MassGenomics

It’s less than a week until the Advances in Genome Biology & Technology meeting (#AGBT2013) in Marco Island, Florida. Historically, this meeting has been like a debutante ball for the sequencing community — the place where new technologies are showcased, promised, and occasionally delivered upon.

The trends of past meetings often set the tone for the year that followed:

• AGBT 2010 highlighted new emerging sequencing technologies like Pacific Biosciences and IonTorrent.
• AGBT 2011 was all about smaller, more affortable benchtop sequencers like the MiSeq and PGRN, culminating with a huge guy literally carrying in a prototype IonTorrent PGM.
• AGBT 2012 focused on sequencing’s clinical applications and saw the stunning announcement of Oxford Nanopore’s jump drive sequencers.

AGBT 2013 Anticipation

This year, AGBT is a bit later in February than usual — good news for the 15 minutes of beach time managed by most attendees — and I won’t be attending myself. Looking at the meeting agenda confused me for a minute. It felt like déjà vu … PacBio talking about structural variation, Liz Worthey on clinical applications, my friend Aaron Quinlan presenting a cleverly-named informatics tool (this year it’s “LUMPY”). I read it and wondered, “Am I looking at an old agenda?”

If we take the agenda as a whole and do some basic text mining, the recurrent themes of most presentations are quick to emerge:

count    phrase
21    sequencing
18    genome
11    cancer
10    analysis
9    whole, human, genomic
8    clinical
7    single
6    gene, cell
5    rna, mutations, discovery
4    medicine, mechanisms, exome, complex
3    tumors, somatic, de novo, metagenomic
3    ngs, genetic, expression, applications

Sequencing, of personal genomes and cancer genomes, is the weather-tested mainstay of agenda topics from recent years. There’s a substantial interest in getting sequencing into the clinic, much like we saw last year. Popular applications of next-gen sequencing, like RNA-seq and cancer profiling, will have their say. Interestingly, exome sequencing seems under-represented… one gets the feeling that this community, at least, is beginning to consider it routine (ho hum). I’m pleased to see the term “metagenomic” a few times, which suggests a growing appreciation of the importance of the human microbiome and similar topics.

Following AGBT Live

Thanks to Twitter and some dedicated “tweeps” (people who tweet things live), this meeting is easy to follow. I’ll have a steady feed of the #AGBT13 hashtag, which isn’t nearly as good as being there, but the best I can manage. There are some good talks to look forward to:

• Eric Boerwinkle (Univ. of Texas) is giving a talk on ““Whole Genome and Exome Sequencing and Analysis of Large Numbers of Deeply-phenotyped Individuals Reveal the Genetic Architecture of Complex Traits: the CHARGE Consortium”.
• Matthew Wiggin of Boreal Genomics will present “Multiplexed Detection of Low Abundance, Tumor Related Nucleic Acids in the Plasma of Cancer Patients”.
• Malachi Griffith, of the Genome Institute at Washington University, has a talk on “Clinical Cancer Sequencing and Integrated Analysis of Whole Genomes, Exomes and Transcriptomes”.
• Mark DePristo of the Broad Institute (a lead contributor to GATK) will discuss “Overcoming Today’s Limitations in Sequencing Technology for Human Medical Genetics” and hopefully commercial attendees won’t have to pay $300K to listen.

The Twitter hashtag is usually cluttered with commercial stuff, so you might want to pick some prolific Twitter-aholics like Nick Loman and Aaron Quinlan.

Update: AGBT 2013 Wordle Tag Cloud

My friends at @nextgenseq made a Wordle tag cloud that nicely illustrates the theme of this year’s AGBT meeting.

This entry was posted on Friday, February 15th, 2013 at 11:17 am by Dan Koboldt + and is filed under Sequencing Technology. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.