gpcr/germvar2

TCGA germline variants

germVar2

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

install.packages("devtools")
library(devtools)
install_github("rj67/germVar2")

Data objects

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

Juptyer notebooks

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

Convenience functions

• plotMutRNASeq -- Plot mutation RNASeq levels
• plotDiseaseDistr -- Plot cancer type distribution given a list of mutations

Dependency

• plyr, dplyr, reshape2, ggplot2, magrittr, RColorbrewer, gridExtra