Posts tagged cancer

The Microbiome of Esophageal Cancer

In anticipation of the International Human Microbiome Congress, our group has diligently worked to generate data to present for our HMP demo project studying the microbiome of patients who have developed esophageal cancer, gastrointestinal reflux disease, and barrett’s esophagus.  We received a large number of samples in December of 2010 which surveyed four body sites (esophagus, fecal, oral and stomach) of twelve patients.  Upon isolation of DNA, we amplified a variable region of the 16S gene for each sample using barcoded PCR primers.  Incorporation of the 454 A and B adaptors to our primers also provided minimal loss of sequence data when compared to previous methods that would ligate the adaptors to amplicons after PCR.  This method also allowed us to generate sequence reads which are all in the same 5’-3’ orientation.  A large dataset with high quality sequence reads was generated and is currently going thru phylogenetic analysis.  Metagenomic data is also currently being generated from DNA extracted from esophageal brushings taken from a healthy individual as well as a patient who has developed esophageal cancer.  This comparative analysis will be scientifically beneficial in identifying key structural and functional elements that are known to increase pathogenesis of a complex disease such as cancer.  We are anxiously awaiting results from the analysis of these sequences and expect to present a thorough investigation on the esophagus microbiome.

HMP Consortium – St. Louis Missouri

Human Microbiome Project Consortium – September 2010 – St Louis, Missouri

We received warm welcome messages from Dr George Weinstock and Dr Jane Petersen as well as a humorous welcome from Dr Larry Shapiro, Dean of Washington University Medical School. 

It was wonderful to see so many scientists come together to share the progress on their individual HMP related demonstration projects.  Our own demonstration project with Dr Zhiheng Pei, involving the esophagus microbiome and how that relates to esophageal adenocarcinoma (EA), was quite unique compared to the other projects as we were the only group to focus on the correlation between bacterial population and a form of cancer. 

With over 400 participants and 59 speakers, the conference was quite successful and very interesting.  JCVI Director Dr Karen Nelson did a wonderful job moderating one of the segments.  Dr Roger Lasken also gave a thorough presentation on his lab’s single cell approaches to genomic sequencing of uncultureable bacteria.  Johannes Goll gave a great presentation on his recent work with an open source tool called METAREP (recently published in Bioinformatics 8/26/2010), which is designed to help scientists with analyzing annotated metagenomic data.  And Dan Haft presented his interesting work with algorithmically tuning protein families from reference genomes for systems discovery. 

Overall the conference was quite interesting and informative.  I continue to wish all of the participating sequencing centers, PIs, and others involved with the HMP much success with their projects. 

Hope to see everyone in Vancouver!!!