One row by sample

No case sensitivity, you can use lowercase and uppercase.

Do not delete nor edit the headers of the columns.

If you have already created the patient case (readable ID), the run template (name) or the oncologist (email) on the OncoKDM platform, they will be reused without creating a new one. 

If a field is not required, you do not have to encode anything. 

run_template__name (*)

readable_id (*), same as the patient id

patient_sex (* only if related to a new patient) must be M or F.

patient_country* must be written in English or ISO code

patient__birthdate* be of the format « YYYY-MM-DD ».

oncologist_firstname

oncologist_lastname

oncologist_email (* only if related to a new patient)

cancer_name (*) must be chosen from the different cancer types of the oncotree standard. Please note that the cancer_primary_site_name and the cancer_name must have the same relationship that on the oncotree standard.

cancer_primary_site_name (*) must be chosen from the different cancer types of the oncotree standard. Please note that the cancer_primary_site_name and the cancer_name must have the same relationship that on the oncotree standard.

external_id (*), is the sample id

 files_names (*): VCF, BAM, or FastQ file name. If you have several files to integrate into the files_names column, you must separate them with a pipe (“|”). Example: sample1.fastq|sample2.fastq

METASTASES: yes; no; unknown

METASTASES_LOCATION: free text (mandatory if the previous answer is yes)

PREVIOUS_MEDICATION: yes; no; unknown

PREVIOUS_MEDICATION_DESCRIPTION: free text (mandatory if the previous answer is yes)

COMORBIDITIES: yes; no; unknown

COMORBIDITIES_WHICH: free text (mandatory if the previous answer is yes)

CONCOMITANT_MEDICATION: yes; no; unknown

MACRO_DISSECTION: yes; no; unknown

TUMOR_CELL_PERCENTAGE number (float number with 2 decimals, e.g. 46,7%)

LABORATORY_ORIGIN

SAMPLE_ORIGIN: free text

COLLECTION_DATE be of the format « YYYY-MM-DD ».

XLSX 

CSV