The Relative Timing of Mutations in a Breast Cancer Genome

Abstract

Many tumors have highly rearranged genomes, but a major unknown is the relative importance and timing of genome rearrangements compared to sequence-level mutation. Chromosome instability might arise early, be a late event contributing little to cancer development, or happen as a single catastrophic event. Another unknown is which of the point mutations and rearrangements are selected. To address these questions we show, using the breast cancer cell line HCC1187 as a model, that we can reconstruct the likely history of a breast cancer genome. We assembled probably the most complete map to date of a cancer genome, by combining molecular cytogenetic analysis with sequence data. In particular, we assigned most sequence-level mutations to individual chromosomes by sequencing of flow sorted chromosomes. The parent of origin of each chromosome was assigned from SNP arrays. We were then able to classify most of the mutations as earlier or later according to whether they occurred before or after a landmark event in the evolution of the genome, endoreduplication (duplication of its entire genome). Genome rearrangements and sequence-level mutations were fairly evenly divided earlier and later, suggesting that genetic instability was relatively constant throughout the life of this tumor, and chromosome instability was not a late event. Mutations that caused chromosome instability would be in the earlier set. Strikingly, the great majority of inactivating mutations and in-frame gene fusions happened earlier. The non-random timing of some of the mutations may be evidence that they were selected.

CAMTA1 is a useful immunohistochemical marker for diagnosing epithelioid haemangioendothelioma

“…The mutations or rearrangements of CAMTA1 have been reported in breast cancers. 22 Such genetic alterations may contribute to the aberrant expression of CAMTA1 in breast cancer, although our case was negative for CAMTA1 rearrangement by FISH.…”

Resolving sub-clonal heterogeneity within cell-line growths by single cell sequencing genomic DNA

“…Both the karyotype and single cell sequencing suggest that the cell line duplicated its entire karyotype after most of the rearrangements seen. The translocations-the 1;3, 1;10;18 and 7;15 translocations-fit the Dutrillaux monosomic pattern of karyotype evolution, in which two normal chromosomes are replaced by one unbalanced translocation, resulting in copy number loss and (if before genome duplication) LOH 6,11 .…”

tHapMix: simulating tumour samples through haplotype mixtures

“…Truth sets representing genomes of different ploidy levels were created by comparison with karyotype data (where available, i.e. Newman et al, 2013) and by manual inspection of coverage, allele ratios and read mappings. The simulation strategy controlled for (1) number of clones, (2) percentage of polyclonal non-root variants, (3) preponderance of the major clone and (4) sample purity (Supplementary Material, Table 1 and 2).…”