Berger #AGBTph18 IMPACT: 468 genes to guide treatment. 1.52Mb, ave 720x coverage. Exons from 468 genes, 20 gene int… https://t.co/gS3Id1wiHI
7:40pm September 8th 2018 via Twitter Web Client
Berger #AGBTph18 Precision oncology req's large-scale molecular profiling; scalable, fast, affordable, low freq sens, flexible.
7:39pm September 8th 2018 via Twitter Web Client
Berger #AGBTph18 BRAF occurs also in lung adenocarcinoma. Observations on dabrafenib and trametinib lead to FDA app… https://t.co/7T1A2m5UwJ
7:38pm September 8th 2018 via Twitter Web Client
Michael Berger (MSKCC) #AGBTph18 Tumor and normal clinical sequencing to guide diagnosis and treatment selection
7:36pm September 8th 2018 via Twitter Web Client
Q: Is lower coverage possible? Nik-Zainal #AGBTph18 10X coverage did drop sens, as well as WES 60-70% sens. Cost: W… https://t.co/f04nl6IWc2
7:34pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 Only 30yo, studying for a PhD, and needs add'l funds to continue treatment (trying to raise 100K)
7:31pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 Oncologists - thinking it was only sarcoma, 3rd-line Rx. Trying to raise funds for Joshua Barn… https://t.co/m79RfhMl4Q
7:30pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 Sig similar to POLE mut, showed phylogenetic tree, POLE sens to checkpt inh; looked at PD-1 ne… https://t.co/l106Eeknv3
7:29pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 Finishes with 'individualized whole cancer genomics' story. Angiosarcoma, 800K mutations in ci… https://t.co/WMPFMEU8Hb
7:28pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 Expect that will go to 'scanning WGS'. HRDetect discriminates pts w/good clin outcome on ACT.
7:25pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 70% explained by BRCA status, HRDetect predicts outcome. MMRd in br ca: an undetected and untreated class of tumors
7:24pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 A collection of signatures - more likely to detect it. '10-'15, 4,077 samples w/treatment, n=2… https://t.co/t7nIqy1cBs
7:20pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 BRCA1 with loss of allele, shows circos plots, and HRDetect ID's add'l BRCA1/2 defective tumors https://t.co/C3It8cQH6I
7:17pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 Validating this: has erythroblast-derived iPSCs, isogenic CRISPR-Cas9 K-O's, and recapitulate… https://t.co/AraVYpApIk
7:14pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 PMS2-null, has thousands of inserts, where MSI may not find. 'WGS can reveal abnormal biology… https://t.co/LXVkDVKYpv
7:12pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 Overlaying MMR, mutational load, and ER status, and some with APOBEC sig '17 ref https://t.co/Y1812PkMk9
7:11pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 But the Circos plots are similar. Unmet need 1: MMR deficiency. MLH1-null circos look similar4k small indel; 49K, 55K.
7:09pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 WGS profiles: 2 pts don't have a single mut in common; but 2k subst each; very few rearr; similar CNV
7:07pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 WGS across 560 samples: ER status, HER2 status. 'No two pts share the same set of drivers or the same qty of sigs'
7:06pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 Not all sigs in all types; focus on breast ca. In 560 br ca samples; fig from '16 Nature https://t.co/RgSq5X4bxm
7:05pm September 8th 2018 via Twitter Web Client
Nik-Zainal #AGBTph18 Found 30 subst mutational signatures. Now up to 45, will increase. Shows a busy slide of signatures x tumor type
7:03pm September 8th 2018 via Twitter Web Client
Oh #AGBTph18 Staph. epidermitus strains tested againt TCR's in their MAIT assay, using CRISPRi with varying specificities
6:45pm September 8th 2018 via Twitter Web Client
Oh #AGBTph18 Looking at naive T-cells, and 'mucosal-assoc'd invariant T-cell' (MAIT) and their activation, could be causing inflammation
6:34pm September 8th 2018 via Twitter Web Client
Oh #AGBTph18 Bacteria that rapidly reproduce have many copies of the replication origin. Non-growing has lower #'s… https://t.co/ifKn9Ce3IN
6:29pm September 8th 2018 via Twitter Web Client
Oh #AGBTph18 Rx targets: could diversify flora, restore oil/pH/moisture balance. Lots of challenges: who to chose as a probiotic organism.
6:26pm September 8th 2018 via Twitter Web Client
Oh #AGBTph18 Observed strong shift in skin disease. '13 ref https://t.co/KxWme9FrWD Loss of diversity, taxonomic restraints.
6:24pm September 8th 2018 via Twitter Web Client
Oh #AGBTph18 Looking at skin stabilityover time: expecting variation in showering, use of antimicrobials. '16 ref:… https://t.co/Y4xDlB3sSo
6:21pm September 8th 2018 via Twitter Web Client
Oh #AGBTph18 Healthy skin: '16 ref https://t.co/ExT0Vu538m Diversity across sites, in detail '14 ref https://t.co/PD9GiANME9
6:20pm September 8th 2018 via Twitter Web Client
Oh #AGBTph18 Major computational challenge - deconvolution. '18 ref https://t.co/qN9td8W5uG
6:18pm September 8th 2018 via Twitter Web Client
Oh #AGBTph18 Studies the skin microbiome - fig from '15 PNAS https://t.co/tLXFG2rffG Diversity; oily, moist and dry surface environments.
6:17pm September 8th 2018 via Twitter Web Client
Oh #AGBTph18 What is a healthy microbiome? What changes in disease, can info then be used to treat disease?
6:14pm September 8th 2018 via Twitter Web Client
Oh #AGBTph18 Obese mice - can recapitulate obese phenotype; red meat broken down by microbes in gut, contrib to heart disease.
Julia Oh (Jackson Laboratory) #AGBTph18 The human skin microbiome: from metagenomes to therapeutics
6:13pm September 8th 2018 via Twitter Web Client
#AGBTph18 Cook-Deegan: And the need for a safe space for sharing info, a looming policy question, and unstable syst… https://t.co/grKz28xPMN
2:48pm September 8th 2018 via Twitter Web Client
#AGBTph18 Cook-Deegan: Everything has been built for research; not well-adapted to indiv users. A complicated design process for end-users.
2:47pm September 8th 2018 via Twitter Web Client
#AGBTph18 Plon: Most physicians not aware that the reports might change. That the physician may need to look; the o… https://t.co/3PUbkU1tkX
2:18pm September 8th 2018 via Twitter Web Client
Q:How does Color look at reinterpretation? #AGBTph18 Topper: No, not legally req'd but ethically so. Trying to wor… https://t.co/eAHwQuoDI2
2:13pm September 8th 2018 via Twitter Web Client
#AGBTph18 Cook-Deegan: Discussion draft, Energy and Commerce depts looking at it; Advamed etc. are chiming in. FDA/… https://t.co/NmG5wmqFtE
2:10pm September 8th 2018 via Twitter Web Client
#AGBTph18 Cook-Deegan: Regulatory: 21st century Cures Act had a section "first to be x-ed out" on regulation of LD… https://t.co/Wzey99dVBh
2:09pm September 8th 2018 via Twitter Web Client
#AGBTph18 Cook-Deegan: Heidi just described the world where we have standards, a professional set; Q's about re-interpretation?
2:08pm September 8th 2018 via Twitter Web Client
#AGBTph18 Cook-Deegan: But other research db's have family cohorts, pathogenic were pedigree-dependant. We have to… https://t.co/mncSCTsiyQ
2:06pm September 8th 2018 via Twitter Web Client
#AGBTph18 Cook-Deegan: Half-empty: 60K tests 'is a mess'. A few genes like BRCA1/2 where 'most of the time' we can… https://t.co/BRnuQXL2Uq
2:05pm September 8th 2018 via Twitter Web Client
#AGBTph18 Cook-Deegan: Also '13 SCOTUS freed-up the patent rights for genetic testing. The half-full picture.
#AGBTph18 Cook-Deegan: in '12-'14: @GA4GH formed to help solve the data-sharing problem. ClinVar got formed, also h… https://t.co/lGSODKwXGd
2:04pm September 8th 2018 via Twitter Web Client
#AGBTph18 Poll note: "In 10 years experience, 67% of LMM’s reported variants were never observed again"
1:59pm September 8th 2018 via Twitter Web Client
RT @Single_Molecule: #AGBTph18 RC_D has no conflicts because he doesn't do anything of interest to anybody
1:56pm September 8th 2018 via Twitter Web Client
RT @Single_Molecule: #AGBTph18 Next up, panel discussion of reinterpretation of clinical results with @splon from Baylor, Scott Topper from…
RT @Single_Molecule: #AGBTph18 ExAC and Gnomad databases enormously useful, led to many reclassifications as benign based on better frequen…
1:55pm September 8th 2018 via Twitter Web Client
RT @agbt: The incredibly popular Great Debate, hosted by @HeidiRehm kicks off now! Panelists include @splon @topper and @cookdeegan "To Rei…
Kollu #AGBTph18 How to integrate into healthcare? A vision for routine clinical sequencing.
1:20pm September 8th 2018 via Twitter Web Client
