Dear Synapse team, I would appreciate if you could help me to navigate through the information in the latest release in order to extract below information: 1. What is the source of tissue of origin for sequencing? 1. For metastatic cases, what is the resectability status of the metastatic deposits at the time of diagnosis? ( i.e. resectable or non-resectable) I have tried to gather this information by searching relevant variables in the "BPC_CRC_v2.0-public_variable_synopsis.xlxs" file, but were not able to located the information that I need. Thanks in advance! Best, Hossein Moosavi

Created by Hossein Moosavi HMOOSAVI
In that case, it isn't possible to know which tissue from one of these multiple anatomic sites is used for NGS, which I am wondering about. In the CPT dataset, the 'sample_type' field only indicates 'Metastasis site unspecified.' Based on the explanation, there are no variables in any other provided accompanying data to disambiguate the site of metastasis for the NGS sample. Thank you for your assistance. Best, Hossein
Dear @HMOOSAVI, The sample in the CPT dataset with PATH_PROC_NUMBER 1 and PATH_REP_NUMBER 2 will correspond to the row in the pathology dataset with PATH_PROC_NUMBER 1 and PATH_REP_NUMBER 2. So in the above example, the NGS sample is associated with multiple anatomic sites in the pathology report. Best, Chelsea
So, if I understood correctly, the **number **in the **[path_rep_number]** column of the **Pathology dataset** corresponds to a **[path_site] column** ending in the same number? In the example above, because **[PATH_REP_NUMBER]** for the second row is **"2"**, it indicates the NGS sample is taken from **"C77.2 Intra-abdominal lymph nodes"**, as listed in **"PATH_SITE2"**. If I'm correct, the next two rows in the cancer panel dataset show a patient (record_id ending with 000147) with two samples: one from 'Primary tumor' and another from 'Metastasis site unspecified.' These can be linked to 'C20.9 Rectum NOS' and 'C22.0 Liver' in the pathology dataset, indicating the samples were taken from these tissue sources for NGS. Thanks for clarifying this! Best
Dear @HMOOSAVI, The cancer panel test dataset can be linked to the pathology dataset using the [record_id], [path_proc_number] and [path_rep_number] fields. In the below example the NGS sample GENIE-SAGE-0001-A is described in the second row of the pathology data set: CPT dataset **RECORD_ID**| CPT_GENIE_SAMPLE_ID | **PATH_PROC_NUMBER** | **PATH_REP_NUMBER** **GENIE-SAGE-0001** | GENIE-SAGE-0001-A | **1** | **2** Pathology dataset **RECORD_ID** | **PATH_PROC_NUMBER** | **PATH_REP_NUMBER** | PATH_SITE1 | PATH_SITE2 | ... | GENIE-SAGE-0001 | 1 | 1 | C48.1 Specified parts of peritoneum | | | **GENIE-SAGE-0001** | **1** | **2** | C18.0 Cecum | C77.2 Intra-abdominal lymph nodes | ... | Let me know if this helps. Best, Chelsea
@chelsea.nayan Dear Chelsea, Thank you for the clarifications. The information I am looking for is related to "**sample_type**" from the **Cancer Panel Test file**. Currently, this variable is indicated by "**Metastasis site unspecified**" or primary tumors. According to the data, it appears that aside from the primary tumors, several biospecimens from different tissues have been obtained for many patients. It also seems that many of these sampled tumors have undergone various analyses, such as pathological examinations. For example, the study by **Yaeger et al**. from **MSK cohort** (10.1016/j.ccell.2017.12.004) provided site-specific tissue of metastases subject to sequencing in the clinical data. Would it be possible to infer this information from the current clinical data, or perhaps will be an scheduled update for the clinical data in CRC cohort? Best.
Dear @HMOOSAVI, Thank you for your interest in the GENIE data. > What is the source of tissue of origin for sequencing? Can you expand on your question? Some of the potential variables of interest are listed below: [Cancer Diagnosis file](https://www.synapse.org/Synapse:syn39802574) - ca_d_site: ICD-O-3 code for the primary cancer site - crc_type: Indicates location of colorectal cancer - ca_first_dmets[1-10]: Site of distant metastases at diagnosis [Cancer Panel Test file](https://www.synapse.org/Synapse:syn39802578) - cpt_oncotree_code: The primary cancer diagnosis code based on the OncoTree ontology - sample_type: Sample type associated with specimen on which NGS was performed Site-specific profiling information can be viewed in the main GENIE [data guide](https://www.synapse.org/Synapse:syn21683345) under the **Genomic Profiling at Each Center** section. More information on the variables available are seen in the [CRC analytical data guide](https://www.synapse.org/Synapse:syn39433168). > For metastatic cases, what is the resectability status of the metastatic deposits at the time of diagnosis? ( i.e. resectable or non-resectable) Unfortunately this variable is not available in the CRC 2.0-public release and there are no plans to include this variable for this cohort. However, there is ca_crc_td which describes the count of colorectal cancer tumor deposits. Let me know if this helps!

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