Sample Type Specification
Summary
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 |
---|---|---|---|
ssm_m |
analyzed_sample_id |
Non-normal | |
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 |
|
exp_seq_m | analyzed_sample_id | Any | |
mirna_seq_m | analyzed_sample_id | Any |