Sample Type Specification


This specification details what the expected specimen_type/reference_sample_type should be for the sample ID fields analyzed_sample_id and matched_sample_id in each of the metadata files.

Specimen Type Categories

We can categorize the terms in the specimen_type codelist into two categories - Normal or Non-Normal. The Non-Normal category encompasses all types of Primary tumour, Recurrent tumour, Metastatic tumour, Xenograft and Cell line tumours.

Normal Non-Normal
Normal - solid tissue Primary tumour - solid tissue
Normal - blood derived Primary tumour - blood derived (peripheral blood)
Normal - bone marrow Primary tumour - blood derived (bone marrow)
Normal - tissue adjacent to primary Primary tumour - additional new primary
Normal - other Primary tumour - other
Normal - lymph node Primary tumour - lymph node
Normal - EBV immortalized Recurrent tumour - solid tissue
Normal - buccal cell Recurrent tumour - blood derived (peripheral blood)
Recurrent tumour - blood derived (bone marrow)
Recurrent tumour - other
Metastatic tumour - NOS
Metastatic tumour - lymph node
Metastatic tumour - metastasis local to lymph node
Metastatic tumour - metastasis to distant location
Metastatic tumour - additional metastatic
Xenograft - derived from primary tumour
Xenograft - derived from tumour cell line
Cell line - derived from tumour
Primary tumour - lymph node
Metastatic tumour - other
Cell line - derived from xenograft tumour

Expected Sample Types

In order to denote a mutation for simple somatic, copy number and structural somatic mutations, a non-normal analyzed sample must be compared against a normal sample. For simple germline variation, the analyzed sample must always be normal.

Data Type File-specific Sample Field Expected specimen_type Expected reference_sample_type


matched_sample_id Normal
cnsm_m analyzed_sample_id Non-normal
matched_sample_id Normal
stsm_m analyzed_sample_id Non-normal
matched_sample_id Normal
sgv_m analyzed_sample_id Normal
jcn_m analyzed_sample_id Any
pexp_m analyzed_sample_id Any
meth_array_m analyzed_sample_id Any
meth_seq_m analyzed_sample_id Any
exp_array_m analyzed_sample_id Any
  • If specimen_type for analyzed_sample_id is Normal:
  • If the specimen_type for analyzed_sample_id is Non-normal:
  • exp_seq_m analyzed_sample_id Any
    mirna_seq_m analyzed_sample_id Any