Johns Hopkins approach to diagnosing breast/colon cancer

Roy Winslow writes in the WSJ of work by the group of Victor Velculescu of Johns Hopkins that appeared in Science Translational Medicine on 18 Feb 2010 on a new approach in screening for cancer:

Much research involving whole-genome sequencing is aimed at finding differences in the individual letters that make up the genetic code. The belief is that those small alterations will point to molecular pathways that regulate disease, which would be potential targets for drug therapies.

The Hopkins researchers, writing in the journal Science Translational Medicine, took a different approach. They scanned the DNA of tumors taken from six patients with breast or colon cancer, looking not for tiny DNA changes, but what they call rearrangements in large sections of the genome of tumor cells. The DNA of tumors varies genetically from that of normal tissue, and the rearrangements are essentially a fingerprint of the cancer.

While this work will (deservedly) get a big splash now, one notes that the relevant information was already available in published patent application 20090123928 which became publicly available on May 14, 2009 and which includes the abstract:

Human cancer is caused by the accumulation of mutations in oncogenes and tumor suppressor genes. To catalogue the genetic changes that occur during tumorigenesis, we isolated DNA from 11 breast and 11 colorectal tumors and determined the sequences of the genes in the Reference Sequence database in these samples. Based on analysis of exons representing 20,857 transcripts from 18,191 genes, we conclude that the genomic landscapes of breast and colorectal cancers are composed of a handful of commonly mutated gene "mountains" and a much larger number of gene "hills" that are mutated at low frequency. We describe statistical and bioinformatic tools that may help identify mutations with a role in tumorigenesis. These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy.

The first claim states: A method of diagnosing breast cancer in a human, comprising the steps of:
determining in a test sample relative to a normal sample of the human, a somatic mutation in a gene or its encoded cDNA or protein, said gene selected from the group consisting of those listed in FIG. 10 (Table S4B) [and]
identifying the sample as breast cancer when the somatic mutation is determined.

Note that federal funding supported the work described in the patent application:
This invention was made using grant funds from the U.S. government. Under the term of the grants, the U.S. government retains certain rights in the invention. Grants used include NIH grants CA 43460, CA 57345, CA 12113, and CA 62924.

Winslow did mention patents in his WSJ article:

Hopkins has filed patents for the technology. Dr. Velculescu and two other co-authors of the paper are entitled to a share of royalties on sales of any products related to the research if it is commercialized. Further research is necessary to validate the approach with more patients and more cancer types, but researchers said such a test could be ready to use within two years and widely available "within several years."

Another patent application from the Hopkins group is 20090208505.

In passing, IPBiz notes that this is another example wherein publishing and filing patent applications co-existed [refer also to LBE's story of the transistor in 8 JMRIPL 80]. Of course, the point is to file the patent application first.