Postcard From the AACR 2012 Annual Meeting - Part 3

AACR 2012 meeting summary - Part 3.
Personalized medicine, diagnosis, whole genome sequencing, NGS, TCGA project, etc




【#AACR 101】 What is next generation sequencing? Not well defined. Any non-Sanger method is technically next gen, it came out early 90s.
                                            —Naoto T. Ueno 上野直人 (@teamoncology) April 2, 2012


【#AACR 101】 The 1st sequencing of DNA came out in 1977 by Sanger. Sanger method is the traditional sequencing.
                                            —Naoto T. Ueno 上野直人 (@teamoncology) April 2, 2012


DIAGNOSTICS



L. Siu:"Histology-independent, aberration-specific. But beware of different degrees of functionality and sensitivity" So provocative! #AACR
                                            — Philippe Aftimos MD (@aftimosp) April 2, 2012


serum/plasma miRNA as biomarkers, important experimental design & data analysis at #AACR. Visit booth 4724 bit.ly/H7b1bq
                                            — SABiosciences (@GeneGlobe) April 2, 2012

WHOLE GENOME SEQUENCING AND BIOMARKERS





【#AACR 101】 Biomarkers have 3 types, predictive, prognostic, or both. Do you know which one you are dealing with? Biomarkers are not equal.
                                            —Naoto T. Ueno 上野直人 (@teamoncology) April 2, 2012


RT @EricTopol: DNA sequencing lays foundation for personalized cancer treatment zite.to/H7k4cP @GenomeInstitute #CDoM #AACR
                                            — Bryant Macy (@bkmacy) April 2, 2012


@wustlmedschool's Dr. Elaine Mardis discusses personalized #cancer treatments at the #AACR annual meeting in Chicago ow.ly/a0DSG
                                           — WUSTL Med St Louis (@WUSTLmedschool) April 1, 2012


Broad's firehouse found at gdac.broadinstitute.org; enterprise level pipeline of pipelines. #TCGA #AACR
                                           — Kenna Shaw (@wyattsgirl) April 1, 2012


Raju kucherlapati reviewing the power on integrated cancer genomics data sets #AACR #TCGA
                                            — Kenna Shaw (@wyattsgirl) April 1, 2012


How do u transform genomics 2 individualized therapies? -> Dev. treatments 4 specific cancer subgroups - Cancer Cell (2011) 20: 384-99 #AACR
                                            — Carole Tactacan (@carole12) April 2, 2012


Cancer GWAS studies no longer coolest kid on block after all the hype a decade ago. Even the GWAS posters look depressed. #AACR
                                            — Mickey Atwal (@MickeyAtwal) April 2, 2012



Bert Vogelstein to hold #aacr press conference at 11am on public health implications of whole genome sequencing - paper published today
                                            — Pieter Droppert (@3NT) April 2, 2012


Whole genome sequencing can be beneficial in identifying genetic basis of monogenic diseases & management of affected families. #AACR
                                            — J Nat'l Cancer Inst (@JNCI_Now) April 2, 2012



Exome sequencing identified prog mutations in 70% of cases.Seq in 385 genes id mutations in 20% of cases. Exome data is informative. #AACR
                                             — Jessica Kao (@SpunkyScientist) April 2, 2012


LESSONS



Horning @genentechnews- Vemurafenib & Vismodegib were successful becauseboth had companion diagnostic & understanding of tumor bio. #AACR
                                            — Iya Khalil (@IyaKhalil) April 2, 2012






CHALLENGES


Well said. RT @wyattsgirl Genomics- making a biology problem a computational problem #AACR
                                             —Naoto T. Ueno 上野直人 (@teamoncology) April 2, 2012



2 petabytes of sequencing data from#TCGA has been uploaded.#AACR
— dominic lahar (@delahar) April 1, 2012


【#AACR Editorial】Next generation seq is def important but how reliable is the technology remains to be tested in rare somatic mutation.
                                               —Naoto T. Ueno 上野直人 (@teamoncology) April 2, 2012



Press briefing at #aacr highlights limits of whole genome sequencing: low prediction of cancer twitter.com/3NT/status/186…
                                                — Pieter Droppert (@3NT) April 2, 2012
<pict press briefing>



【#AACR Editorial】Whole genome seq will provide too much info that it may not be easy 2 find the triggers. Not a criticism, a reality check.
                                            —Naoto T. Ueno 上野直人 (@teamoncology) April 2, 2012




TCGA project 


【#AACR 101】 What is TCGA? The Cancer Genome Atlas is a large effort to understand the molecular basis of cancer by genome analysis.
                                               —Naoto T. Ueno 上野直人 (@teamoncology) April 1, 2012


【#AACR 101】 TCGA includes large-scale genome sequencing. It is supported by NCI and the NHGRI, NIH, US Dept of HHS.
                                              —Naoto T. Ueno 上野直人 (@teamoncology) April 1, 2012


【#AACR 101】The link to TCGA. fb.me/YOHX73WF
                                               —Naoto T. Ueno 上野直人 (@teamoncology) April 2, 2012


TPCGA: the pre-cancer genome atlas. Bronch. Epithelial cells RNA extracted and gene expression compared in smokers/former smokers/non. #AACR
                                                 — David Woessner (@pinfoto) April 2, 2012 


SG: grateful that TCGA started with serous ovarian cystadenocarcinoma; looking at 489 high grade serous ovarian tumors #TCGA #AACR
                                                — Kenna Shaw (@wyattsgirl) April 2, 2012


Josh Stuart now talking about cross tumor type analysis- pan cancer analysis just starting #AACR #TCGA
                                              — Kenna Shaw (@wyattsgirl) April 1, 2012

#TCGA announced 12 new rare tumors added to pipeline; possible shift to biopsies or FFPE in next year #AACR
                                              — Kenna Shaw (@wyattsgirl) April 1, 2012

AK: makes it clear that we need to make sure to look at geographic origin too in terms of PC analysis #TCGA #AACR
                                               — Kenna Shaw (@wyattsgirl) April 2, 2012



eQTLs


SG: one thing that is clearly coming out is that its clear that eQTLs are going to be both disease and TISSUE specific #AACR
                                           — Kenna Shaw (@wyattsgirl) April 2, 2012


SG: reviews the eQTL locus they've done in OV cancer looking at 19p13 locus. #AACR
                                            — Kenna Shaw (@wyattsgirl) April 2, 2012



SOBERING THOUGHTS, REALITY CHECK 

#AACR Whole genome sequencing "not magic bullet" for predicting cancer risk, according to data from extensive twin study. #epigenetics
                                             — Manuel Caceres (@Quetzaltwit) April 2, 2012 



My conclusion from Vogelstein #aacr press conf: don't rely on whole genome sequencing to predict if you will get cancer
                                              — Pieter Droppert (@3NT) April 2, 2012



"Whole genome sequencing cannot substitute for conventional risk management strategies." #AACR
                                               — J Nat'l Cancer Inst (@JNCI_Now) April 2, 2012


【#AACR Editorial】Accurate whole genome seq will not translate to clinic asap. Genetic changes will require validation by basic research.
                                             —Naoto T. Ueno 上野直人 (@teamoncology) April 2, 2012


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Postcard From the AACR 2012 Annual Meeting - Part 1
Postcard From the AACR 2012 Annual Meeting - Part 2
Postcard From the AACR 2012 Annual Meeting - Part 4
Postcard From the AACR 2012 Annual Meeting - Part 5