Biospecimen data refers to information associated with the physical sample taken from a participant and its processing down to the aliquot level for sequencing experiments. This data falls into several key categories:
For major NCI CCG programs, biospecimen data is provided by a Biospecimen Core Resource (BCR) under contract to the NCI. Data is submitted in an established, schema-valid XML format. This data includes program and project identifiers, UUIDs, and the relationships between case, sample, and aliquot. UUIDs submitted by BCRs are typically adopted by the GDC.
For other submitters, data in the BCR XML format is accepted. However, the GDC also provides a simpler means for submission of a minimal set of biospecimen data, in which a data may be formatted in a JSON or tab-delimited (TSV) text file and submitted to the GDC Submission Portal.
The GDC Data Model uses a graph representation that has no technical limits on adjusting the entities and relationships. However there may be effects on quality control, reporting, accounting and user interface/experience. Therefore, major changes to the model needed to support new biospecimen information will undergo review by the GDC Data Model Change Control Board.
Links to the dictionary entry for each biospecimen entity are listed below. Each entry contains information about each field and a downloadable template for submission.
Term | Category | CDE | Required? |
---|---|---|---|
a260 a280 ratio | Analyte | 5432595 | Optional |
adapter name | Read group | --- | Optional |
adapter sequence | Read group | --- | Optional |
aliquot quantity | Aliquot | --- | Optional |
aliquot volume | Aliquot | --- | Optional |
amount | Aliquot | --- | Optional |
amount | Analyte | --- | Optional |
analyte quantity | Analyte | --- | Optional |
analyte type | Aliquot | 2513915 | Optional |
analyte type | Analyte | 2513915 | Required |
analyte volume | Analyte | --- | Optional |
base caller name | Read group | --- | Optional |
base caller version | Read group | --- | Optional |
biospecimen anatomic site | Sample | 4742851 | Optional |
biospecimen laterality | Sample | 2007875 | Optional |
bone marrow malignant cells | Slide | --- | Optional |
catalog reference | Sample | --- | Optional |
chipseq antibody | Read group | --- | Optional |
chipseq target | Read group | --- | Optional |
composition | Sample | 5432591 | Optional |
concentration | Aliquot | 5432594 | Optional |
concentration | Analyte | 5432594 | Optional |
consent type | Case | --- | Optional |
creation datetime | Portion | 5432592 | Optional |
current weight | Sample | 5432606 | Optional |
days to collection | Sample | 3008340 | Optional |
days to consent | Case | --- | Optional |
days to lost to followup | Case | 6154721 | Optional |
days to sample procurement | Sample | --- | Optional |
days to sequencing | Read group | --- | Optional |
diagnosis pathologically confirmed | Sample | --- | Optional |
disease type | Case | 6161017 | Required |
distance normal to tumor | Sample | 3088708 | Optional |
distributor reference | Sample | --- | Optional |
experiment name | Read group | --- | Required |
experimental protocol type | Analyte | --- | Optional |
flow cell barcode | Read group | --- | Optional |
fragment maximum length | Read group | --- | Optional |
fragment mean length | Read group | --- | Optional |
fragment minimum length | Read group | --- | Optional |
fragment standard deviation length | Read group | --- | Optional |
fragmentation enzyme | Read group | --- | Optional |
freezing method | Sample | 5432607 | Optional |
growth rate | Sample | --- | Optional |
includes spike ins | Read group | --- | Optional |
index date | Case | 6154722 | Optional |
initial weight | Sample | 5432605 | Optional |
instrument model | Read group | 5432604 | Optional |
intermediate dimension | Sample | --- | Optional |
is ffpe | Portion | 4170557 | Optional |
is ffpe | Sample | 4170557 | Optional |
is paired end | Read group | --- | Required |
lane number | Read group | --- | Optional |
library name | Read group | --- | Required |
library preparation kit catalog number | Read group | --- | Optional |
library preparation kit name | Read group | --- | Optional |
library preparation kit vendor | Read group | --- | Optional |
library preparation kit version | Read group | --- | Optional |
library selection | Read group | --- | Required |
library strand | Read group | --- | Optional |
library strategy | Read group | --- | Required |
longest dimension | Sample | 5432602 | Optional |
lost to followup | Case | 6161018 | Optional |
method of sample procurement | Sample | --- | Optional |
multiplex barcode | Read group | --- | Optional |
no matched normal low pass wgs | Aliquot | --- | Optional |
no matched normal targeted sequencing | Aliquot | --- | Optional |
no matched normal wgs | Aliquot | --- | Optional |
no matched normal wxs | Aliquot | --- | Optional |
normal tumor genotype snp match | Analyte | 4588156 | Optional |
number expect cells | Read group | --- | Optional |
number proliferating cells | Slide | 5432636 | Optional |
oct embedded | Sample | 5432538 | Optional |
passage count | Sample | --- | Optional |
pathology report uuid | Sample | --- | Optional |
percent eosinophil infiltration | Slide | 2897700 | Optional |
percent follicular component | Slide | --- | Optional |
percent granulocyte infiltration | Slide | 2897705 | Optional |
percent inflam infiltration | Slide | 2897695 | Optional |
percent lymphocyte infiltration | Slide | 2897710 | Optional |
percent monocyte infiltration | Slide | 5455535 | Optional |
percent necrosis | Slide | 2841237 | Optional |
percent neutrophil infiltration | Slide | 2841267 | Optional |
percent normal cells | Slide | 2841233 | Optional |
percent rhabdoid features | Slide | 6790120 | Optional |
percent sarcomatoid features | Slide | 2429786 | Optional |
percent stromal cells | Slide | 2841241 | Optional |
percent tumor cells | Slide | 5432686 | Optional |
percent tumor nuclei | Slide | 2841225 | Optional |
platform | Read group | --- | Required |
portion number | Portion | 5432711 | Optional |
preservation method | Sample | 5432521 | Required |
primary site | Case | 6161019 | Required |
prostatic chips positive count | Slide | --- | Optional |
prostatic chips total count | Slide | --- | Optional |
prostatic involvement percent | Slide | --- | Optional |
read group name | Read group | --- | Required |
read length | Read group | --- | Required |
ribosomal rna 28s 16s ratio | Analyte | --- | Optional |
rin | Read group | 5278775 | Optional |
rna integrity number | Analyte | --- | Optional |
sample ordinal | Sample | --- | Optional |
section location | Slide | --- | Required |
selected normal low pass wgs | Aliquot | --- | Optional |
selected normal targeted sequencing | Aliquot | --- | Optional |
selected normal wgs | Aliquot | --- | Optional |
selected normal wxs | Aliquot | --- | Optional |
sequencing center | Read group | --- | Required |
sequencing date | Read group | --- | Optional |
shortest dimension | Sample | 5432603 | Optional |
single cell library | Read group | --- | Optional |
size selection range | Read group | --- | Optional |
source center | Aliquot | --- | Optional |
specimen type | Sample | C70713 | Required |
spectrophotometer method | Analyte | 3008378 | Optional |
spike ins concentration | Read group | --- | Optional |
spike ins fasta | Read group | --- | Optional |
target capture kit catalog number | Read group | --- | Optional |
target capture kit name | Read group | --- | Optional |
target capture kit target region | Read group | --- | Optional |
target capture kit vendor | Read group | --- | Optional |
target capture kit version | Read group | --- | Optional |
target capture kit | Read group | --- | Required |
time between clamping and freezing | Sample | 5432611 | Optional |
time between excision and freezing | Sample | 5432612 | Optional |
tissue collection type | Sample | --- | Optional |
tissue microarray coordinates | Slide | --- | Optional |
tissue type | Sample | 5432687 | Required |
to trim adapter sequence | Read group | --- | Optional |
tumor code id | Sample | --- | Optional |
tumor code | Sample | --- | Optional |
tumor descriptor | Sample | 3288124 | Required |
weight | Portion | 5432593 | Optional |
well number | Analyte | 5432613 | Optional |
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