Inaccurate read count prediction in peak regions

[lindashirley99]

Hi,
we found it several times that when we have both SNP6.0 data and WES data for the same sample, there is inconsistent CN results in high coverage (peak) regions. CopywriteR was not able to reflect high CN values in these regions whereas the mapped bam files do have high peaks. It seems that the off-target read-based approach might have limitation in this case.

Looking forward to your reply.
Thanks!

[PeeperLab2]

Dear Linda Shirley, Thank you for using CopywriteR and thank you for informing us regarding inconsistencies between SNP6.0 and CopywriteR. So if I understand your email correctly you have high peaks (amplifications) with SNP6.0 that are not captured correctly by CopywriteR? I would love to see the profiles and look further into this discrepancy. Would it be possible to share these with me? Maybe even for one chromosome only? Kind regards, Oscar Oscar Krijgsman, PhD Postdoctoral research fellow Division of Molecular Oncology & Immunology The Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam, the Netherlands Phone: +31 20 512 2028 o.krijgsman@nki.nl<mailto:o.krijgsman@nki.nl> On 22 Feb 2019, at 03:46, lindashirley99 <notifications@github.com<mailto:notifications@github.com>> wrote: Hi, we found it several times that when we have both SNP6.0 data and WES data for the same sample, there is inconsistent CN results in high coverage (peak) regions. CopywriteR was not able to reflect high CN values in these regions whereas the mapped bam files do have high peaks. It seems that the off-target read-based approach might have limitation in this case. Looking forward to your reply. Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#26>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AH9-xO4DrwAf_oQ8AgwbM9gEFKbtDjXSks5vP1oLgaJpZM4bIv79>.

[lindashirley99]

Dear Linda Shirley, Thank you for using CopywriteR and thank you for informing us regarding inconsistencies between SNP6.0 and CopywriteR. So if I understand your email correctly you have high peaks (amplifications) with SNP6.0 that are not captured correctly by CopywriteR? I would love to see the profiles and look further into this discrepancy. Would it be possible to share these with me? Maybe even for one chromosome only? Kind regards, Oscar Oscar Krijgsman, PhD Postdoctoral research fellow Division of Molecular Oncology & Immunology The Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam, the Netherlands Phone: +31 20 512 2028 o.krijgsman@nki.nlmailto:o.krijgsman@nki.nl On 22 Feb 2019, at 03:46, lindashirley99 <notifications@github.commailto:notifications@github.com> wrote: Hi, we found it several times that when we have both SNP6.0 data and WES data for the same sample, there is inconsistent CN results in high coverage (peak) regions. CopywriteR was not able to reflect high CN values in these regions whereas the mapped bam files do have high peaks. It seems that the off-target read-based approach might have limitation in this case. Looking forward to your reply. Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#26>, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AH9-xO4DrwAf_oQ8AgwbM9gEFKbtDjXSks5vP1oLgaJpZM4bIv79.

Thank you very much for your quick response! What kind of data do you need to check? The segment-level CN result files from both techniques or the input bam files for CopywriteR?

Best,
Linda

[PeeperLab2]

Dear Linda, To start I would like to see the profiles, segment-level CN data will do for this. To really dig into the underlying cause the bam file would be preferred. But only if you want/can share this data. Otherwise we need to think of another solution (sending bam file for a part of the data for example). Also, could you provide me with a bit more information about the data? Did you use a Human targeted panel, whole exome? Ands what was the coverage/total reads? Could you also include the .log file from the CopywriteR run? Best Oscar On 25 Feb 2019, at 10:59, lindashirley99 <notifications@github.com<mailto:notifications@github.com>> wrote: Dear Linda Shirley, Thank you for using CopywriteR and thank you for informing us regarding inconsistencies between SNP6.0 and CopywriteR. So if I understand your email correctly you have high peaks (amplifications) with SNP6.0 that are not captured correctly by CopywriteR? I would love to see the profiles and look further into this discrepancy. Would it be possible to share these with me? Maybe even for one chromosome only? Kind regards, Oscar Oscar Krijgsman, PhD Postdoctoral research fellow Division of Molecular Oncology & Immunology The Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam, the Netherlands Phone: +31 20 512 2028 o.krijgsman@nki.nl<mailto:o.krijgsman@nki.nl>mailto:o.krijgsman@nki.nl On 22 Feb 2019, at 03:46, lindashirley99 <notifications@github.com<mailto:notifications@github.com>mailto:notifications@github.com> wrote: Hi, we found it several times that when we have both SNP6.0 data and WES data for the same sample, there is inconsistent CN results in high coverage (peak) regions. CopywriteR was not able to reflect high CN values in these regions whereas the mapped bam files do have high peaks. It seems that the off-target read-based approach might have limitation in this case. Looking forward to your reply. Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#26<#26>>, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AH9-xO4DrwAf_oQ8AgwbM9gEFKbtDjXSks5vP1oLgaJpZM4bIv79. Thank you very much for your quick response! What kind of data do you need to check? The segment-level CN result files from both techniques or the input bam files for CopywriteR? Best, Linda — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#26 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AH9-xO-I_qI44gU06kAvgFp7brTMs8_9ks5vQ7QBgaJpZM4bIv79>.

[lindashirley99]

segment_CopywriteR.txt
segment_SNP6.0.txt
Dear Oscar,
here are two respective segment-based CN result files from CopywriteR and PICNIC (SNP6.0) for one human sample. We checked the CN values of ERBB2 (chr17:37,842,393-37,886,915) for both, the result is inconsistent. And we do observe peaks in this region in WES data. If you need to check the bam file or fastq data further, please let me know.
Thanks!
Best,
Linda