McKenzie #AGBTph18 With Ras, BRAF, MET ampl, this says 'cancer doing everything to survive'.
8:48pm September 7th 2018 via Twitter Web Client
McLeod #AGBTph18 Sees TP53, KRAS, MYC ampl, BRAF and MET ampl, EGFR muts incl T790M. McKenzie: loathe to focus on one mutation
8:47pm September 7th 2018 via Twitter Web Client
McLeod #AGBTph18 Shows chart of case 1 w/list of genes mutated, AF, protein domain, MSS (stable), TMB intermediate 16.
8:46pm September 7th 2018 via Twitter Web Client
McKenzie #AGBTph18 Talking about 'the mission field', where oncologists in rural settings seeing all kinds of cance… https://t.co/dos126H7vM
8:45pm September 7th 2018 via Twitter Web Client
McKenzie #AGBTph18 Liq Biopsy - 'just b/c it's easy doesn't mean it is something we need to do' balanced with 'better than nothing'.
Rehm #AGBTph18 Other types of controls at the Broad: individual signatures for each pt, an individual MRD assay.
8:43pm September 7th 2018 via Twitter Web Client
Rehm #AGBTph18 One thing to think about is contamination rate, when very low levels are being detected. Positive controls are problematic.
8:42pm September 7th 2018 via Twitter Web Client
Berger #AGBTph18 Some level of discordance to expect; driver muts. Cancer community has adopted this.
8:41pm September 7th 2018 via Twitter Web Client
Berger #AGBTph18 Most MSK seq is tissue. Spec of liquid biopsy has improved; lack of concordance has been extensive… https://t.co/1oX5X5lZbA
8:40pm September 7th 2018 via Twitter Web Client
McLeod #AGBTph18 ...switched to osimertinib, progressed 5mo later. Options: carboplatin, chemo, Nivo (plus Ipi if t… https://t.co/7Gr3bugbDN
8:38pm September 7th 2018 via Twitter Web Client
McLeod #AGBTph18 First case: 46yo fem, never smoker Stg IV lung adenocarc. EGR exon 19, PD-L1 neg, erlotinib. 4 mo,… https://t.co/FzSL9lR21C
8:37pm September 7th 2018 via Twitter Web Client
Howard McLeod (Moffit) moderator #AGBTph18 A mock tumor board, with Heidi Rehm (MGH) Michael Berger (MSKCC) Andrew McKenzie (Sarah Cannon)
8:36pm September 7th 2018 via Twitter Web Client
Kathiresan #AGBTph18 Polygenic risk scores, '16 ref https://t.co/5twWIAUb73 '18 ref https://t.co/qUsqHwIo0T Polyeni… https://t.co/oe3YjXrjbs
6:47pm September 7th 2018 via Twitter Web Client
Kathiresan #AGBTph18 Polygenic looking at SNPs: 60K cases, 120K controls and genotyped; 95 gene regions. 1 of many… https://t.co/OkXy9AyeiQ
6:44pm September 7th 2018 via Twitter Web Client
Kathiresan #AGBTph18 LPL, APOA5, LPA; four genes. Of 100 pts, monogenic familial hypercholesterolemia in 1.7% (manuscript in review)
6:43pm September 7th 2018 via Twitter Web Client
Kathiresan #AGBTph18 Genetic paths: case/controls n=5000/5000: LDLR 3.2x-fold '15 Nature https://t.co/aHpAh0SD8V
6:41pm September 7th 2018 via Twitter Web Client
Kathiresan #AGBTph18 MI is complex; 1/2 of MI cases, 1st presentation is fatal. '97 MGH started enrolling early-onset MI <50yo
6:39pm September 7th 2018 via Twitter Web Client
Kathiresan #AGBTph18 ACC/AHA ASCVD risk: pt was only 1.7%. Was it monogenic to MI? Polygenic component? Do somatic muts contribute?
6:37pm September 7th 2018 via Twitter Web Client
Kathiresan #AGBTph18 Starts w/42yo male, VF arrest, taken to hospital, received angioplasty + stent. Anoxic injury… https://t.co/Btt8byIoHu
6:36pm September 7th 2018 via Twitter Web Client
Sekar Kathiresan (MGH) #AGBTph18 Genetic basis for heart attack
6:35pm September 7th 2018 via Twitter Web Client
Flicek #AGBTph18 htsget: a standardized interface for secure data streaming, part of the large-scale genomics workstream.
6:26pm September 7th 2018 via Twitter Web Client
Flicek #AGBTph18 Shows busy slide of driver projects - @AllofUsResearch BRCA Challenge, NCI Genomic Data Commons...
6:19pm September 7th 2018 via Twitter Web Client
Flicek #AGBTph18 Upcoming @GA4GH 6th plenary 3-5 Oct '18 https://t.co/RUzfi2paei
6:17pm September 7th 2018 via Twitter Web Client
Flicek #AGBTph18 Federation allows analysis moved to data; reciprocal access; transfer of methods into healthcare.
6:14pm September 7th 2018 via Twitter Web Client
Flicek #AGBTph18 Challenges: healthcare not used to volume of data; clinical data not interoperable; retooling to g… https://t.co/PqAEY5QDEa
Flicek #AGBTph18 We can get a >60M virtual cohort by 2025; humans 'will be the best studied organisms on the planet due to healthcare'
6:12pm September 7th 2018 via Twitter Web Client
Flicek #AGBTph18 BioRxiv preprint on GA4GH looks to 2022: https://t.co/hwnbX5lEyK
6:11pm September 7th 2018 via Twitter Web Client
Flicek #AGBTph18 Infrastructure is 'just engineering'; but not trivial (Tesla as an example). GA4GH Connect: 5y pla… https://t.co/MOaSbqTKfe
6:10pm September 7th 2018 via Twitter Web Client
Flicek #AGBTph18 Informatics is infrastructure: archives, standards, formats, metadata. 1984: a print-out of EMBL's GenBank.
6:07pm September 7th 2018 via Twitter Web Client
Flicek #AGBTph18 'Infrastructure works when it is entirely invisible.' "Fund us so we can build something that no o… https://t.co/JF12tHHZTy
Flicek #AGBTph18 Infrastructure building: highways in the '20's, '30's. Bridge from 1935. All of us assume our phon… https://t.co/pRDjx7I9SQ
6:06pm September 7th 2018 via Twitter Web Client
Flicek #AGBTph18 "Growth repeatedly exposes inadequate infrastructure to support the needs of new technologies"
6:05pm September 7th 2018 via Twitter Web Client
Flicek #AGBTph18 1909 "The automobile has reached the limit of its development" Scientific American
6:04pm September 7th 2018 via Twitter Web Client
Flicek #AGBTph18 History of a foundational modern tech; 1879 first gasoline engine (Benz); 1885 first automobile; 1908 Ford model T.
Paul Flicek (EBI-EMBL) #AGBTph18 Empowering data sharing for genomic medicine
6:01pm September 7th 2018 via Twitter Web Client
Hi #AGBTph18 - @Pillar_Bio will present ‘Eval of a high-thruput NGS SLIMamp CFTR assay’ poster at the break #155 https://t.co/y8uPkcYLqq
4:25pm September 7th 2018 via Twitter for iPhone
Ramakrishnan #AGBTph18 Confirmed segmental duplication. Partial reciprocal translocation near ETV1/FOXA1.
4:19pm September 7th 2018 via Twitter Web Client
Ramakrishnan #AGBTph18 Shows complex plot, shows animation of SW pulling ROI of transposition. Can hone in easily.… https://t.co/H1FbOsBeZF
4:18pm September 7th 2018 via Twitter Web Client
Ramakrishnan #AGBTph18 Case study with Arul Chinnaiyan of UMich; 6 Pr Ca lines; 4 FF primary tissues, likely FOXA1.… https://t.co/NsqWyv79Th
4:15pm September 7th 2018 via Twitter Web Client
Ramakrishnan #AGBTph18 The problem w/large SVs: complex, repetitive around breakpoints, FFPE fragmentation. Gene re… https://t.co/GXkxyumI4v
4:13pm September 7th 2018 via Twitter Web Client
Ramakrishnan #AGBTph18 Read-pairs can span up to Mb in size. Chr-level assy; large/complex struct var; profile 3D f… https://t.co/qeZ4uGY5yu
4:12pm September 7th 2018 via Twitter Web Client
Ramakrishnan #AGBTph18 Covers core proximity-ligation tech; Chicago libraries (gDNA), Fix-C (FFPE), Hi-C (post-fixa… https://t.co/qNBLHTBfMn
4:11pm September 7th 2018 via Twitter Web Client
Ramesh Ramakrishnan (Dovetail Genomics) #AGBTph18 High confidence identification and visualization of genomic rearr… https://t.co/iED4YAVaVo
4:06pm September 7th 2018 via Twitter Web Client
Bick #AGBTph18 Soldier had collapsed after 12 mi run with 80lbs of gear, had 107F fever and ICU. Heterozygous for g… https://t.co/QGc7JHRKl1
3:42pm September 7th 2018 via Twitter Web Client
David Bick (Envision Genomics AL) #AGBTph18 Interesting comparison of diagnostic yield between WES and WGS. Presented case of rhabdomyelitis
3:41pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 of n=165, 151 was able to help interpret info from WGS/WES. Concludes on interesting Noonan syndrome… https://t.co/vtBuRb1zXz
3:04pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 RNA at UDN: n=66, 165 variants, 51% were deep intronic. Shows busy stacked bars for other types (exon… https://t.co/SkOyTRwyUf
2:56pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 37% adding metabolomics provided information helpful to var interpretation.
2:53pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 Not quantitative but still valuable, Dx and cost to replace existing tests. 1300 samples, 53% no othe… https://t.co/ILC17tv2w7
2:52pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 Metabolome: how to report, worked with Metabolon to validate across known diseased samples. Impt scre… https://t.co/fhi7EySN0N
2:50pm September 7th 2018 via Twitter Web Client
