This database contains variants from the Cancer Genome Project. It is “an ongoing effort to catalogue those genes for which mutations have been causally implicated in cancer. The original census and analysis was published in Nature Reviews Cancer and supplemental analysis information related to the paper is also available. Currently, more than 1% of all human genes are implicated via mutation in cancer. Of these, approximately 90% have somatic mutations in cancer, 20% bear germline mutations that predispose to cancer and 10% show both somatic and germline mutations.” {1}
Not all genes are available in the knownGene or refGene database so you will lose a few genes if you try to find all variants within these cancer genes through location information of knownGene or refGene. The latest version of Cancer Gene Census lists the following genes that are not available in refGene.name2: AMER1, C12orf9, CDKN2a, FAM22B, H3F3AP4, IGH, IGK@, IGL@, KMT2A, KMT2B, KMT2C, NUTM1, NUTM2A, TCRB, TRA, TRD.
This database should be linked to a field of common gene name, e.g. refGene.name2. You can use load it by
vtools use refGene
vtools use CancerGeneCensus --linked_by refGene.name2
NFO: Downloading annotation database from http://vtools.houstonbioinformatics.org/annoDB/CancerGeneCensus-20130711.DB.gz
INFO: Using annotation DB CancerGeneCensus in project ra.
INFO: This database contains variants from the Cancer Genome Project. It is
an ongoing effort to catalogue those genes for which mutations have been causally
implicated in cancer. The original census and analysis was published in Nature
Reviews Cancer and supplemental analysis information related to the paper is also
available. Currently, more than 1% of all human genes are implicated via mutation
in cancer. Of these, approximately 90% have somatic mutations in cancer, 20% bear
germline mutations that predispose to cancer and 10% show both somatic and
germline mutations.
INFO: 471 out of 23242 refgene.name2 are annotated through annotation database CancerGeneCensus
WARNING: 16 out of 487 values in annotation database CancerGeneCensus are not linked to the project.
If you would like to use the knownGene database, you will have to link through knownGene.name. The command to use would be
vtools use knownGene
vtools use CancerGeneCensus --linked_by knownGene.name --linked_field kgID
INFO: Using annotation DB CancerGeneCensus in project ra.
INFO: This database contains variants from the Cancer Genome Project. It is
an ongoing effort to catalogue those genes for which mutations have been causally
implicated in cancer. The original census and analysis was published in Nature
Reviews Cancer and supplemental analysis information related to the paper is also
available. Currently, more than 1% of all human genes are implicated via mutation
in cancer. Of these, approximately 90% have somatic mutations in cancer, 20% bear
germline mutations that predispose to cancer and 10% show both somatic and
germline mutations.
INFO: 433 out of 80922 knowngene.name are annotated through annotation database CancerGeneCensus
WARNING: 54 out of 487 values in annotation database CancerGeneCensus are not linked to the project.
Description: Cancer Genome Project
Database type: field
Number of records: 487
Number of distinct entries: 485
Reference genome *: ['kgID']
Field: GeneSymbol
Type: string
Missing entries: 0
Unique Entries: 484
Field: kgID
Type: string
Missing entries: 0
Unique Entries: 485
Field: Name
Type: string
Missing entries: 0
Unique Entries: 487
Field: GeneID
Type: string
Missing entries: 0
Unique Entries: 485
Field: Chr
Type: string
Missing entries: 0
Unique Entries: 24
Field: ChrBand
Type: string
Missing entries: 0
Unique Entries: 343
Field: CancerSomaticMut
Type: string
Missing entries: 0
Unique Entries: 2
Field: CancerGermlineMut
Type: string
Missing entries: 0
Unique Entries: 3
Field: TumourTypesSomatic
Type: string
Missing entries: 0
Unique Entries: 230
Field: TumourTypesGermline
Type: string
Missing entries: 0
Unique Entries: 59
Field: CancerSyndrome
Type: string
Missing entries: 0
Unique Entries: 66
Field: TissueType
Type: string
Missing entries: 0
Unique Entries: 26
Field: CancerMolecularGenetics
Type: string
Missing entries: 0
Unique Entries: 9
Field: MutationType
Type: string
Missing entries: 0
Unique Entries: 77
Field: TranslocationPartner
Type: string
Missing entries: 0
Unique Entries: 159
Field: OtherGermlineMut
Type: string
Missing entries: 0
Unique Entries: 3
Field: OtherSyndromeOrDisease
Type: string
Missing entries: 0
Unique Entries: 33
Abbreviation Term
A amplification
AEL acute eosinophilic leukemia
AL acute leukemia
ALCL anaplastic large-cell lymphoma
ALL acute lymphocytic leukemia
AML acute myelogenous leukemia
AML* acute myelogenous leukemia (primarily treatment associated)
APL acute promyelocytic leukemia
B-ALL B-cell acute lymphocytic leukaemia
B-CLL B-cell Lymphocytic leukemia
B-NHL B-cell Non-Hodgkin Lymphoma
CLL chronic lymphatic leukemia
CML chronic myeloid leukemia
CMML chronic myelomonocytic leukemia
CNS central nervous system
D large deletion
DFSP dermatofibrosarcoma protuberans
DLBCL diffuse large B-cell lymphoma
DLCL diffuse large-cell lymphoma
Dom dominant
E epithelial
F frameshift
GIST gastrointestinal stromal tumour
JMML juvenile myelomonocytic leukemia
L leukaemia/lymphoma
M mesenchymal
MALT mucosa-associated lymphoid tissue lymphoma
MDS myelodysplastic syndrome
Mis Missense
MLCLS mediastinal large cell lymphoma with sclerosis
MM multiple myeloma
MPD Myeloproliferative disorder
N nonsense
NHL non-Hodgkin lymphoma
NK/T natural killer T cell
NSCLC non small cell lung cancer
O other
PMBL primary mediastinal B-cell lymphoma
pre-B All pre-B-cell acute lymphoblastic leukaemia
Rec reccesive
S splice site
T translocation
T-ALL T-cell acute lymphoblastic leukemia
T-CLL T-cell chronic lymphocytic leukaemia
TGCT testicular germ cell tumour
T-PLL T cell prolymphocytic leukaemia
vtools use CancerGeneCensus --linked_by refGene.name2
vtools select variant 'GeneSymbol is not NULL' -t CancerVariants
If you are interested in only some of the cancer genes, but would like to get variants not only within the genes, but also up and downstream of these genes, you will first have to get a list of genes.
For example, you can run
vtools execute select GeneSymbol from CancerGeneCensus
to get a list of cancer genes.
Then, to locate variants in a different region as the default range of the refGene database (from txStart to txEnd), you will need to re-use the refGene database using command
vtools use refGene --linked_fields chr 'txStart-5000', 'txEnd+5000'
Then, you can use the following commands to create tables of variants for each gene:
for gene in GENE1 GENE2 GENE3
do
vtools select variant "refGene.name2='${gene}'" -t \\({gene}_ext
done