% of region capture needed for LD analysis?

[JWJH]

I was really torn between posting this in the bioinformatics section or here but decided on here since this would be the platform I'm using for my study. If anyone thinks this topic/question should be somewhere else pls feel free to let me know.

I'm currently thinking of doing a targeted resequencing study on a approx. 1Mb region on a certain chromosome using Life Technologies' Ion TargetSeq custom capture probes and have sent my region in for probe design. The design came back to me for approval about a week ago and I couldn't help but realize that the design only offered me approx. 75% capture for my specified region.
I tried to ask if they could improve the capture % but was told that to increase the capture they would need to use non-specific probes, which would increase the chances of capturing other unwanted regions.

What I'd like to know is whether this 75% capture will be enough for me to compare LD in my region with other, already studied populations? Is there a 'recommended' amount of sequence capture for LD analysis?

Sorry if my question seems vague or strange but I'm still new to the whole NGS thing, if any further information is required, pls feel free

Thanks in advance!

[IonTorrent]

Hello JWJH,

Have you considered an AmpliSeq custom panels approach as an alternative to TargetSeq? It may be the better approach for you given the size of your capture. For regions of up to 1 Mb, this approach is an excellent choice as an enrichment technology for PGM sequencing. You can access the AmpliSeq Designer tool at http://www.ampliseq.com and may also find related information there. AmpliSeq Designer will allow you to enter a design, which when returned, will highlight the coverage you can expect if you employ this approach.

I was really torn between posting this in the bioinformatics section or here but decided on here since this would be the platform I'm using for my study. If anyone thinks this topic/question should be somewhere else pls feel free to let me know.

I'm currently thinking of doing a targeted resequencing study on a approx. 1Mb region on a certain chromosome using Life Technologies' Ion TargetSeq custom capture probes and have sent my region in for probe design. The design came back to me for approval about a week ago and I couldn't help but realize that the design only offered me approx. 75% capture for my specified region.
I tried to ask if they could improve the capture % but was told that to increase the capture they would need to use non-specific probes, which would increase the chances of capturing other unwanted regions.

What I'd like to know is whether this 75% capture will be enough for me to compare LD in my region with other, already studied populations? Is there a 'recommended' amount of sequence capture for LD analysis?

Sorry if my question seems vague or strange but I'm still new to the whole NGS thing, if any further information is required, pls feel free

Thanks in advance!

[JWJH]

Thanks for the suggestion, I have actually looked at the Ion Ampliseq panels and had them design the primers for my region (I'm also looking at another 1.1Mb region on another chromosome in parallel) and the report that came back didn't look too good.

The number of primers were staggering and the cost was too expensive for my lab to agree with (my prof almost had a heart attack) and after looking around, I found the Ion TargetSeq that seemed to be a good trade-off between capture and cost. I kinda pooled the regions together into one single Custom 2Mb capture kit to lower the cost to something more reasonable.

Not to mention, I'm actually quite pressed for time as well...

Thanks for the suggestion though, appreciate it! Looking forward to more responses!

Hello JWJH,

Have you considered an AmpliSeq custom panels approach as an alternative to TargetSeq? It may be the better approach for you given the size of your capture. For regions of up to 1 Mb, this approach is an excellent choice as an enrichment technology for PGM sequencing. You can access the AmpliSeq Designer tool at http://www.ampliseq.com and may also find related information there. AmpliSeq Designer will allow you to enter a design, which when returned, will highlight the coverage you can expect if you employ this approach.