This forum is moderated by staff at Sage Bionetworks and additional scientists involved in Project Genie.   Please **start a new thread** for your question, rather than responding to this thread.

Created by Kristen Dang kkdang
Dear @yiming1967, Please create a new thread for your post so that it is easier for others to find your question and answer.
In data_clinical_sample.txt, the CANCER_TYPE of lung has three types: [1] "Non-Small Cell Lung Cancer" "Small Cell Lung Cancer" [3] "Lung Cancer, NOS" What is the last one: "Lung Cancer, NOS"? what does "NOS" mean here? Thx Ming
Question about CNV data, per description in the data guide "-2: deep loss, possibly a homozygous deletion -1: single-copy loss (heterozygous deletion) 0: diploid 1: low-level gain 2: high-level amplification." Could I know how GENIE harmonized such CNV data? I assume they were produced with GISTIC, but GISTIC has completely different definition of -2/-1. In particular, -1 is low-level loss, and -2 is high level loss equivalent to hemizygous (single-copy loss). This is very different from the description from GENIE.
Hormone receptors are not publicly available for GENIE data. The available clinical data is described here: https://www.synapse.org/#!Synapse:syn7222066/wiki/409778.
Is there any information available for hormone receptors (ER, PR and HER2) in the GENIE project for breast cancer patients? Thanks
Dear all, anyone knows when will the survival and drug treatment data be available ? Thanks
Dear @dchakrob, No, there is no gene expression data available or planned in the GENIE project. Thanks for your question.
Thank you for releasing the dataset publicly. I had a couple of quick questions: 1) Is there some associated gene expression data for the samples? 2) If yes, then where and how can I access it? If not, then are there any plans to release it in the near future?
Dear Kahn, The file you are looking for is the [genie_combined.bed](syn7851252) file. This file has Hugo_Symbol and SEQ_ASSAY_ID column, where the SEQ_ASSAY_ID is the panel name. Best, Thomas
In the Data Guide pdf on page 5, there are several files listed that seems to contain the genes tested by each panel. When will those files be made available?
Hi Coco, Please create a new thread for your post. This makes it easier to see and respond to new messages. Thanks.
What a great news of sharing the Genie database publicly!! I have successfully downloaded the file but am wondering which software that I need to download/purchase in order to open and analyze all these documents. Would you mind guiding me through this? Unfortunately, we don't have a colleague working in this particular field.

Create a new thread for any questions about the GENIE dataset. page is loading…