Supplementary materials for
Pan-cancer sequencing analysis reveals frequent germline mutations in cancer genes
Ruomu Jiang, William Lee, Nadeem Riaz, Chris Sander, Timothy J Mitchison^, Debora S Marks^
install.packages("devtools")
library(devtools)
install_github("rj67/germVar2")
Dataframes that can be loaded
- list_goi -- candidate gene list
|
Gene |
Approved.Name |
Ensembl.Gene |
MDG |
CPG |
Class |
83 |
ATM |
ATM serine/threonine kinase |
ENSG00000149311 |
TRUE |
TRUE |
H-TSG |
135 |
BRCA1 |
breast cancer 1, early onset |
ENSG00000012048 |
TRUE |
TRUE |
H-TSG |
- all_patients -- all the patient information
Patient |
disease2 |
age |
agez |
EA |
race2 |
gender |
P6-A5OG |
ACC |
45 |
-0.2248333 |
TRUE |
WHITE |
FEMALE |
OR-A5JY |
ACC |
68 |
1.0679583 |
TRUE |
WHITE |
FEMALE |
- LoF_vars -- variant information, each row is a variant and columns are various annotation
|
Gene |
uid |
EFF |
TAC2 |
AN2 |
rare |
AAChange |
Transcript |
3444 |
BRCA1 |
17-41199682-C-T |
stop_gained |
1 |
17630 |
TRUE |
p.Trp711*/c.2133G>A |
ENST00000491747 |
3445 |
BRCA1 |
17-41201208-TG-T |
frameshift_variant |
1 |
17630 |
TRUE |
p.Gln1732fs/c.5194delC |
ENST00000493795 |
- LoF_muts -- variant carrier information, each row corresponds to the carrier of a particular variant.
|
Gene |
uid |
Patient |
disease2 |
AAChange |
DP |
AB |
N_hom |
nA |
nB |
8 |
BRCA1 |
17-41247941-T-G |
04-1336 |
OV |
c.453A>C |
39 |
0.9411765 |
FALSE |
3 |
0 |
205 |
BRCA1 |
17-41201208-TG-T |
09-2045 |
OV |
p.Gln1732fs/c.5194delC |
96 |
0.8541667 |
FALSE |
1 |
0 |
- nsSNP_vars -- variant information, each row is a variant and columns are various annotation
|
Gene |
uid |
EFF |
TAC2 |
AN2 |
rare |
AAChange |
Transcript |
dele |
RCVaccession |
cosm_scount |
17-41201181-C-A |
BRCA1 |
17-41201181-C-A |
missense_variant |
1 |
17630 |
TRUE |
p.Gly1788Val/c.5363G>T |
ENST00000357654 |
TRUE |
RCV000048961;RCV000031241 |
NA |
17-41215920-G-A |
BRCA1 |
17-41215920-G-A |
missense_variant |
1 |
17630 |
TRUE |
p.Ala1708Val/c.5123C>T |
ENST00000357654 |
FALSE |
NA |
NA |
- nsSNP_muts -- variant carrier information, each row corresponds to the carrier of a particular variant.
|
Gene |
uid |
Patient |
disease2 |
AAChange |
DP |
AB |
N_hom |
nA |
nB |
3 |
BRCA1 |
17-41245027-G-A |
02-0047 |
GBM |
p.Arg841Trp/c.2521C>T |
330 |
0.4575758 |
FALSE |
1 |
1 |
89 |
BRCA1 |
17-41245027-G-A |
05-5425 |
LUAD |
p.Arg841Trp/c.2521C>T |
195 |
0.5179487 |
FALSE |
3 |
1 |
Reproduce most of the analysis/figures in the paper
- project_overview -- Samples, candidate gene, all variants overview.
- known_cancer_gene_variants -- Summary variants in known cancer genes.
- loss_of_heterozygousity_analysis -- LOH of all germline variants
- low_frequency_variants_association -- Assocation test of low frequency missense and truncation variants comparing to 1000G and ESP
- plotMutRNASeq -- Plot mutation RNASeq levels
- plotDiseaseDistr -- Plot cancer type distribution given a list of mutations
- plyr, dplyr, reshape2, ggplot2, magrittr, RColorbrewer, gridExtra