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Researchers Finding Mutations in Second AML Genome

DENVER (GenomeWeb News) – Researchers are wrapping up their analysis of the second acute myeloid leukemia genome, Elaine Mardis, co-director of Washington University's Genome Sequencing Center, told attendees at the American Association for Cancer Research meeting in Denver yesterday.

Researchers started using targeted re-sequencing to assess the genetics of AML, a blood-forming cell cancer, in 2002. While that approach turned up a handful of genes frequently mutated in AML, it did not provide a complete picture of somatic mutations, structural changes, and other genetic alterations associated with the cancer, Mardis explained during her presentation.

In an effort to obtain a more complete view of AML genetics, she and her colleagues have been assessing entire AML genomes — an approach that provides an unbiased view of AML genetics. Last November, the team reported in Nature that they had sequenced the complete tumor and normal genome from the same AML patient, a woman with cytogenetically normal AML. The team identified eight somatic mutations and two indels in the AML1 genome.

Now, Mardis said the researchers have just finished analyzing the second AML genome. For that study, the researchers sequenced normal and tumor tissue from a Caucasian man with de novo M1 AML using the Illumina Genome Analyzer II platform.

Mardis touted the value of paired end reads for deciphering information on everything from single base mutations to structure variations and copy number changes, all using the same dataset.

Although she noted that the sequencing throughput was lower when the team sequenced the first AML genomes, Mardis said the current sequencing output is roughly 18 gigabases per instrument run. Read length has also improved and is currently about 75 base pairs, she added.

Their work uncovered dozens of somatic mutations as well as a couple of somatic indels in the AML2 genome. Mardis did not disclose details of the genes affected, noting the team plans to submit the work for publication.

Along with DNA sequencing, the team is working on RNA sequencing studies aimed at unraveling the AML2 transcriptome. In addition, Mardis said the researchers are currently sequencing a third AML genome and have selected several patients with AML M1 and M3 subtypes for additional genome studies.