By Monica Heger
Washington University scientists have made progress on a number of cancer sequencing projects, including the sequencing of 50 acute myeloid leukemia tumors and the sequencing of breast cancer metastatic tumors, one of the scientists said at the Biology of Genomes meeting at Cold Spring Harbor last week.
Li Ding, a research instructor at the Genome Sequencing Center at Washington University, said at the conference that 26 of the sequenced AML tumors are part of the National Institutes of Health-funded Cancer Genome Atlas.
Ding also said the researchers have sequenced metastatic tumors from the lung and liver of a breast cancer patient, adding to a previously reported metastatic tumor from the brain of a different breast cancer patient (IS 4/20/2010). In addition, Elaine Mardis, co-director of Wash U's Genome Center, reported at the meeting on initial results of the sequencing of an AML relapse tumor (IS same issue).
To sequence the 50 AML tumors, the researchers used paired-end sequencing on the Illumina Genome Analyzer and achieved around 30-fold coverage of the genomes with 100 base pair reads.
The researchers are currently in the process of analyzing the AML sequencing data using an algorithm called PathScan, developed by statistical geneticist Michael Wendl at Wash U, which seeks to find significant mutational pathways. They have not yet published the results of the analysis.
The Wash U researchers are also sequencing 100 matched tumor/normal pairs from breast, lung, glioblastoma, and ovarian cancers. All of these recent sequencing efforts have allowed them to characterize mutational rate and spectrum, and profile different tumor types, said Ding.
For instance, she said, pediatric cancers seem to have the lowest mutational rate and, while AML has the second lowest mutational rate, secondary AML has an 8- to 10-fold higher mutational rate, she said.
Being able to characterize cancer tumors will "help us understand the etiology of cancer," she said. "Different mutational spectrums may reflect different pathogenic mechanisms." For example, a smoker who develops lung cancer has up to a 100-fold higher mutational rate and also a very different mutational spectrum than a non-smoker who develops lung cancer. However, AML and glioblastoma have a similar mutational spectrum, sharing several highly mutated genes.
Going forward, Ding said that sequencing tumors at different stages of disease progression, such as metastasis and relapse, and also combining whole-genome sequencing with methylome and transcriptome sequencing will be important for gaining a comprehensive view of cancer.
"Whole-genome sequencing provided a lot of clues in terms of understanding cancer," Ding said. "That's a big first step… Now, we can analyze a population of cancer cases from multiple individuals and cancer types, and we can look at the genetic changes across all levels."