CRONACA

Il genoma personale, ovvero quando Twitter e la scienza si incontrano

CRONACA – Twitter e gli altri social network hanno senz’altro un forte impatto sul nostro modo di fruire le informazioni che ogni giorno circolano sul web. Selezionare un argomento di nostro interesse e raccontare in diretta un evento sono azioni a cui gli utenti di Twitter sono ormai abituati. E la scienza non sta certo a guardare. Sempre più spesso ai grandi convegni sono proprio i ricercatori a twittare o postare sui blog i commenti alle presentazioni dei colleghi. E anche i premi Nobel non si sottraggono alle regolo del web, come Dan Shechtman che ha ringraziato da Twitter i membri della Fondazione Nobel per avergli assegnato il premio.

Pochi giorni fa si è svolto a Cold Spring Harbour il quarto meeting Personal Genomes in cui si sono discussi i recenti progressi della genomica e le implicazioni, etiche ed economiche che le nuove tecnologie hanno sulla salute. E oggi grazie a Twitter possiamo tracciare la sequenza degli interventi di maggior rilievo e che hanno destato l’interesse dei partecipanti “più tecnologici”, che in diretta hanno condiviso in rete critiche e impressioni. Un vero e proprio riassunto dell’evento, che potete seguire nella twitter-cronaca in fondo a questo articolo.

Ma veniamo agli aspetti più significativi emersi dai tre giorni di conferenze.

Genetic info isn’t really that much different from other clinical data

La necessità di considerare i dati genetici allo stesso livello degli altri dati clinici è emerso da diversi interventi. Il prezzo del sequenziamento è in continua diminuzione, basta fare un salto sul sito dell’ormai nota 23&Me, dove per 999dollari viene offerto il servizio di sequenziamento dell’intero esoma (la parte di DNA che codifica per le proteine).

Richard Gibbs estimates around 4,000 whole human genomes now sequenced, expects 30K in 2012.

Mark Boguski: discussing the transition to routine clinical sequencing. Who will be interpreting clinical genomic data? Pathologists, primary care physicians, someone else?

Una mappa del DNA sempre più facile da ottenere, semplice quasi come farsi fare una radiografia? Nonostante un “accesso più democatico” ai dati del DNA, il problema centrale resta l’interpretazione dei dati e l’affidabilità del laboratorio che si occupa di effettuare l’analisi, come spiegato in un recente articolo pubblicato sul sito di Nature Avere la sequenza delle lettere che compongono il nostro genoma non equivale alla capacità di interpretare quello che c’è scritto e un problema cruciale riguarda chi debba occuparsi dell’interpretazione dell’enorme quantità di dati che derivano dal sequenziamento completo del genoma.

Un progetto di cui forse sentiremo parlare più avanti è quello del sequenziamento completo del genoma degli abitanti delle Isole Faroe, presentato proprio in occasione del meeting. Al momento è in corso il progetto pilota di sequenziamento dei primi 100 genomi, come spiegato sulla rivista Science e ai restanti 50mila abitanti sarà offerta la possibilità di sequenziare completamente il proprio genoma gratis nei prossimi 5 anni. I dati dell’analisi del DNA saranno collegati ai dati clinici contenuti nel database del sistema sanitario nazionale e saranno accessibili su richiesta dei medici, ma anche se il proprietario vorrà analizzare la propria sequenza del DNA.

Ed eccovi qui di seguito la cronaca minuto per minuto dei twit dei partecipanti alla conferenza.

2011 CSHL Meeting on Personal Genomes

Organizers:Paul Flicek, European Bioinformatics Institute, UKJim Lupski, Baylor College of Medicine Elaine Mardis, Washington University School of Medicine We are pleased to host the fourth annual meeting on Personal Genomes, which will begin in the morning (9am) on Friday, September 30, 2011 and conclude in the late afternoon of Sunday October 2.
Inizia il primo giorno della conferenza
Elaine Mardis is kicking off CSHL Personal Genomes (#cshlpg) with a keynote on whole genome sequencing for cancer diagnostics.
dgmacarthur
September 30, 2011
The plot thickens on @PathwayGenomics’ claims of FDA registration for its DNA collection kit: http://bit.ly/p1LiMv
dgmacarthur
September 30, 2011
OK, Atul Butte confirmed with me in person that his talk is tweetable except where otherwise specified. #cshlpg
dgmacarthur
September 30, 2011
Lots of fun tweets coming from the Cold Spring Harbor Personal Genome meeting look for #cshlpg
digitalbio
September 30, 2011
Atul Butte launches his talk with an extensive financial disclaimer slide – meaning “don’t believe a word I say”. #cshlpg
dgmacarthur
September 30, 2011
DD: clinical labs rely on the accuracy of research data. If you publish a false mutation it can affect patient care. #cshlpg
dgmacarthur
September 30, 2011
DD: less happy example: mutations in young girl indicated disease would not be cured by transplant; allowed her to die with dignity. #cshlpg
dgmacarthur
September 30, 2011
Want fantastic tweets from the #cshlpg? Follow @dgmacarthur, very insightful, wish I were there. If only to find Jim at the bar at night.
alalejandro
September 30, 2011
DM: Huge amount of complexity in genome interpretation, summarized in one slide: DNA -> Function #cshlpg
konrad_jk
September 30, 2011
Q&A after DD’s talk includes reality checks on bringing WGS to the clinic. CLIA, FDA, gene patents all obstacles. #cshlpg
dgmacarthur
September 30, 2011
@dgmacarthur: most of us are walking around with about 100 loss-of-function variants, but only about 20 are homozygous #cshlpg
Erika_Check
September 30, 2011
E si prosegue con il secondo giorno
Second day of personal genomes #cshlpg about to start. Keynote by David Valle, Johns Hopkins Med.
finchtalk
October 1, 2011
Valle: have opportunity to move from viewing the patient as a classic case and from avg medicine towards individualized med #cshlpg
genomeresearch
October 1, 2011
DV starting session on how to think differently about the individualization of medicine: enabled by HGP, WGS, & evolution in med #cshlpg
bffo
October 1, 2011
DV: each individual has their own disease #cshlpg
genomeresearch
October 1, 2011
@Erika_Check “sequence at birth? ‘why not?’ #cshlpg” Most seq info not clinically useful; may be used to profile/discriminate
KTKeith
October 1, 2011
That tweeting break was brought to you by laptop battery failure, and having to climb >200 steps to retrieve my power adaptor… #cshlpg
dgmacarthur
October 1, 2011
@joltdude I really don’t think it’s a gamble to bet on the value of genomic information increasing over time. #cshlpg
dgmacarthur
October 1, 2011
@joltdude Let’s not be alarmist. Genetic info isn’t really that much different from other clinical data. #cshlpg
dgmacarthur
October 1, 2011
Over-elaborate protection of genetic info will simply reinforce genetic exceptionalism. #cshlpg
dgmacarthur
October 1, 2011
Peer Bork now talking about microbiomes…has a new company that will sequence yours for $2100 http://t.co/qR4kbeIV #cshlpg
Erika_Check
October 1, 2011
Peer Bork is talking about analysing personal microbiomes. Very complex data, immature technology. #cshlpg
dgmacarthur
October 1, 2011
PB: how different are individual gut microbiomes? Analysis of 39 samples from France, Italy, Denmark, Spain, Japan, US. #cshlpg
dgmacarthur
October 1, 2011
PB discussing clustering of the gut microbiome into “enterotypes”, recent Nature paper (http://t.co/t3yjDObR). #cshlpg
dgmacarthur
October 1, 2011
Jim Watson’s in the House!! #cshlpg
kfakhro
October 1, 2011
Although Kayser’s talk is untweetable it sounds as though a lot of this is close to publication – so stay tuned. #cshlpg
dgmacarthur
October 1, 2011
Joris Veltman is up now, discussing the transition from disease gene identification to diagnostic testing. #cshlpg
dgmacarthur
October 1, 2011
JV starts with analogy between agriculture and Mendelian gene discovery – now all the fruit is hanging much lower. #cshlpg
dgmacarthur
October 1, 2011
JV: exome sequencing is most complicated for sporadic dominant diseases. Discussing this paper: http://t.co/vBG67sC2 #cshlpg
dgmacarthur
October 1, 2011
Manfred Kayser is talking about the genetics of human appearance, but his talk is untweetable. #cshlpg
dgmacarthur
October 1, 2011
(For those who missed it, these #cshlpg tweets are coming from the Cold Spring Harbor Personal Genomes meeting: http://t.co/LbNO4BEn)
dgmacarthur
October 1, 2011
Steven Brenner is discussing the CAGI project on predicting phenotype from genetic data: http://t.co/lRtB0iFD #cshlpg
dgmacarthur
October 1, 2011
James Watson is asking a question. At least I think it’s a question. #cshlpg
dgmacarthur
October 1, 2011
Terzo e ultimo giorno
First up this morning at #cshlpg is Richard Gibbs with a keynote on “Personal genomes as a commodity”
dgmacarthur
October 2, 2011
RG estimates around 4,000 whole human genomes now sequenced, expects 30K in 2012. #cshlpg
dgmacarthur
October 2, 2011
RG: demographic expansion in humans has resulted in far more rare variants than expected. #cshlpg
dgmacarthur
October 2, 2011
RG: every genome contains 100-300 potentially functional variants never seen in any other sequenced genome. #cshlpg
dgmacarthur
October 2, 2011
RG emphasising genetic complexity: genes involved in both Mendelian and complex diseases, diff. modes of inheritance. #cshlpg
dgmacarthur
October 2, 2011
R Gibbs talking about “clan genomics”: the idea that more recent variants have greater effect on one’s health http://t.co/CZQ0nfT5 #cshlpg
Erika_Check
October 2, 2011
@dgmacarthur #GWAS completely ignored complexity and failed to deliver on tranforming medicine. Will #NGS take the same path? #cshlpg
moorejh
October 2, 2011
Follow the #cshlpg hashtag for cold spring harbor lab personal genomes conference tweets
Symbiologica
October 2, 2011
#cshlpg We have oversold genetics to the public since the HGP. Once patient advocacy groups sour on genetics it is all over.
moorejh
October 2, 2011
#NGS data are great. Let’s be careful not to promise patients too much. Human health IS a complex system. The public knows this. #cshlpg
moorejh
October 2, 2011
@moorejh Happy to engage in scientific debate. But please, fewer slurs on the motives of genomics researchers – it’s not useful. #cshlpg
dgmacarthur
October 2, 2011
First up in the clinical implementation session is Mark Boguski, discussing the transition to routine clinical sequencing. #cshlpg
dgmacarthur
October 2, 2011
MB starts with a (deliberately) dense wall of text on lab test regulation. Notes CLIA was last amended in 1988… #cshlpg
dgmacarthur
October 2, 2011
Acronyms that clinical genomicists need to know and understand: CLIA, LDT, FDA, CPT. #cshlpg
dgmacarthur
October 2, 2011
This meeting has been very US-health policy centric. #cshlpg
sbmontgom
October 2, 2011
Attitudes towards genetic testing are changing – a recap of #cshlpg tweets by @digitalbio: http://bit.ly/qXOcyc
dgmacarthur
October 4, 2011
MB: who will be interpreting clinical genomic data? Pathologists, primary care physicians, someone else? #cshlpg
dgmacarthur
October 2, 2011
MB: there are 1,000 medical geneticists, 3,000 genetic counsellors and 17,000 pathologists in the US. #cshlpg
dgmacarthur
October 2, 2011
MB: currently unclear whether gene patent problem will be resolved by licensing, legislation or litigation. #cshlpg
dgmacarthur
October 2, 2011
Next up is Gholson Lyon on the return of incidental findings to next-gen sequenced patients. #cshlpg
dgmacarthur
October 2, 2011
GL: woman in disease family arrives 4 months pregnant. GL knew she was carrier but couldn’t return results. Baby affected, died. #cshlpg
dgmacarthur
October 2, 2011
Incredibly understated story – but emphasises the moral horror of blocking return of research findings. #cshlpg
dgmacarthur
October 2, 2011
Worth coming to #cshlpg for the last two talks alone. Great illustrations of the subtle complexities of clinical seq.
dgmacarthur
October 2, 2011
G Lyon: researchers should sequence in clinically certified labs so that they can return “incidental” findings to study subjects #cshlpg
Erika_Check
October 2, 2011
Final talk of #cshlpg is Dennis Lo, on prenatal diagnosis through sequencing of fetal DNA in maternal blood. #cshlpg
dgmacarthur
October 2, 2011
DL: fetuses leak DNA into maternal blood – about 5% of DNA in maternal blood comes from the fetus. #cshlpg
dgmacarthur
October 2, 2011
DL: diagnosing trisomy 21 using this fetal DNA is very challenging – requires incredibly accurate quantitation. #cshlpg
dgmacarthur
October 2, 2011
That was another incredible talk. Early leavers just missed the three best presentations of #cshlpg, IMO.
dgmacarthur
October 2, 2011
DL: using sequencing approach can use dosage of chrX to determine fetal sex. Proof of principle for trisomy 21 diagnosis. #cshlpg
dgmacarthur
October 2, 2011
DL: half-life of fetal DNA in maternal blood is 15 minutes. Two hours after birth, no detectable fetal DNA left. #cshlpg
dgmacarthur
October 2, 2011
That’s it from #cshlpg. Great meeting – thanks to the conference organisers and my fellow tweeters.
dgmacarthur
October 2, 2011
Fantastic collection of talks #cshlpg – enjoyed every minute.
Para_Dhillon
October 4, 2011
Meetings & Courses Home

Cold Spring Harbor Asia Conferences represent the Laboratory’s new venture to develop a hub for the life sciences in Asia. Programs will be held at Suzhou Dushu Lake Conference Center in Suzhou, China, sixty miles west of Shanghai and in easy reach of international and domestic airports.

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