Hello DepMap team, I am seeing a lot of cell lines with copy number values of 0 since the 2020 Q4 releasing. A lot of these cell lines did not have these low copy number values a few releases ago. Can you check if this could be a mistake? Thank you, Artur

Hello, That certainly sounds suspicious. We’ll investigate and will let you know once we understand whether this is accurate or a mistake. Thanks, Phil

Hi Phil, I was wondering if you have any updates on this issue. Thanks, Artur

Hi Artur, Sorry for the delay! Are you seeing genes for which the copy number changed dramatically for most cell lines, to a lower level? I will also say that there is a couple things to know with this new release that might have an influence in the number of zeroes. We used to only report CN on …

[image] Hi, Just to confirm the zeros problem. Best, Saed

Hi, To add to this thread, I found a relevant example. Some well-known ERBB2 amplified breast cancer cell lines have a CN count of 0 in the 20Q4 release (e.g. BT-474 and HCC1954). In previous releases these cell lines had a high CN count (5.78 for HCC1954 and 3.79 for BT-474 in the 20Q3 release). …

Thanks all for reporting this issue. Please see the following post for more information: [image] [IMPORTANT UPDATE] Issues with DepMap 20Q4 data Issues and Bugs We have discovered issues with files in the original 20Q4 data release that have now been addressed on the publi…

Hi, I was using the 20Q1 data for an analysis in my project. Can you please let me know if 20Q1 version does not contain this bug? Regards, Arkajyoti

@Arkajyoti this issue only affected 20Q4, so 20Q1 is Ok to use.

High number of cell lines with copy number equal to 0

Issues and Bugs

jnoorbak December 11, 2020, 9:36pm 7

Thanks all for reporting this issue. Please see the following post for more information:

Topic		Replies	Views
[IMPORTANT UPDATE] Issues with DepMap 20Q4 data Issues and Bugs	5	3939	January 9, 2021
Values in OmicsCNGene.csv 24Q2 release Issues and Bugs	1	241	July 3, 2024
Missing copy number values from the last 5 genes from all the cell lines Report an Issue	1	234	February 21, 2023
ACH001956 removed from 22Q4 entirely Issues and Bugs genetic-screens	3	381	May 1, 2023
Issues with copy number data Report an Issue	1	322	June 7, 2022

High number of cell lines with copy number equal to 0

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