Structural variation in human genome...

[Patrick]

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

[henry]

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]

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]

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]

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]

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

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]

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.

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]

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]

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

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]

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]

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
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]

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]

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 Patrick,

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

Best

Jing

[henry]

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]

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 ^^

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