Cancer Genome Sequencing and Amazing Progress
May 23, 2012
The field of cancer genome sequencing has exploded due to amazing early progress in identifying new mutations in cancer, patterns of how tumours change over time and identification of new disease subtypes. The work my team and I have done has contributed to this progress due to innovations in computationally modeling these datasets to infer mutations responsible for disease.
Currently my work is focused on analysis of ovarian, breast and lymphoid cancers. There is so much we do not yet understand about the behaviour of these diseases in the context of chemotherapeutic response, progression and metastasis.
It is our mission to find answers buried in their genomes.
The amazing progress in sequencing technology and installed capacity at the Genome Sciences Centre allowed my colleagues and I to study, for the first time, the complete set of mutations in the most aggressive and hardest to treat type of breast cancer: triple negative breast cancer.
This is a disease with no targeted therapies and where the long-term survival rate for afflicted women is very poor. When we started this project we knew very little about what gene mutations contributed to triple negative breast cancer and mutations are often the key to unlocking the secrets of tumour biology.
Together with Dr. Sam Aparicio, we set out to understand the genomic underpinnings of this disease and generated DNA sequences for 65 samples – effectively ‘decoding’ the most important parts of their genomes with literally millions of datapoints per sample. This was both exhilarating and incredibly challenging since it was new technology producing new types of data for which there was no instruction manual for analysis.
My research team at the BC Cancer Agency set to work and developed new ways to detect mutations in this enormous dataset. What we found was quite amazing: triple negative breast cancers varied widely in the number and content of their mutations. This at first seemed quite daunting, but we noticed that approximately 20% of the samples had mutations in genes that we know a lot about, with targeted therapies indicated for other types of cancer, or with targeted therapies in development.
This means that, for at least some women with triple negative breast cancer, there is hope that tailored therapies existing today, may be effective in the future – but this will take a lot more work to determine if that is the case.
In addition, we were able to determine that these cancers at presentation are already at widely different stages of their genomic evolution. This is important because these cancers are currently considered the same in clinical practice. Our results suggest that more individualized cancer care will be needed for triple negative breast cancer. You can read more about the results here.