Korlach: With increased ZMWs come much higher multiplexing capability. #AGBT16
1:49pm February 12th 2016 via Hootsuite
Korlach: Presents specs of Sequel: QV50, RL similar to RSII, 5-10GB/cell, 1-16 cells/run #AGBT16
RT @infoecho: AA, quoted 'Jim Lupski: "The Goal is De Novo Assembly in Clinic"' #AGBT16
1:47pm February 12th 2016 via Hootsuite
Jonas Korlach (PacBio) - some concluding comments: 75% of variation is not captured by SNVs. There are SVs, Haplotypes, epigenetics #AGBT16
Ameur: #AGBT16 Targeted PacBio of FADS region '12 AJHG https://t.co/QmJh12Ft1X Able to do phasing of functional variant, results submitted
1:39pm February 12th 2016 via Hootsuite
Ameur: will monitor HCV drug resistance. Also screen for TP53 mutations. Will be working on a hyb-based protocol w/Agilent #AGBT16
1:35pm February 12th 2016 via Hootsuite
Ameur: Offers this as routine service, ~4 samples/week. 100 samples to-date. 100% consistent w/Sanger. Wants to go to 0.1% sens #AGBT16
1:34pm February 12th 2016 via Hootsuite
RT @euanashley: Best "any questions" slide ever. #AGBT16 https://t.co/BTjJmf5WKp
1:33pm February 12th 2016 via Hootsuite
Ameur: Can go down to 1% allele freq. Showed instances of mutations showing up over time, some compound #AGBT16
Ameur: First example is CML Drug resistance is due to point mutations. '15 BMC Cancer ref https://t.co/NC7227MPux #AGBT16
1:30pm February 12th 2016 via Hootsuite
Ameur: One of the most well-equipped NGS facilities in Europe, have two RSII. >3K SMRT cells to-date. Majority is non-human research #AGB
1:26pm February 12th 2016 via Hootsuite
Adam Ameur (Uppsala Univ Sweden) "Clinical SMRT Sequencing - from single genes to complete genomes" #AGBT16
1:25pm February 12th 2016 via Hootsuite
Murrell: Showing 9.2kb full-length HCV assembly from full-length reads at 99% accuracy. #AGBT16
1:20pm February 12th 2016 via Hootsuite
Murrell: Appears to have some recombination between strains as well.Very complex, able to multiplex 6 timepoints. #AGBT16
1:17pm February 12th 2016 via Hootsuite
Murrell: 2nd donor, N332 'glycan supersite' antibody lineage, 34 mAbs. Infected by 2 founder variants. V00 through V60 #AGBT16
1:14pm February 12th 2016 via Hootsuite
Murrell: Interesting plot of V00 through V48 with size of var frequency in size of bubble, and trees of relatedness #AGBT16
1:12pm February 12th 2016 via Hootsuite
Murrell:Individual donors - full-length env sequencing, Ab heavy-chain NGS. Will present on 2 donors. #AGBT16
1:11pm February 12th 2016 via Hootsuite
Murrell: Presents some HIV-1 biology about how antibodies are targeting envelope, but an 'arms race'. Rev: https://t.co/kXf7cUQDDe #AGBT16
1:10pm February 12th 2016 via Hootsuite
Murrell:Showed actual longitundinal HIV env data - amazing illustration. 2.6kb amplicon. CCS method. #AGBT16
1:08pm February 12th 2016 via Hootsuite
Ben Murrell (UCSD) "Deeply sequencing entire genes from rapidly evolving viruses" #AGBT16
1:06pm February 12th 2016 via Hootsuite
Sebra: Showed side-by-side RSII and Sequel somatic calls were very close to each other by AF, ranging from 5% to 50% #AGBT16
1:02pm February 12th 2016 via Hootsuite
Sebra: Somatic var detection from bulk - CCS reads. 4 germline confirmed, 16 som confirmed. 3 mutants by WES FN, 1 somatic WES FP #AGBT16
1:01pm February 12th 2016 via Hootsuite
Sebra: Bar chart showed 100's of deletions picked up. Last case: risk of WES to miss clinically important things. #AGBT16
12:59pm February 12th 2016 via Hootsuite
Sebra:Took 3 cases: good concordance across 3 platforms (Ion and ILMN), but large # of indels picked up by PacBio #AGBT16
Sebra: Whole-gene BRCA 1/2: 'most current dbSNP entries are highly biased toward exonic coverage' (WGS, WES cohorts) #AGBT16
12:57pm February 12th 2016 via Hootsuite
Sebra: Ended up validating w/jumping libraries AGBT16
12:55pm February 12th 2016 via Hootsuite
Sebra: Will be publishing soon - huge MB-sized inverted duplication LINE element. SMRT correctly assembled breakpts, rearrangement #AGBT16
12:54pm February 12th 2016 via Hootsuite
Sebra: Goldenhar Syndrome (rare disease) "Large SVs matter". Long surgical history (7 of them, every 5 years). #AGBG16
12:53pm February 12th 2016 via Hootsuite
Sebra: Can resolve from 50 to 150 repeats. showed very comparable data between RSII and Sequel #AGBT16
12:52pm February 12th 2016 via Hootsuite
Sebra: 3rd example, C9orf72 ALS G4C2 challenging repeat. '13 Science https://t.co/wgWWaJOohb #AGBT16
12:51pm February 12th 2016 via Hootsuite
Sebra: GBA and its pseudogene - a 6.4kb product, to do single full-length amplicon, #AGBT16
12:50pm February 12th 2016 via Hootsuite
Sebra: Shows CYP2D6 ref from '10 JMD https://t.co/lQLN6pKBOd and how SMRT clarified the 2D6 genotype #AGBT16
12:48pm February 12th 2016 via Hootsuite
Sebra: Population-scale PGx: CYP2D6 metabolism to phase, importance of 2D6 as it metabolizes some 25% of all drugs #AGBT16
12:47pm February 12th 2016 via Hootsuite
Sebra: Similar chart as Ashley's - cancer, immunology, infectious disease, so many areas to tackle. #AGBT16
12:46pm February 12th 2016 via Hootsuite
Sebra: Long list of known disease ass'n 'that require long reads'; and bigger cohorts. #AGBT16
12:45pm February 12th 2016 via Hootsuite
Sebra: Points to this '15 Nature Methods paper https://t.co/dnMebYsznA with a host of single-molecule approaches (BioNano Genomics) #AGBT16
Sebra: They have 2 PacBio SEQUELS. Tackled NA12878, impt for variety of haplotypes to completion, to design precise approaches #AGBT16
12:44pm February 12th 2016 via Hootsuite
Sebra: They are driving toward precision med. 7 HiSeq 2500/4000; 2 MiSeq, 10 Protons, 5 S5 XL, 2 PGM, 11 Ion Chefs 3 PacBio RSII #AGBT16
12:42pm February 12th 2016 via Hootsuite
Bobby Sebra (Mt Sinai Icahn SOM) "Leveraging SMART sequencing technology for developing niche assays with diagnostic potential" #AGBT16
12:41pm February 12th 2016 via Hootsuite
Ashley:Q:What's the priority? A:Know that one size does not fit all. NB: Livestream this here https://t.co/mQUAYs6wlG #AGBT16
Ashley: Concludes: complexity of the genome; ideal germline Dx is adequate coverage, solution to complex areas #AGBT16
12:38pm February 12th 2016 via Hootsuite
Ashley: Precision gene silencing - silencing mutant alleles, has generated data in a mouse model with iPS #AGBT16
12:37pm February 12th 2016 via Hootsuite
Ashley: Finishes with video of cardiac hypermyopathy. Looking at silencing genes in iPS cadiomycytes. then RNA-Seq #AGBT16
12:36pm February 12th 2016 via Hootsuite
Ashley: The ideal may be a multiple tech's. Scottish: "The right horse for the right course." #AGBT16
12:33pm February 12th 2016 via Hootsuite
Ashley: Shows figure from this Nature '15 https://t.co/Pezv6K7601 for structural var of size and number resolved via @pacbio #AGBT16
12:32pm February 12th 2016 via Hootsuite
Ashley: Shows sensitivity as a fn of indel length - striking decline the larger the indel #AGBT16
12:31pm February 12th 2016 via Hootsuite
Ashley: Assembly not good, and variant calling. Some solutions are graph references #AGBT16
Ashley: Onto HLA/MHC - makes a comment about complexity of HLA and many words on his slide. Capture not work well - polymorphisms. #AGBT16
12:30pm February 12th 2016 via Hootsuite
Ashley: What about Huntington's, w/expanding sequence? (CAG)n - there are 31 repeat conditions. List here: https://t.co/6p3eIJlUHf #AGBT16
12:29pm February 12th 2016 via Hootsuite
Ashley: Haploid? Risk alleles comes from real diploid people. But Factor V risk factor is in the ref genome. Homoz won't be called #AGBT16
12:28pm February 12th 2016 via Hootsuite