Cardoso: Used Shiina Tissue Antigens 2012 primers for LR PCR (4.6kb) and PGM sequencing for HLA-B #ionworld2013
11:38am October 22nd 2013 via Hootsuite
Cardoso: Aim to survey 4500 samples across MesoAmerica; and apply NGS to HLA typing, reduce cost and time for HLA-B #ionworld2013
11:37am October 22nd 2013 via Hootsuite
Cardoso: New protective and risk alleles in Mexican and Guatemalan cohorts discovered #ionworld2013
11:36am October 22nd 2013 via Hootsuite
Cardoso: Set of protective and risk HLA alleles, differing plasma viral loads, CD4 Tc #ionworld2013
11:35am October 22nd 2013 via Hootsuite
Cardoso: Collaborating with others in S America, looking at CTL response restricted by HLA class I alleles #ionworld2013
Cardoso: Ion Reporter with 16S analysis can produce a nice corona plot #ionworld2013 http://t.co/EF5YQrqeOY
11:34am October 22nd 2013 via Hootsuite
Cardoso: Can now put in a user-defined workflow with parameters, to the genus and species level. "Very promising" #ionworld2013
11:32am October 22nd 2013 via Hootsuite
Cardoso: An 'all-in-one' pipeline is desirable for her - 'now possible with Ion Reporter metagenomics', early access #ionworld2013
Cardoso: PCA shows anti-retroviral naiive compare nicely to uninfected controls #ionworld2013
11:31am October 22nd 2013 via Hootsuite
Cardoso: Used modified version of cutadapt (courtesy George Watts Univ AZ), QIIME, then STAMP (Parks and Beiko 2011) #ionworld2013
11:29am October 22nd 2013 via Hootsuite
Cardoso: V3 fusion primers, 200bp, 5 samples/316 chip, 355Mb Q20 bases. #ionworld2013
11:28am October 22nd 2013 via Hootsuite
Cardoso: Dysbiosis of the gut - correlates with HIV disease progression. Use PGM to examine 37 HIV+ pts #ionworld2013
11:27am October 22nd 2013 via Hootsuite
Cardoso: Aug Science Trans Med - shown gut bacterial composition differs in HIV+ pts. #ionworld2013 PubMed: http://t.co/PBMFN2E0w3
11:26am October 22nd 2013 via Hootsuite
Cardoso: T-cells in the gut - a 'leaky gut' where microbiome products get into circulation. Known to play a role in inflamm. #ionworld2013
11:24am October 22nd 2013 via Hootsuite
Cardoso: CD4+ T-cells and viral load monitored in periph. blood, but virus found in the gut, co-express CD4 and CCR5 #ionworld2013
Cardoso: CIENI is located in Mexico City MX, HIV infection and 16S sequencing #ionworld2013
11:21am October 22nd 2013 via Hootsuite
Up next: Sandra Maria Pinto Cardoso, Res. Center for Infect. Dis., 16S rRNA gene-based profiling of the gut microbiota of HIV #ionworld2013
11:20am October 22nd 2013 via Hootsuite
Steve Glavas speaking about Influenza A at the Swedish equivalent of the US CDC #ionworld2013 http://t.co/1HdMOZhehE
11:17am October 22nd 2013 via Hootsuite
Glavas: Workflow goal is 'any user capable', with less hands-on, and fully automated data reporting #ionworld2013
11:13am October 22nd 2013 via Hootsuite
Glavas: Evaluation of Ion Chef, they prepared libraries and Ion did the template and seq; 'data looked good' similar accuracy #ionworld2013
Glavas: "I don't know if any of you have written a plug-in; it's easy, give a holler if you want any help" #ionworld2013
11:10am October 22nd 2013 via Hootsuite
Glavas: Sample failure correlated to older samples. Created PathogenAnalyzer plugin for Ion Server #ionworld2013
11:09am October 22nd 2013 via Hootsuite
Glavas: Uses AB Library Builder for library prep. Goal was to run 105 isolates (enough for 1 season) from sample to report #ionworld2013
11:06am October 22nd 2013 via Hootsuite
Glavas: Sanger method takes 3 days, only H, N, M fragments. Manual assembly method for analysis, determine clade and deviation #ionworld2013
11:03am October 22nd 2013 via Hootsuite
Glavas: Influenza has 8 gene fragments, 12kb genome, 14K deaths in 2009 pandemic. #ionworld2013
11:02am October 22nd 2013 via Hootsuite
Next up: Steve Glavas, Swedish Inst. for Communicable Disease Control. Retrospective study of 100 influenza A using NGS. #ionworld2013
11:00am October 22nd 2013 via Hootsuite
Photo of Joe Petrosino, Baylor, on the comparison between 454 and PGM for 16S of microbiome samples. #ionworld2013 http://t.co/CcvIcAyB07
10:59am October 22nd 2013 via Hootsuite
Petrosino: Next steps: using same amplicon for 454 and PGM #ionworld2013
10:58am October 22nd 2013 via Hootsuite
Petrosino: Different area, torso, difference can be observed in days. #ionworld2013
10:55am October 22nd 2013 via Hootsuite
Petrosino: Time-course to see change in communities - by week, can see a large change between 1 week and 2/3 week frames #ionworld2013
Petrosino: Heat signatures of bodies from sunlight, shade, very complex and interesting project. Look at microbiome mix. #ionworld2013
10:54am October 22nd 2013 via Hootsuite
Petrosino: Useful for forsensics - look at entemology, tell whether the body has been moved. Yikes, he has photos. #ionworld2013
10:53am October 22nd 2013 via Hootsuite
Petrosino: Microbiome of decomposition: called a 'body farm' north of Houston, place cadavers and let them decompose (!) #ionworld2013
Petrosino: No PCA cluster for T1D of controls vs >1 yr cases. Comparison of 454 vs. PGM: 'congruent'. #ionworld2013
10:52am October 22nd 2013 via Hootsuite
Petrosino: Type 1 Diabetes in Mexico (T1D) - ID an environmental trigger; another idea is different triggers by geography #ionworld2013
10:50am October 22nd 2013 via Hootsuite
Petrosino: Relative abundance by day: very similar data from 454 vs. PGM for this application. #ionworld2013
10:49am October 22nd 2013 via Hootsuite
Petrosino: Patient cured within 24h. Cp 454 and PGM data, PCA of 1 sample over time. Day 40 sample very different #ionworld2013
10:48am October 22nd 2013 via Hootsuite
Petrosino: Goal - use probiotics to accomplish the same for C.diff. Targeted microbiome transplant. Collect samples / compare #ionworld2013
10:47am October 22nd 2013 via Hootsuite
Petrosino: Recurring C.diff - a huge problem. Issue is antibiotics only 30% effective. Fecal transplants are 90% successful #ionworld2013
10:46am October 22nd 2013 via Hootsuite
Petrosino: Details: QIIME pipeline dev for Sanger, 454, adapted for PGM. #ionworld2013
10:45am October 22nd 2013 via Hootsuite
Petrosino: Stats: every read counts (no 'consensus'); C.diff, T1D, Cadaver datasets. #ionworld2013
Petrosino: Comparison - including a project on 'human decomposition'. PGM used V4 (515-806bp) #ionworld2013
10:44am October 22nd 2013 via Hootsuite
Petrosino: 400bp RL on PGM: WT vs KO mouse, comparing 200, 300, 400 RL compared to 454. 400 RL on PGM now feasible for 16S #ionworld2013
10:43am October 22nd 2013 via Hootsuite
Petrosino: Platforms over the years; 454 gold std, across the 9 regions; paired-end and single read cartoon. #ionworld2013
10:42am October 22nd 2013 via Hootsuite
Petrosino: 16S rRNA gene; 9 variable regions, a fingerprinting effort. Sanger reads capture 9 regions; NGS with shorter reads #ionworld2013
10:41am October 22nd 2013 via Hootsuite
Petrosino: >100 collaborators studying body sites worldwide. Laundry list of diseases they are looking at. #ionworld2013
10:40am October 22nd 2013 via Hootsuite
Petrosino: Photo of Houston: "MILLIONS OF SAMPLES" - stool samples galore! (And a 'we are here' arrow) #ionworld2013
10:39am October 22nd 2013 via Hootsuite
Petrosino: Review of Human Microbiome approach, 16S sequencing to ID organism(s) or genes that indicate disease #ionworld2013
10:38am October 22nd 2013 via Hootsuite
Up next: Joe Petrosino, Baylor. "Novel approaches in infectious disease res. and microbial sequencing" on Human Microbiome #ionworld2013
10:36am October 22nd 2013 via Hootsuite
Nils Homer speaking on Claritas Genomics' efforts in evaluation of the Ion Proton and AmpliSeq Exome #ionworld2013 http://t.co/q9oB6mUyjN
9:43am October 22nd 2013 via Hootsuite
