As usual, the meeting had a really busy schedule with several parallel sessions, so my report is not a complete survey but it's based only on talks I've attended.
In this area the two sponsored sections of both Life Tech and Illumina had interesting data to show. Indeed, under the pressure of the producers, the speakers also reported technical details on the protocols and performance, aspects that usually not receive a lot of attention. Benchtop sequenchers from both sides (essentially Life's Ion PGM and Illumina's MiSeq) have demonstrated that they are almost ready for a diagnostic and clinical debut, both with its own fallbacks that have been deeply discussed in the last months (see for example 1, 2, 3). Speaking for myself, I see a ready-to-go future for both platforms in the field of target re-sequencing of already known mutations or disease genes, with disease-targeted validated panels as the best option. This is in agreement to the trends emerged from Q&A sessions: small gene panels can guarantee higher coverage and so higher confidence in variant calling and moreover you get information only on the specific disease gene(s), avoiding more complex counseling and ethical issues. Even if exome sequencing proved to be an effective approach for syndromes showing extreme genetic heterogeneity or even better for rare conditions caused by private mutations, this approach still remain on the research side of the line. Technical difficulties related to data interpretation and accuracy, cost-benefit considerations and ethical issues raised by the genetic data not strictly related to the pathology have to be resolved before this approach could develop in a "routine" genetic test (however initiatives in this direction are already in testing, such as the Baylor College's Exome diagnostic service which has been running for a about one year and have already receive more than a hundred request for exome test from clinicians. See this interview on GenomeWeb).
Going back to presentations, it worth mentioning that Illumina made the move in clinical market, announcing that its MiSeq have received CLIA certification and so they are ready to sell a certified version of the machine (and the sequencing kits) from the second half of 2013. We'll see how Life Technologies will respond on its PGM to avoid the risk of being cut out of the market...I think that IonTorrent's community based panels (target amplicon resequencing kits tailored on a specific pathology or cancer type and developed with the support and collaboration of research community) should allow them to rapidly develop robust disease oriented panels, but an official certification is still an essential requisite to compete in the clinical market.
In another talk Gustincich from Trieste showed how lncRNA could also act in stimulating translation. The fact itself confirm new possibilities for the regulatory role of non-coding RNA, since until now they have been mostly implicated in repression of transcription. This enrich the picture of protein level regulation that appear to occur at three distinct levels (plus post-traductional mechanisms of course): mRNA transcription, regulated by historically studied mechanisms such as TF binding and chromatin remodeling which made the transcript available; RNA stability and traduction, regulated by availability of specific RNA-binding factors; and a fine regulation of mRNA levels and mRNA traduction based on ncRNA or more complex mechanism such as RNA editing. Things are made even more complicated by the fact that often a single ncRNA could target multiple mRNAs with different affinity and so its effect on protein level depends on the final equilibrium of all the possible interactions, as illustrated by the theory of competing endogenous RNA (ceRNA) appeared on Cell.
Keep your genetic enthusiasm alive!