Journal
Nature Communications
Publication Date
2015
Volume
6
Inclusive Pages
10086
Document Type
Open Access Publication
DOI
10.1038/ncomms10086
Rights and Permissions
C. Lu, et al. 22 December 2015. Patterns and functional implications of rare germline variants across 12 cancer types. Nature communications. Art. No. 10086. DOI: 10.1038/ncomms10086. http://www.nature.com/ncomms/2015/151209/ncomms10086/full/ncomms10086.html
Recommended Citation
Lu, Charles; Xie, Mingchao; Wendl, Michael C.; Wang, Jiayin; McLellan, Michael D.; Huang, Kuan-lin; Wyczalkowski, Matthew A.; Jayasinghe, Reyka; Ning, Jie; Tripathi, Piyush; Zhang, Qunyuan; Niu, Beifang; Ye, Kai; Schmidt, Heather K.; Fulton, Robert S.; McMichael, Joshua F.; Batra, Prag; Kandoth, Cyriac; Bharadwaj, Maheetha; Koboldt, Daniel C.; Miller, Christopher A.; Kanchi, Krishna L.; Eldred, James M.; Larson, David E.; Welch, John S.; Ozenberger, Bradley A.; Govindan, Ramaswamy; Walter, Matthew J.; Ellis, Matthew J.; Mardis, Elaine R.; Graubert, Timothy A.; Dipersio, John F.; Ley, Timothy J.; Wilson, Richard K.; Chen, Feng; and Ding, Li, "Patterns and functional implications of rare germline variants across 12 cancer types." Nature Communications. 6, 10086. (2015).
https://digitalcommons.wustl.edu/open_access_pubs/4472
Supplementary Figures 1-6, Supplementary Note 1 and Supplementary References
ncomms10086-s2.xlsx (55 kB)
Coverage and variant calling stats for discovery and control cohorts.
ncomms10086-s3.xlsx (135 kB)
Summary of germline truncation variants identified in 624 cancer associated genes. Rare germline truncation variants (<0.05% MAF in discovery case and control combined) identified in 624 cancer associated genes across 4,034 cancer cases.
ncomms10086-s4.xlsx (59 kB)
Rare germline truncation variants (<0.05% MAF in case and control combined) identified in 32 genes of interest across 1,627 validation cancer cases.
ncomms10086-s5.xlsx (55 kB)
69 germline truncations validated using whole genome sequencing data.
ncomms10086-s6.xlsx (43 kB)
Cancer associated gene lists used in this study, including 624 cancer associated genes, 114 cancer susceptibility genes reported in Rahman et al., 47 genes from Fanconi Anemia pathway.
ncomms10086-s7.xlsx (34 kB)
Frequencies of rare truncation variants in 3 gene lists across 12 cancer types.
ncomms10086-s8.xlsx (72 kB)
Burden analysis results for Pan-Cancer discovery cohort using rare truncation variants from 624 cancer associated genes in 3,125 Caucasian samples. The control cohort is 1039 WHI Caucasian cases.
ncomms10086-s9.xlsx (76 kB)
Burden analysis results for Pan-Cancer discovery cohort using rare truncation variants from 624 cancer associated genes in 4,034 cases. The control cohort is ESP 6503 sample set.
ncomms10086-s10.xlsx (44 kB)
Gene-based LOH analysis using rare truncation variants in significant genes from burden analysis.
ncomms10086-s11.xlsx (74 kB)
Site-based LOH analysis for rare truncation variants in 624 cancer associated genes.
ncomms10086-s12.xlsx (38 kB)
Gene-based LOH analysis for rare missense variants in 624 cancer associated genes.
ncomms10086-s13.xlsx (217 kB)
Site-based LOH analysis for rare missense variants in 624 cancer associated genes.
ncomms10086-s14.xlsx (58 kB)
LOH analysis of rare missense variants for discovering hotspot clusters.
ncomms10086-s15.xlsx (36676 kB)
Somatic mutations discovered in 3,368 out of 4,034 cancer cases.
ncomms10086-s16.xlsx (45 kB)
Somatic and Germline Mutation Relationship (mutual exclusive/co-occuring) across 12 cancer types. The genes used are 34 burden test significant genes and recurrent mutated genes (>= 5 somatic mutations across all cancer types).
ncomms10086-s17.xlsx (49 kB)
Somatic and Germline Mutation Relationship (mutual exclusive/co-occuring) for individual cancer types. The genes used are 34 burden test significant genes and recurrent mutated genes (>=2 somatic mutations in particular cancer type).
ncomms10086-s18.xlsx (40 kB)
Distribution of BRCA1, BRCA2, and ATM germline truncation variants and somatic mutations across 12 cancer types.
ncomms10086-s19.xlsx (59 kB)
Genes with rare germline truncation variants associated with somatic mutation frequencies.
ncomms10086-s20.xlsx (44 kB)
Genes with rare germline truncation variants associated with younger age of initial diagnosis with cancer type as a covariate.
ncomms10086-s21.xlsx (54 kB)
Genes with rare germline truncation variants associated with younger age of initial diagnosis for each cancer type.
ncomms10086-s22.xlsx (49 kB)
Primers used for creating 72 BRCA1 expression constructs with 68 rare missense variants introduced and 4 control truncation constructs.
ncomms10086-s23.xlsx (52 kB)
Homologous directed recombination assay results for 68 missense constructs, and 4 truncations as positive controls.
ncomms10086-s24.xlsx (55 kB)
Summary of BRCA1 validation status for A.I./non A.I. events and the enrichment factor.
ncomms10086-s25.xlsx (50 kB)
