Blog @ Illumina
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The Real Buzz

Gustav Karlberg, Luc Smink
| Jun 24, 2012

ILMN workshopThat cancer research and genetics is a hot topic does not come as a surprise to most. ESHG is no exception and several sessions today focused on cancer and cancer genetics. In the session around Basic Research in Cancer Genetics, several talks focused on the use of Next Generation Sequencing (NGS) to unravel the genetics of cancer.

Dr. Kuiper (Radboud University, Nijmegen) focused on exome sequencing of leukemia patients to show how recurring leukemias can be completely unrelated, and is most likely due to germline predisposition. Dr. Sascha Dierks (Department of Human Genetics, Gotttingen) presented on prostate cancer, showing how leupaxin is a mediator in cancer progression, which is over expressed in roughly 20% of prostate carcinomas. In mouse models, a leupaxin knockdown leads to reduced invasion of prostate cancer cells. As part of this focus on cancer, more and more vendors are developing cancer panels for clinical testing. However, it is clear from data presented that not all cancer panels are the same. The Illumina workshop included a presentation from Dr. Andrew Fellowes from Peter Macallum in Melbourne. Dr. Fellowes highlighted their results from beta testing the Illumina TruSeq Amplicon Cancer panel on the MiSeq system. Not only did the speed and ease of use impress these researchers, but the level of sensitivity is what really stood out. Dr Fellowes showed that they were able to call variants down to 1%, allele frequency, far better than any other data presented.

All the talks weren’t just on panels though. Tumour heterogeneity confounds research and clinical diagnosis. Nicholas Navin from MD Anderson Cancer Center talked about the use of single cell sequencing to understand the extent of clonal diversity and how to reconstruct the cell lineages. In a published study, they sequenced hundreds of single cells from triple negative breast cancer to assess genomic copy number. To validate the technique, single cells were compared to millions of cells, and the profiles look extremely similar. They have now developed a technique to use Whole Genome Sequencing (WGS) on single cells to detect point mutations and indels. Dr. Navin showed data from ductal carcinoma at 40-50x coverage. He highlighted that approximately 20% of de novo mutation events occurred in single cells. This technique is now being used to investigate several areas of cancer biology, such as metastasis and response to therapy.