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Sunday, 23 December 2012

Genome biology highlights for 2012


We are coming to the end of a big year in the field of genome science, one which was dominated by the swarm of papers from the ENCODE consortium. (The number of ENCODE articles, mostly in Nature, has reached 92! and has no sign of slowing down.) If you haven't had time an read them all, do so here.

Apart from ENCODE, there has been a quite astonishing pace in genomic studies. Here are just a few highlights from me:
  • The 1000 genomes project published it's main findings in Nature (link).
  • Non-invasive prenatal genome sequencing was described in PNAS (link), triggering a debate about the ethics of genomic studies of the unborn.
  • Single cell sequencing techniques improve with better methods of amplification, even allowing sequencing of 99 individual sperm (link) giving new insights into patterns of recombination, and opening new avenues for IVF testing.
  • Metagenomics analysis takes off. Whether it's environmental samples from the sea, hot springs or soil (JGI website) or even microbiomes of humans, insects, plants - there are new microbes being discovered by the day.
  • Big chunks of the wheat genome are finished thanks to advanced in chromosomal flow sorting sequencing techniques (link).
  • Barley genome sequence and comprehensive transcriptome analysis described in Nature (link)
  • Ribo-Seq goes mainstream with novel applications of ribosome profiling including identification of novel viral encoded proteins (link).
On the instrument side, the upgrade to Illumina HiSeq platforms allowing rapid run allowing 2 x 150 bp in 27 hrs is something that has gotten our lab fairly excited. Life Technologies started shipping the Proton sequencer, superseding the Ion Torrent. On the whole 3rd gen systems have failed to overtake the mature players while Helicos is more or less broke.

What have been your top 5 papers of the year?

Merry Christmas!