Housman: Idea: 'Direct to Wallet' get a test, device, or Rx into the market w/o payment from trad reimbursement channels #NGDx16
5:03pm August 23rd 2016 via Hootsuite
Housman: Quotes '16 Health Affairs survey https://t.co/gC07n17ptn 75% no connection between cost and quality of care #NGDx16
5:01pm August 23rd 2016 via Hootsuite
Laura Housman (Access Solutions) Direct to wallet: understanding and managing pt responsibilities assoc'd w/NGS testing #NGDx16
5:00pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: Even with freeze-thaws, still nice match via non-param Wilcoxon and ANOVA. #NGDx16
4:07pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: Showing indels not better on one platform; homopolymer SNVs still very low CVs 'really positive to see' #NGDx16
4:06pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: Indels: four indels to challenge system to adjust pipeline during validation, also see over time. #NGDx16
4:04pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: AF10, 2% Coeff of var; AF20 2.5%. Pleased to see such small CVs across labs. #NGDx16
4:03pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: Gives a 'shout out' to VCU lab 6 - all 26 mutations picked up. SNVs tight correlations, regardless of platform #NGDx16
4:02pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: Interlaboratory study ran 72 samples over 8 weeks, with 7 labs. Clinical smpls run also #NGDx16 https://t.co/pEF1HnZkQA
4:00pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: iQ software from SeraCare, something that needs to be considered - how to track and trend reported %'s over time #NGDx16
3:58pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: Presenting @SeraCare inter-laboratory study at #NGDx16 https://t.co/DRRmpiFLNc
3:57pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: 10.3% and 18% measurement by ddPCR. Showed list of 26 mutations, combination of common and rare var's #NGDx16
3:56pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: The 10% allele frequency was good for them, while 20% useful in case something went wrong. ddPCR quantitation #NGDx16
3:55pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: Points out the entire workflow, ability to look at variation across the process. 26 muts at fixed Allele Freq #NGDx16
3:53pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: Brings up two recent FDA guidances; here's the GenomeWeb commentary https://t.co/RYM2uTg11Y #NGDx16
3:50pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: Two more draft guidances - starting to regulate LDT in a more flexible way, but the details. Use of db's #NGDx16
3:47pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: Rapidly changing regulatory landscape. CAP has started efforts; now FDA giving guidelines to IVD mfrs #NGDx16
3:45pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: Tech is advancing; lack of assay/platform standardization; lack of control/ref materials. Over 20y: same prob's #NGDx16
3:43pm August 23rd 2016 via Hootsuite
Ferreira-Gonzalez: Have to look at all the parameters; credited @SeraCare in helping bring this study. #NGDx16
3:42pm August 23rd 2016 via Hootsuite
Andrea Ferreira-Gonzalez (VCU) An NGS inter-laboratory study to assess performance and QC #NGDx16
3:41pm August 23rd 2016 via Hootsuite
Simonyan: HIVE will move to open source in Fall 2016, freeing it of limitations to implement. #NGDx16
3:31pm August 23rd 2016 via Hootsuite
Simonyan: Submissions to the FDA can then refer back to the HIVE data computation. Will have a conf Spring '17 to invite opinion #NGDx16
3:30pm August 23rd 2016 via Hootsuite
Simonyan: Shows input, parametric, and output domains. Described in a simple text file. With GW Univ: create db, portal, source code #NGDx16
3:29pm August 23rd 2016 via Hootsuite
Simonyan: Input and output domains are limited / described by the datatypes. Outputs give range of errors. Can map usability domains #NGDx16
3:27pm August 23rd 2016 via Hootsuite
Simonyan: Ex of an instantiation of a human (himself) as a data-type, going onto data-type hierarchy. Framework: descriptive types #NGDx16
3:25pm August 23rd 2016 via Hootsuite
Simonyan: From a scientific method, to a protocol (parameterized instantiations of a method); in other words a recipe #NGDx16
3:23pm August 23rd 2016 via Hootsuite
Simonyan: Goes into a generized experiment concept - inputs, parameters, and outputs. #NGDx16
3:22pm August 23rd 2016 via Hootsuite
Simonyan: Now they can use external platforms (with HIVE underlying) that can integrate / emulate the same compute inside #NGDx16
3:21pm August 23rd 2016 via Hootsuite
Simonyan: Every year, there are 15K clinical trials worldwide (!) #NGDx16
3:20pm August 23rd 2016 via Hootsuite
Simonyan: FDA regulatory loop: industry to FDA ma be multiple issues, re-submitted, iterated. FDA to regulatory analysis. 8w = $2M #NGDx16
3:19pm August 23rd 2016 via Hootsuite
Simonyan: Under 4 different HIVEs, all are identical. Can also run under Amazon cloud. Beware of just a cloud provider for HW #NGDx16
3:18pm August 23rd 2016 via Hootsuite
Simonyan: Multiple deployments - maxi-HIVE (2 PB, 3K cores); public-HIVE 400TB, 500 cores. 35 pubs in past 3y #NGDx16
3:17pm August 23rd 2016 via Hootsuite
Simonyan: Able to handle not only DNA, RNA, also proteomic working on immunoseq data. Visualization is open-ended #NGDx16
3:16pm August 23rd 2016 via Hootsuite
Simonyan: Outside sources, parsed and parallelized. Databases - instead of 30 tables, 3mos to implement; 4-5 tables, 1d instead #NGDx16
3:15pm August 23rd 2016 via Hootsuite
Simonyan: FDA's platform called HIVE - archiving data, security, an encapsulated cloud hosted by the FDA. HTP infiniband - 40Gb/s #NGDx16
3:14pm August 23rd 2016 via Hootsuite
Simonyan: The FDA perspective - covers the 4V's of Big Data (high volume, velocity, variety, veracity); keeping data alive is hard #NGDx16
3:10pm August 23rd 2016 via Hootsuite
Vahan Simonyan (FDA) NGS Harmonization manifold: from data to ontologies, from computations to knowledge #NGDx16
3:06pm August 23rd 2016 via Hootsuite
Kulkani: Points to this '15 ref https://t.co/9lmChFUbtL 'optimizing cancer genome sequencing and analysis' in AML #NGDx16
3:03pm August 23rd 2016 via Hootsuite
Kulkani: Shows data from '15 JAMA https://t.co/pxH5dfBxb1 with mutation clearning in response to AML Rx #NGDx16
3:02pm August 23rd 2016 via Hootsuite
Kulkani: Impt Q's remain for AML - how to integrate clonality into risk assessment; to use 'enhanced' WES to detect 1% allele freq #NGDx16
3:00pm August 23rd 2016 via Hootsuite
Kulkani: AML - easy to access, relatively free of normal cell contamination, heterogeneous. Shows the 'long tail' of muts #NGDx16
2:58pm August 23rd 2016 via Hootsuite
Kulkani: Thymic carcinoma - fast growing, pts die w/in a year. Found KIT del, responded to imatinib, stable since '12. #NGDx16
2:56pm August 23rd 2016 via Hootsuite
Kulkani: Reviews 5-levels of somatic variant classification (AMP's is coming soon) #NGDx16
2:55pm August 23rd 2016 via Hootsuite
Kulkani: "There is a new career path for clinical genomics interpretation people. #NGDx16
2:54pm August 23rd 2016 via Hootsuite
Kulkani: EMR integration - you want the data, links, not just a PDF. Many SW business models exist, need for var curation too #NGDx16
2:53pm August 23rd 2016 via Hootsuite
Kulkani: Clinical bioinformatics doesn't have a single off-the-shelf solution. 'We need creative, cost-effective solutions' #NGDx16
2:52pm August 23rd 2016 via Hootsuite
Kulkani: The data deluge: a lifetime of Hubble data is less than a single whole genome (!) #NGDx16
2:51pm August 23rd 2016 via Hootsuite
Kulkani: Shows heterogeneity of genomic aberrations. Translocations via intronic probes; more labs moving toward RNA/DNA NGS assays #NGDx16
Kulkani: Cp 17 pairs of FF and FFPE using PE sequencing to show insert-size distribution, coverage '13 JMD https://t.co/4JtoUIfJh5 #NGDx16
2:49pm August 23rd 2016 via Hootsuite
Kulkani: Sample qty, quality, purity. WGA isn't ideal, thousands of var's can be introduced. Quality, samples have necrotic cells #NGDx16
2:47pm August 23rd 2016 via Hootsuite
