Nickerson: Mosaicism is important - could explain incomplete penetrance. Hemizygosity in males '13 ref https://t.co/CVbT1lXsxg #AGBT16
3:24pm February 12th 2016 via Hootsuite
Nickerson: Otitis Media - chronic ear infections '15 Nat Genet https://t.co/EZxvZLqffu Novel dupl var, LOD 7.5 Circular pedigree! #AGBT16
3:22pm February 12th 2016 via Hootsuite
Nickerson: Congen heart disease - H3K4 ass'd, Science '15 paper https://t.co/QjhzkIVqfZ 'every child w/this needs to be sequenced' #AGBT16
3:20pm February 12th 2016 via Hootsuite
Nickerson: One case:acromelic frontonasal dysostosis, where father had a slightly flat nose but child severe https://t.co/1npZb5TZMj #AGBT16
3:18pm February 12th 2016 via Hootsuite
Nickerson: Analysis - WES of affecteds, filter var's based on genetic model (de novo, dominant or recessive), filter on allele freq #AGBT16
3:12pm February 12th 2016 via Hootsuite
Nickerson: Genetic models: never sure if it's de novo or dominant, because they are so rare. #AGBT16
Nickerson: There is a 'need for more and robust phenotype information' due to the difficulty of association with low-penetrant genes #AGBT16
3:11pm February 12th 2016 via Hootsuite
Nickerson: ~7700 in OMIM, ~300/y solved, 1/100,000 rare, and hard due to incomplete penetrance or multi-gene effects #AGBT16
3:10pm February 12th 2016 via Hootsuite
Debbie Nickerson, (Univ Washington) “Scaling Mendelian genomics” #AGBT16
3:09pm February 12th 2016 via Hootsuite
Varmus: Splicing pattern of U2AF1-S34F (knock-in, inducible mutant) in mouse resembles human cancer, no obvious phenotype in mice. #AGBT16
2:26pm February 12th 2016 via Hootsuite
Varmus: Build mouse models that had inducible splicing-factor mutations. Data shows WT-U2AF1 essential for viability. #AGBT16
2:24pm February 12th 2016 via Hootsuite
RT @mason_lab: #AGBT16 My slides from Plenary Session: Space Genetics, long reads, and inter-planetary technology! https://t.co/TFAU0ViZCu
2:18pm February 12th 2016 via Hootsuite
Varmus: Story 2: Splicing factor genes in myeloid neoplasms: implications for U2AF1 found in many tumor types. a surprise #AGBT16
2:17pm February 12th 2016 via Hootsuite
Varmus: Ref to this '06 Cancer Res https://t.co/XGNhLArXDD work on melanoma #AGBT16
2:15pm February 12th 2016 via Hootsuite
Varmus: BRAF and NRAS Q61C in melanoma do not co-express, perhaps another oncogene combination #AGBT16
2:14pm February 12th 2016 via Hootsuite
Varmus' work on synthetic lethality explanation of KRAS and EGFR mutation exclusivity MT @frapaport: eLife https://t.co/GZho1Z2B19 #AGBT16
2:12pm February 12th 2016 via Hootsuite
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
