Questions about WM regions on mutiplesamples

[ame...@b612.email]

Hi Yuchao,

Thank you for the most interesting paper and useful tool Canopy.

But I have some questions on Canopy input about multiple samples.

If I have 5 points samples from the same patient, every sample I get different mutations, when I make the R and X matrix, should I make a union or an intersection for the 5 samples? May I should select informative SNAs among samples.

secondly, Maybe I get different CNA segments among 5 samples, should I make a union or an intersection for the 5 samples? For example the sample1 and sample2 from the same patient.

If I make WM matrix, should the WM matrix like this?

These questions have been confused me for a long time, hoping for your replay.

Sincerely,

minfang

[Yuchao Jiang]

See my reply below.

On Tue, Nov 20, 2018 at 3:47 AM <ame...@b612.email> wrote:

Hi Yuchao,

Thank you for the most interesting paper and useful tool Canopy.

But I have some questions on Canopy input about multiple samples.

If I have 5 points samples from the same patient, every sample I get different mutations, when I make the R and X matrix, should I make a union or an intersection for the 5 samples? May I should select informative SNAs among samples.

secondly, Maybe I get different CNA segments among 5 samples, should I make a union or an intersection for the 5 samples? For example the sample1 and sample2 from the same patient.

Union. You should get the total read counts for the samples that don't have the mutations called. If this is not available, you can use a median coverage across all samples as an approximate.

 

If I make WM matrix, should the WM matrix like this?

Yes, the WM and Wm matrix should have the same row entry across all samples, if you don't consider overlapping CNAs. This means that often times you need to curate the copy number calls, e.g., combining adjacent copy number regions that share similar copy number profiles or merge two different breakpoints that are close to each other across different samples.

 How to deal with overlapping CNA events is non-trivial and at this stage it still needs a lot of manual inspection and selection. Let me try to answer your question here and let me know if you need more clarification:

For the MDA231 dataset, we know chr7 has two CNA events (supplementary Figure S13 in our paper) with different breakpoints. However for this CNA region shown in Figure S13, we only have one CNA input (from WM and Wm) for a specific sample, i.e., we won’t know the chr7_1 and chr7_2 input for each sample until we perform the deconvolution. Therefore, we name them chr7_1 and chr7_2 just so we know that there are two CNA events on chr7 that are overlapping, as specified by the C matrix.

For WM and Wm matrix, there will be only one major copy and one minor copy for one genomic segment that harbors any CNA (it’s not a value per chromosome but per copy number segment). However, multiple CNA events can overlap with this genomic segment/region. In matrix C, each row is one copy number REGION and each column is one copy number EVENT. You can only correctly assign this if you manually visualize and inspect the data otherwise it won’t be identifiable. For example, a homozygous deletion can always be treated as two consecutive heterozygous deletion but in this case we wouldn’t separate these as two events. However, for the case below (three samples from patient GBM9, with ASCN results loaded into IGV for visualization), for example, we know that there is a duplication, followed by a loss-of heterozygosity (and thus two copy number EVENTS) in the yellow copy number REGION.

These questions have been confused me for a long time, hoping for your replay.

Sincerely,

minfang

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[ame...@b612.email]

Hi Yuchao,

I am really grateful for your answer, which is helpful to me. I want to more classfiy the overlapping CNAs, for example (supplementary Figure S13 in your paper), how should I make C and Wm /WM matirx ?

  

 WM matrix

                       sample1  sample2  sample3

CNAregion1

C matrix

                         CNA(E1)   CNA(E2)   CNA(E3)

CNA region1           1                1            1

Sincerely,

minfang

在 2018年11月21日星期三 UTC+8上午4:24:15，Yuchao Jiang写道：

[Yuchao Jiang]

This example is just for illustration and we have not implemented the auto-parsing and auto-curation step.

For the current setting of Canopy, each WM, Wm, and C row corresponds to a CNA “region”. Each column of C corresponds to a CNA “event”. For the example in Supplementary Figure S3, there are three CNA events and six copy number segments (separated by breakpoints across all samples). More details here https://github.com/yuchaojiang/Canopy/blob/master/instruction/overlapping_CNA.md

On Nov 21, 2018, at 10:53 PM, ame...@b612.email wrote:

Hi Yuchao,

I am really grateful for your answer, which is helpful to me. I want to more classfiy the overlapping CNAs, for example (supplementary Figure S13 in your paper), how should I make C and Wm /WM matirx ?

  

 WM matrix

                       sample1  sample2  sample3

CNAregion1

C matrix

                         CNA(E1)   CNA(E2)   CNA(E3)

CNA region1           1                1            1

To view this discussion on the web visit https://groups.google.com/d/msgid/canopy_phylogeny/8c5cbe67-9481-49f7-8aee-0584d129987b%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

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