reorg

As detailed in Supplemental Table S5, many of the studies contributing to our gene lists did not have matched germline DNA from every sample. It has been shown that some genes have disproportionately higher numbers of rare germline variants. The genes with the highest number of rare variants overall have been described in a recent study as FrequentLy mutAted GeneS (FLAGS)@shyrFLAGSFrequentlyMutated2014. These genes should be considered with caution in any study that associates them with a phenotype. Insufficient removal of germline variants in the studies explored herein could explain some of the genes in Tiers 2 and 3. To evaluate this, we used the ranking of the frequency of rare mutations in all genes covered by common exome panels. This "FLAGS rank" assignes the lowest rank to genes with the highest number of rare variants (e.g. TTN = 1, MUC16 = 2, OBSCN = 3, etc). We used the distribution of ranks across the three tiers of DLBCL genes to evaluate the relative extent to which the genes on each list may be explained, in part, by inadequate removal of rare germline variants. If there is no influence on genes, the FLAGS_rank is expected to follow a uniform distribution. Accordingly, we compared each of the four gene lists to a uniform distribution using a negative binomial regression. Interestingly, the distributions of FLAGS_rank for Tier 2 and Tier 3 and the Cosmic Cancer Gene Census (CGC)@futrealCensusHumanCancer2004 genes were significantly different than the uniform distribution. In contrast, the distribution for Tier 1 genes was not significantly different from a uniform distribution. This is consistent with the Tier 1 DLBCL genes having minimal contamination of genes due to rare germline variants. To evaluate whether the separation of genes into Tiers 2 and 3 offers some benefit in this regard, we compared the Tier 2 DLBCL genes to the other lists. Indeed, Tier 2 showed a significant difference when compared to Tier 3 (P=3.86e-06). Based on this, we conclude that the Tier 3 gene list is dominated by FLAGS whereas Tier 2 represents a mixture of true DLBCL genes and FLAGS.

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<figcaption><strong>Supplemental Figure S2. Comparing FLAGS rank in the DLBCL genes.</strong> <br>

The FLAGS rank of DLBCL genes in Tier 1, 2 and 3 is compared. The genes in the COSMIC CGC list are included for comparison. Values closer to 1 indicate the gene has a higher number of rare germline variants.

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