T of origin could not be determined. The omitted mutations comprised eight non-synonymous missense and two truncating mutations. Even if we consider the most unfavorable case, that the 10781694 two truncating mutations were classified as later, the MLE for the number of nonrandom truncation mutations in the earlier group is is n = 9, with a 95 lower bound of 3 when p = 0.4, and n = 5 or 6 with a 95 lower bound of 0 when p = 0.59.Timing of Genetic Instability and Other FunctionsThis earlier versus later classification may help us to understand a variety of issues including the timing and origins of chromosome instability and the drivers versus passengers problem for this particular tumor. There has been much discussion of when chromosomal instability occurs, for example some have suggested it as a key facilitator of early tumorigenesis, notably causing loss of heterozygosity of APC in colorectal cancers [21]. In contrast, some suggest that the extensive rearrangements of carcinoma karyotypes might be late progression events [7,8]. Others favor a Title Loaded From File transient period of chromosome instability, either at `crisis’ Title Loaded From File caused by telomere loss, or at some other catastrophic event such as `chromothripsis’, in which one or more chromosomes undergo massive rearrangement, apparently in a single event [9,10]. We observed roughly equal ratios of structural to sequence-level mutations earlier and later. Although there are other possibilities, a reasonable explanation is that both mutational processes were happening at approximately the same rate for much of the evolution of the tumour. We did not see, for example, a much higher ratio of rearrangements to point mutations in the earlierTable 1. Summary of Mutations in HCC1187 and their timing.Total Reported Total Classifiable Unclassifiable All Mutations All Structural mutations Translocation Deletion (,2 Mb) Duplication (,2 Mb) All Sequence-level mutations Synonymousa Missense Nonsense INDEL Mutation Classification Nonsense and INDEL mutations Missense classifiable by SIFT SIFT non-functional SIFT Functional CAN genes Expressed fusion transcripts In-frame transcriptb Out of Frame transcriptbaEarlier 61 27 13 7 7 34 0 23 3Later 62 21 9 5 7 41 4 35 2Earlier 50 56 59 58 50 45 0 40 60144 59 22 13 24 85 4 66 5123 48 22 12 14 75 4 58 521 11 0 1 10 10 0 8 015 52 30 22 9 12 413 47 28 19 9 9 32 5 2 3 0 3 011 16 9 7 6 7 32 31 19 12 3 2 085 34 32 37 67 77 100Few synonymous mutations are known since they were not reported in the main survey of point mutations [3]. In-frame and out-of-frame expressed fusion transcripts. doi:10.1371/journal.pone.0064991.tbTiming of Mutations in a Breast Cancer Genomeclass, as expected if most of the rearrangements had occurred during a telomere crisis before endoreduplication. An important value of the classification is that mutations that may cause ongoing chromosome instability must generally be in the `earlier’ group as, by definition, they must pre-date almost all chromosome changes, which were quite numerous before endoreduplication. Among the mutated genes that might contribute to chromosome instability were TP53, BAP1 and PAXIP1, and all were indeed classified as earlier. BAP1/UCHL2 (BRCA1associated protein1/ubiquitin carboxy-terminal hydrolase 2) was discovered as a binding partner of BRCA1 and appears to participate in the DNA damage response by interacting with BRCA1 and BARD1 [25;26]. It is a deubiquitinase that controls ubiquitination of Histone H2A, and is also a component of the Po.T of origin could not be determined. The omitted mutations comprised eight non-synonymous missense and two truncating mutations. Even if we consider the most unfavorable case, that the 10781694 two truncating mutations were classified as later, the MLE for the number of nonrandom truncation mutations in the earlier group is is n = 9, with a 95 lower bound of 3 when p = 0.4, and n = 5 or 6 with a 95 lower bound of 0 when p = 0.59.Timing of Genetic Instability and Other FunctionsThis earlier versus later classification may help us to understand a variety of issues including the timing and origins of chromosome instability and the drivers versus passengers problem for this particular tumor. There has been much discussion of when chromosomal instability occurs, for example some have suggested it as a key facilitator of early tumorigenesis, notably causing loss of heterozygosity of APC in colorectal cancers [21]. In contrast, some suggest that the extensive rearrangements of carcinoma karyotypes might be late progression events [7,8]. Others favor a transient period of chromosome instability, either at `crisis’ caused by telomere loss, or at some other catastrophic event such as `chromothripsis’, in which one or more chromosomes undergo massive rearrangement, apparently in a single event [9,10]. We observed roughly equal ratios of structural to sequence-level mutations earlier and later. Although there are other possibilities, a reasonable explanation is that both mutational processes were happening at approximately the same rate for much of the evolution of the tumour. We did not see, for example, a much higher ratio of rearrangements to point mutations in the earlierTable 1. Summary of Mutations in HCC1187 and their timing.Total Reported Total Classifiable Unclassifiable All Mutations All Structural mutations Translocation Deletion (,2 Mb) Duplication (,2 Mb) All Sequence-level mutations Synonymousa Missense Nonsense INDEL Mutation Classification Nonsense and INDEL mutations Missense classifiable by SIFT SIFT non-functional SIFT Functional CAN genes Expressed fusion transcripts In-frame transcriptb Out of Frame transcriptbaEarlier 61 27 13 7 7 34 0 23 3Later 62 21 9 5 7 41 4 35 2Earlier 50 56 59 58 50 45 0 40 60144 59 22 13 24 85 4 66 5123 48 22 12 14 75 4 58 521 11 0 1 10 10 0 8 015 52 30 22 9 12 413 47 28 19 9 9 32 5 2 3 0 3 011 16 9 7 6 7 32 31 19 12 3 2 085 34 32 37 67 77 100Few synonymous mutations are known since they were not reported in the main survey of point mutations [3]. In-frame and out-of-frame expressed fusion transcripts. doi:10.1371/journal.pone.0064991.tbTiming of Mutations in a Breast Cancer Genomeclass, as expected if most of the rearrangements had occurred during a telomere crisis before endoreduplication. An important value of the classification is that mutations that may cause ongoing chromosome instability must generally be in the `earlier’ group as, by definition, they must pre-date almost all chromosome changes, which were quite numerous before endoreduplication. Among the mutated genes that might contribute to chromosome instability were TP53, BAP1 and PAXIP1, and all were indeed classified as earlier. BAP1/UCHL2 (BRCA1associated protein1/ubiquitin carboxy-terminal hydrolase 2) was discovered as a binding partner of BRCA1 and appears to participate in the DNA damage response by interacting with BRCA1 and BARD1 [25;26]. It is a deubiquitinase that controls ubiquitination of Histone H2A, and is also a component of the Po.
