(
Can you roughly explain the back story and the important finding of the "The diploid genome sequence of an Asian individual"?
Besides that, can you roughly share with me about the relationship between the SVs concept with the "The diploid genome sequence of an Asian individual".
Thanks a lot for your sharing info.

Quote:

Originally Posted by BENM (Post 8067)
SVs concept come from CNV and CNP, you can find more details at DGV database: http://projects.tcag.ca/variation/
I had developed a kind of models to detect SVs by Paired-Ends mapping(PEM) before, which the results published with YH papers(Jun Wang, Wei Wang, Ruiqiang Li, et al. The diploid genome sequence of an Asian individual. Nature 2008; 456(7218): 60-5.). I am also glad to communicate with others who are insterested in SVs detection.


henry 09-08-2009 02:36 AM

Quote:

Originally Posted by Patrick (Post 8090)
Hi, Henry.

Thanks for sharing.
Do you have the softcopy of the " structural variation in the human genome" paper?
I got try do download it from internet.
Unfortunately, I only can read the abstract of this paper but can't read the full article :(
Thanks a lot for your help again :)

Hi, patrick

I'm sorry. I don't have pdf copy of that nature paper. I read the hard copy in the library. Why not ask the corresponding author for that nature paper?

Best

Jing

Patrick 09-08-2009 04:34 AM

Hi, Henry.
Never mind. I will try to find out the soft-copy of the paper from the author.
Anywhere thanks a lot for your sharing.
I'm appreciate it.
Hope that we can share a lot of bioinformatics knowledge in future :)


Quote:

Originally Posted by henry (Post 8109)
Hi, patrick

I'm sorry. I don't have pdf copy of that nature paper. I read the hard copy in the library. Why not ask the corresponding author for that nature paper?

Best

Jing


henry 09-08-2009 06:02 PM

Quote:

Originally Posted by Patrick (Post 8120)
Hi, Henry.
Never mind. I will try to find out the soft-copy of the paper from the author.
Anywhere thanks a lot for your sharing.
I'm appreciate it.
Hope that we can share a lot of bioinformatics knowledge in future :)

Hi, Patrick
You are welcome. Surely, we can share a lot of experiences in processing and analyzing data cohorts. All people can benefit from communications. ^ ^

Best

Jing

Patrick 09-08-2009 06:13 PM

Hi, Jing.

You are right. "All people can benefit from communications".
Hope that we can share a lot of experiences in processing and analyzing data in future.
Normally, what fields you prefers to do research on it?

regards
Patrick

Quote:

Originally Posted by henry (Post 8140)
Hi, Patrick
You are welcome. Surely, we can share a lot of experiences in processing and analyzing data cohorts. All people can benefit from communications. ^ ^

Best

Jing


henry 09-08-2009 09:16 PM

Quote:

Originally Posted by Patrick (Post 8141)
Hi, Jing.

You are right. "All people can benefit from communications".
Hope that we can share a lot of experiences in processing and analyzing data in future.
Normally, what fields you prefers to do research on it?

regards
Patrick

Hi Patrick,

At present, we mainly focus on oncogenesis, hoping to identify potential drug target. What are your research interests?

Best

Jing

Patrick 09-08-2009 10:25 PM

Hi Jing,

Glad to hear that you research on oncogenesis now.
If I got any latest info about it, sure will told you d!
I recently focus on the research of breast cancer and related it with bioinformatics.
Do you have any idea or suggestion that can link the breast cancer disease with bioinformatics tools?!
thanks again :)


Quote:

Originally Posted by henry (Post 8144)
Hi Patrick,

At present, we mainly focus on oncogenesis, hoping to identify potential drug target. What are your research interests?

Best

Jing


henry 09-09-2009 02:30 AM

Quote:

Originally Posted by Patrick (Post 8145)
Hi Jing,

Glad to hear that you research on oncogenesis now.
If I got any latest info about it, sure will told you d!
I recently focus on the research of breast cancer and related it with bioinformatics.
Do you have any idea or suggestion that can link the breast cancer disease with bioinformatics tools?!
thanks again :)

Hi Partrick,
How would you like to investigate breast cancer? First, we need to determine how we will investigate tumor, like from DNA level, RNA level, protein level, or from angle of pathology, et al. Then what kind of data we expect from the research. Finally, we can decide what methods we may use to analyze the data. Because bioinformatics methods are data-driven. In addition, research framework (namely, how we wanna perform research) is more important, though data-mining is also difficult and important. Could you tell us how you would like to investigate breast cancer?

Best

Jing

Patrick 09-09-2009 03:03 AM

Hi,

Thanks a lot for your concern.
I just try to link the breast cancer research with the available online bioinformatics tools.
My supervisors want me to use the available online bioinformatics tools to verify the result of some breast cancer research that have been done before.
I just try to make a good back story to link the breast cancer research that have been done before with the available online bioinformatics tools now.
It seems like quite difficult to do it :(
Do you have any suggestion or advice?
I very appreciate it ^^


Quote:

Originally Posted by henry (Post 8163)
Hi Partrick,
How would you like to investigate breast cancer? First, we need to determine how we will investigate tumor, like from DNA level, RNA level, protein level, or from angle of pathology, et al. Then what kind of data we expect from the research. Finally, we can decide what methods we may use to analyze the data. Because bioinformatics methods are data-driven. In addition, research framework (namely, how we wanna perform research) is more important, though data-mining is also difficult and important. Could you tell us how you would like to investigate breast cancer?

Best

Jing


henry 09-09-2009 03:38 AM

Quote:

Originally Posted by Patrick (Post 8170)
Hi,

Thanks a lot for your concern.
I just try to link the breast cancer research with the available online bioinformatics tools.
My supervisors want me to use the available online bioinformatics tools to verify the result of some breast cancer research that have been done before.
I just try to make a good back story to link the breast cancer research that have been done before with the available online bioinformatics tools now.
It seems like quite difficult to do it :(
Do you have any suggestion or advice?
I very appreciate it ^^

You mean you wanna obtain statistical data on which bioinformatics tools have been used among the previous breast cancer researches?

Patrick 09-09-2009 04:46 PM

For example: "In particular, carriers of the breast cancer susceptibility genes, BRCA1 and BRCA2, are at a 30-40% increased risk for breast and ovarian cancer, depending on in which portion of the protein the mutation occurs."

My task is like download the breast cancer gene sequence from NCBI and used the available online bioinformatics tools to prove that from the whole breast cancer sequence, mutation in BRCA1 and BRCA2 is the main key factor that causes the breast cancer to occur. After this, I want to make a back story about the breast cancer and link it with the online bioinformatics tools.

In your opinion, besides the BRCA1 and BRCA2 gene, any other genes that is very interesting at the breast cancer research?

Thanks again :)




Quote:

Originally Posted by henry (Post 8172)
You mean you wanna obtain statistical data on which bioinformatics tools have been used among the previous breast cancer researches?


henry 09-09-2009 05:24 PM

Quote:

Originally Posted by Patrick (Post 8206)
For example: "In particular, carriers of the breast cancer susceptibility genes, BRCA1 and BRCA2, are at a 30-40% increased risk for breast and ovarian cancer, depending on in which portion of the protein the mutation occurs."

My task is like download the breast cancer gene sequence from NCBI and used the available online bioinformatics tools to prove that from the whole breast cancer sequence, mutation in BRCA1 and BRCA2 is the main key factor that causes the breast cancer to occur. After this, I want to make a back story about the breast cancer and link it with the online bioinformatics tools.

In your opinion, besides the BRCA1 and BRCA2 gene, any other genes that is very interesting at the breast cancer research?

Thanks again :)

Whole genome sequencing of breast carcinoma sample can help us identify breast-carcinoma specific SNPs and indels. Among these identified SNPs and indels, there may be some novel mutations. Whether these novel mutation can actually affect the expression of genes, and further influence protein functions. We may design biological validation experiment. Hopefully, whole genome sequencing of breast carcinoma sample can provide some clues on genes/proteins we wanna further track.
As for whole genome sequencing software, there are many software available, like MAQ, BWA, Bowtie, BFAST, SOAP, ZOOM, SeqMap,SHRimp, NovoALign, Mosaik, et al. We can derive SNPs and indels using these software. However, we will usually obtain thousands of SNPs/indels. Further manipulating those SNPs/indels will require ourselves to write codes (using perl, C/C++, R, Matlab)according to our own research interests. We may also add other prior knowledge into the analysis.
In regards to potential breast carcinoma susceptibility genes, I have no idea. I haven't done any research on breast carcinoma. But many cancer involves genes related to angiogenesis, cell proliferation, immune responce. Cancer seems to share some common pathways while maintaining their own specific features. You may have a try to prescreen genes you care from those pathways.
Do you have idea of how you would like to search for potential breast carcinoma susceptibility genes?

Best

Jing

Patrick 09-09-2009 05:44 PM

Hi henry,

I very thanks and appreciate for your info.
I learn a lot from you :)
To search for potential breast carcinoma susceptibility genes, I maybe will try to use the mgrc company free online bioinformatics tools to help me analyze it.
I still in process to explore and try it now.
I will share it with you once I found any interesting findings :)



Quote:

Originally Posted by henry (Post 8212)
Whole genome sequencing of breast carcinoma sample can help us identify breast-carcinoma specific SNPs and indels. Among these identified SNPs and indels, there may be some novel mutations. Whether these novel mutation can actually affect the expression of genes, and further influence protein functions. We may design biological validation experiment. Hopefully, whole genome sequencing of breast carcinoma sample can provide some clues on genes/proteins we wanna further track.
As for whole genome sequencing software, there are many software available, like MAQ, BWA, Bowtie, BFAST, SOAP, ZOOM, SeqMap,SHRimp, NovoALign, Mosaik, et al. We can derive SNPs and indels using these software. However, we will usually obtain thousands of SNPs/indels. Further manipulating those SNPs/indels will require ourselves to write codes (using perl, C/C++, R, Matlab)according to our own research interests. We may also add other prior knowledge into the analysis.
In regards to potential breast carcinoma susceptibility genes, I have no idea. I haven't done any research on breast carcinoma. But many cancer involves genes related to angiogenesis, cell proliferation, immune responce. Cancer seems to share some common pathways while maintaining their own specific features. You may have a try to prescreen genes you care from those pathways.
Do you have idea of how you would like to search for potential breast carcinoma susceptibility genes?

Best

Jing


henry 09-10-2009 03:48 AM

Quote:

Originally Posted by Patrick (Post 8213)
Hi henry,

I very thanks and appreciate for your info.
I learn a lot from you :)
To search for potential breast carcinoma susceptibility genes, I maybe will try to use the mgrc company free online bioinformatics tools to help me analyze it.
I still in process to explore and try it now.
I will share it with you once I found any interesting findings :)

Hi patrick,
you are welcome. Good luck to your research.

Best

Jing


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