Beyond the Genome conference

Genome Biology, in conjunction with Genome Medicine, is pleased to host the second annual Beyond the Genome conference in Washington DC from 19 - 22 September 2011. This year’s conference will focus on cancer genomics, the human microbiome and exome and genomic sequencing and how these approaches are being used to identify common and rare disease-causing mutations. Technological as well as medical or biological perspectives will be discussed.

DNAvision offers Human WGS for 7,500 euros

I had imagined exome sequencing would still have a good run for the next 2-3 years but seeing how commercial service providers are throwing caution to the wind and offering Whole genome sequencing at ever decreasing costs, I think many will soon revert to WGS instead. Exome sequencing kits will have a lot to catch up in terms of price and useful data if they are to match up with quickly plummeting WGS prices.
DNAVision to Offer $10K Human Genome Sequencing Services; Purchases Four SOLiDs
Landed: First Illumina HiSeq Machines Advertised (By Nick Loman on February 10, 2010)

The $1,000 Genome Debate is 'Already ... Irrelevant'

excerpted from GenomeWeb
Matthew Herper and Daniel MacArthur are at odds over the $1,000 genome. Forbes' Herper argues that even though sequencing is becoming cheaper, analyzing a genome still costs much more than $1,000. Over at Genetic Future, MacArthur responds that as sequencing costs continue to fall, "a substantial niche will develop for innovators providing affordable, intuitive, accurate interpretation tools." 

My thoughts on this later.. 

Bioinformatics. 2011 Jan 7. [Epub ahead of print]

A fast, lock-free approach for efficient parallel counting ofoccurrences of k-mers.

Marçais G, Kingsford C.

Program in Applied Mathematics & Statistics, and Scientific Computation, University of Maryland, College Park, MD, USA.

Abstract

MOTIVATION: Counting the number of occurrences of every k-mer (substring of length k) in a long string is a central subproblem in many applications, including genome assembly, error correction of sequencing reads, fast multiple sequence alignment, and repeat detection. Recently, the deep sequence coverage generated by next-generation sequencing technologies has caused the amount of sequence to be processed during a genome project to grow rapidly, and has rendered current k-mer counting tools too slow and memory intensive. At the same time, large multi-core computers have become commonplace in research facilities allowing for a new parallel computational paradigm.

RESULTS: We propose a new k-mer counting algorithm and associated implementation, called Jellyfish, which is fast and memory efficient. It is based on a multi-threaded, lock-free hash table optimized for counting k-mers up to 31 bases in length. Due to their flexibility, suffix arrays have been the data structure of choice for solving many string problems. For the task of k-mer counting, important in many biological applications, Jellyfish offers a much faster and more memory efficient solution.

AVAILABILITY: The Jellyfish software is written in C++ and is GPL licensed. It is available for download at http://www.cbcb.umd.edu/software/jellyfish.

CONTACT: gmarcais@umd.edu.

PMID: 21217122 [PubMed - as supplied by publisher]

Cell. 2011 Jan 7;144(1):27-40.

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development.

Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, McLaren S, Lin ML, McBride DJ, Varela I, Nik-Zainal S, Leroy C, Jia M, Menzies A, Butler AP,Teague JW, Quail MA, Burton J, Swerdlow H, Carter NP, Morsberger LA, Iacobuzio-Donahue C, Follows GA, Green AR, Flanagan AM, Stratton MR, Futreal PA, Campbell PJ.

Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.

Abstract

Cancer is driven by somatically acquired point mutations and chromosomal rearrangements, conventionally thought to accumulate gradually over time. Using next-generation sequencing, we characterize a phenomenon, which we term chromothripsis, whereby tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. Rearrangements involving one or a few chromosomes crisscross back and forth across involved regions, generating frequent oscillations between two copy number states. These genomic hallmarks are highly improbable if rearrangements accumulate over time and instead imply that nearly all occur during a single cellular catastrophe. The stamp of chromothripsis can be seen in at least 2%-3% of all cancers, across many subtypes, and is present in ∼25% of bone cancers. We find that one, or indeed more than one, cancer-causing lesion can emerge out of the genomic crisis. This phenomenon has important implications for the origins of genomic remodeling and temporal emergence of cancer. PAPERCLIP:

Copyright © 2011 Elsevier Inc. All rights reserved.

PMID: 21215367 [PubMed - in process]

AGBT Meeting is Sold out!!

Not attending the 2011 AGBT but am curious about the speakers. Was surprised to find that the meeting is sold out!
http://agbt.org/

I guess Sequencing and Genomics is all the prime focus now in Biology and everyone is interested to find new applications or produce reagents for high throughput sequencing.

Search and clustering orders of magnitude faster than BLAST, Bioinformatics.

Hmmm must check out this... Edgar, R.C. (2010), Search and clustering orders of magnitude faster than BLAST, Bioinformatics.
doi: 10.1093/bioinformatics/btq461
http://www.drive5.com/usearch/usearch_docs.html