PolITiGenomics » Search Results » AML

What the Crisis Nursery does

dd — Thu, 11 Mar 2010 21:09:59 +0000

Below is a nice interview with DiAnne Mueller, CEO of the St. Louis Crisis Nursery, talking about what the Crisis Nursery does and how you can help.

State of cancer genome sequencing

dd — Wed, 28 Oct 2009 17:38:42 +0000

The Genome Center’s Elaine Mardis and Rick Wilson have just published a review article on cancer genome sequencing. The article focuses on the application of next-generation sequencing technologies to the study of cancer, covering structural variation studies using low coverage paired-end sequence data, targeted gene sequencing studies using PCR and Sanger sequencing, transcriptome sequencing using RNA-seq, and whole-genome sequencing, e.g., our AML publications. The article concludes with a brief discussion of the future of cancer sequencing and the functional genomics required to determine the role identified mutations play in cancer progression.

AML in the news

dd — Wed, 12 Aug 2009 13:48:25 +0000

For those interested, here is a collection of stories in the press about the recent article in the New England Journal of Medicine on the sequencing of the second whole cancer genome discussed previously in this post: Washington University Medical News (the source, not always referenced, for many other stories), BBC, Cancer Research UK, NCI Cancer Research Highlights, and Bio-IT World.

Second whole cancer genome published

dd — Thu, 06 Aug 2009 15:26:33 +0000

Today in the New England Journal of Medicine the second paper detailing the whole genome sequencing of a tumor and its matched normal was published: Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome. Accompanying the article is an editorial well worth reading by Jim Downing from St. Jude Children’s Research Hospital discussing the significance of these whole genome sequence efforts from the medical researcher and practitioner’s perspective. Dan Koboldt has posted a nice summary of the journal article.

The most interesting finding from this research was the recurring mutation in a gene called IDH1. The likelihood of the same mutation randomly occurring in 16% of similar AML patients in vanishingly small. In other words, it is quite likely that this mutation plays a role in AML biology. Mutations in this gene have been previously described in glioblastomas (brain cancer) where they were associated with improved outcome for patients. In contrast, correcting for other mutations which are associated with better outcomes in AML, the IDH1 mutation is associated with poorer outcomes in AML. Thus, while IDH1 seems to play a role in glioblastomas and AML, its role in each may be quite different.

Yesterday’s news

dd — Wed, 03 Jun 2009 05:24:36 +0000

Well, I took a bit of a jab at St. Louis Magazine for being late to the party on reporting about the first cancer genome sequence, so it is only fair that I also poke a little fun at Outlook, a quarterly publication of Washington University in St. Louis School of Medicine, for waiting until their Spring 2009 issue to report on the AML genome: Dangerous Transformations. I guess they are a quarterly and deserve a little more slack, but surely it could have been in the winter issue. With the recent completion of the second AML tumor and normal genomes, perhaps it is true what they say, “everything old is new again”.

It is worth noting that the picture in the article (linked below) of Rick Wilson, Elaine Mardis, and Tim Ley was taken in our data center. Or as Tim calls it, the holodeck.

The local press

dd — Mon, 01 Jun 2009 03:06:28 +0000

Some media outlets take a little longer to recognize a story, even one in their own back yard. St. Louis Magazine, a local culture and dining monthly, has an article in the June 2009 issue about our whole-genome sequencing approach to studying AML entitled The Code Breakers. You can tell from the tenor of the interview, they’re not exactly targeting a scientific audience (given their target audience this is neither surprising nor a bad thing).

Sequencing AML with paired-end reads

dd — Wed, 29 Apr 2009 14:20:25 +0000

When The Genome Center performed the sequencing of the first whole cancer genome, the state of the art for next-generation sequencing was single-end, or fragment, reads. While these data allowed the discovery of single nucleotide variants and small indels, they do not allow discovery of structural variation, e.g., indels larger than a few bases, inversions, and translocations. With the advent of pair-end sequencing on the next-generation sequencing platforms, i.e., two reads sequenced from each end of a DNA fragment of known size, you are now able to detect these more complicated types of variation. When you align the two end reads back to the reference human genome, if they map the expected distance apart with the appropriate orientation, then all is as expected. If, however, they map at a greater distance, then there is possibly a deletion in the genome with respect to the reference. If the two end reads map at a distance closer than expected, there is possibly an insertion in the genome with respect to the reference. If their orientation is not as expected, there could have been an inversion. If one end maps to one chromosome and the other maps to another chromosome, it indicates a possible translocation. Using paired-end sequencing, this is exactly the sort of analysis we have done when sequencing the second AML genome. The ability to detect these types of variations opens the door to whole new sets of analysis and genomic comparisons, allowing us to more deeply probe the mutations that convert a healthy genome into a cancerous genome.

AML at ASH

dd — Wed, 10 Dec 2008 16:03:17 +0000

It seems the publication of the first whole cancer genome sequence is getting a good reception in hematology circles. This past Saturday at the 50^th Annual Meeting of the American Society of Hematology, Dr. Tim Ley presented our AML sequencing work to a packed room of over 2000 people. In fact, there was such demand to see the talk that they scheduled a second time for Dr. Ley to give the talk so that all those that were turned away the first time could get a chance to see it. There is a lot of excitement in these oncology circles because the initiating events for many of these tumors are not known and an unbiased, whole-genome sequencing approach is currently the best chance to discover them.

Junk DNA no more

dd — Thu, 13 Nov 2008 16:32:03 +0000

The New York Times has a good article, Now – The Rest of the Genome, on the latest research on genes and the non-protein-encoding parts of the genome. As reported in our recent AML paper, while we found many somatic variants (i.e., variants specific to the cancer genome) throughout the genome, at present we are really only able to interpret those variants that fall in genes. Research such as that described in the New York Times article, e.g., ENCODE, will help us to be able to interpret all the other variations that may play a role in cancer and other diseases.

AML on NPR

dd — Fri, 07 Nov 2008 16:22:01 +0000

Dr. Tim Ley of The Genome Center is going to be a guest on NPR’s Talks of the Nation Science Friday today. He will be talking about the AML paper published in Nature yesterday. The show starts at 2 p.m. EST but will be interrupted on our local NPR station, KWMU 90.7 FM, for President-elect Obama’s press conference at 2:20 p.m. EST. So if you want to listen, it might be better to listen on-line (although other stations may be interrupted as well) or get the podcast.