Data type |
Data attributes |
Inclusion level1 |
Recommended standards or vocabularies |
|
|
|
|
Gene |
Name |
MIASM |
HGNC (HUGO Gene Nomenclature Committee) (www.genenames.org/) |
|
RefSeq/LRG |
MIASM |
NCBI gene reference sequence (www.ncbi.nlm.nih.gov/refseq/) |
|
|
|
|
Variant (mutation) |
Genomic location |
MIASM |
Genomic coordinates (indicate genome build) HGVS format2 (g.) (www.hgvs.org/mutnomen/) |
|
Genomic reference and altered sequence |
MIASM |
|
|
Description variant on DNA or RNA level |
MIASM |
HGVS format2 (c. and r.) |
|
Deduced amino-acid change |
R |
HGVS format2 (p.) |
|
Predicted impact on protein activities |
R |
SIFT, PolyPhen-2, … |
|
|
|
|
Tumor sample |
Topography (organ site) |
MIASM |
International Classification for Disease in Oncology, 3rd ed. (ICD-O-3) (www.seer.cancer.gov/) |
|
Morphology (histological type) |
MIASM |
ICD-O-3 (www.seer.cancer.gov/) |
|
Source of specimen |
MIASM |
Surgery, biopsy, xenograft, cell-line, body fluid, … |
|
Origin of tumor |
MIASM |
primary, recurrent, secondary, metastasis, … |
|
Grade |
R |
Use most popular international system for each type of cancer |
|
Stage |
R |
TNM, SEER |
|
|
|
|
Patient |
Age at diagnosis |
R |
Time from birth to cancer diagnosis or surgery in years |
|
Sex |
R |
M/F (male/female) |
|
Country of living |
R |
UN population demographics (unstats.un.org/unsd/methods/m49/m49.htm); use country of hospital where recruited |
|
Ethnicity |
R |
SEER (seer.cancer.gov/manuals/2007/SPCSM_2007_AppendixD.pdf) |
|
Family history |
D |
Cancer or syndrome name using OMIM nomenclature |
|
Known germline mutation |
D |
Name of altered gene (HUGO nomenclature) |
|
|
|
|
Study design |
Type |
MIASM |
Retrospective, prospective, case-control, clinical trial, … |
|
Sample inclusion criteria |
R |
- |
|
Hospital/institution name |
R |
- |
|
Recruitment period |
R |
Years |
|
Variant (mutation) detection method |
MIASM |
Sanger sequencing, Next-generation sequencing (type), pre-screening method if any. |
|
region of the gene(s) that has been screened |
MIASM |
Exons and introns numbers, |
|
tissue sampling |
MIASM |
Fresh, frozen, paraffin-embedded, … |
|
starting material for variant detection |
MIASM |
DNA, RNA, protein, … |
|
Somatic status verification |
R |
Indicate if and how somatic origin of variants has been assessed |
|
|
|
|
Clinical Information3 |
Treatment |
D |
Drug/protocol name |
|
Treatment response |
D |
Response Evaluation Criteria in Solid Tumors (RECIST) vocabulary |
|
Follow-up time (range and median) |
D |
Months |
|
Overall survival |
D |
Time between diagnosis or surgery and death or last follow-up in months |
|
Disease-free survival |
D |
Time between diagnosis or surgery and first recurrence or last follow-up in months |
|
|
|
|
Life-style and exposures |
Smoking habit |
D |
- |
|
Drinking habit |
D |
- |
|
Infections |
D |
- |
|
Occupation/Job activity |
D |
Bureau of Labor Statistics, Standard Occupational Classification System (www.bls.gov/soc/) |
|
Chemical and radiation exposures |
D |
- |
|
Reproductive factors |
D |
- |