Paul Flicek (EBI-EMBL) #AGBTph18 Empowering data sharing for genomic medicine
6:01pm September 7th 2018 via Twitter Web Client
Ramakrishnan #AGBTph18 Confirmed segmental duplication. Partial reciprocal translocation near ETV1/FOXA1.
4:19pm September 7th 2018 via Twitter Web Client
Ramakrishnan #AGBTph18 Shows complex plot, shows animation of SW pulling ROI of transposition. Can hone in easily.… https://t.co/H1FbOsBeZF
4:18pm September 7th 2018 via Twitter Web Client
Ramakrishnan #AGBTph18 Case study with Arul Chinnaiyan of UMich; 6 Pr Ca lines; 4 FF primary tissues, likely FOXA1.… https://t.co/NsqWyv79Th
4:15pm September 7th 2018 via Twitter Web Client
Ramakrishnan #AGBTph18 The problem w/large SVs: complex, repetitive around breakpoints, FFPE fragmentation. Gene re… https://t.co/GXkxyumI4v
4:13pm September 7th 2018 via Twitter Web Client
Ramakrishnan #AGBTph18 Read-pairs can span up to Mb in size. Chr-level assy; large/complex struct var; profile 3D f… https://t.co/qeZ4uGY5yu
4:12pm September 7th 2018 via Twitter Web Client
Ramakrishnan #AGBTph18 Covers core proximity-ligation tech; Chicago libraries (gDNA), Fix-C (FFPE), Hi-C (post-fixa… https://t.co/qNBLHTBfMn
4:11pm September 7th 2018 via Twitter Web Client
Ramesh Ramakrishnan (Dovetail Genomics) #AGBTph18 High confidence identification and visualization of genomic rearr… https://t.co/iED4YAVaVo
4:06pm September 7th 2018 via Twitter Web Client
Bick #AGBTph18 Soldier had collapsed after 12 mi run with 80lbs of gear, had 107F fever and ICU. Heterozygous for g… https://t.co/QGc7JHRKl1
3:42pm September 7th 2018 via Twitter Web Client
David Bick (Envision Genomics AL) #AGBTph18 Interesting comparison of diagnostic yield between WES and WGS. Presented case of rhabdomyelitis
3:41pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 of n=165, 151 was able to help interpret info from WGS/WES. Concludes on interesting Noonan syndrome… https://t.co/vtBuRb1zXz
3:04pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 RNA at UDN: n=66, 165 variants, 51% were deep intronic. Shows busy stacked bars for other types (exon… https://t.co/SkOyTRwyUf
2:56pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 37% adding metabolomics provided information helpful to var interpretation.
2:53pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 Not quantitative but still valuable, Dx and cost to replace existing tests. 1300 samples, 53% no othe… https://t.co/ILC17tv2w7
2:52pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 Metabolome: how to report, worked with Metabolon to validate across known diseased samples. Impt scre… https://t.co/fhi7EySN0N
2:50pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 Recent exomes (>'16) are 'generally comparable'. WGS at least as good as WES. Murdoch poster here.
2:49pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 Difference in capture quality; shows box-and-whiskers between 4 providers of WES enrichment. OMIM, ACMG59 genes
2:48pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 278 infnats; <100d NICU; 36.7% Dx yield; 52% cases Dx affected medical care. '17 https://t.co/OaAhJyMWhA
Lee #AGBTph18 Cites data from '13 https://t.co/XR3AFK9DhB and '14 NEJM
2:46pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 Clin phenotype is 'still absolutely req'd' - var expressivity, incomplete penetrance
2:44pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 Functionalizing the gneome - metabolomics clinically avail; transcriptomics 'ready for prime-time'. S… https://t.co/jPNvUZH17b
Lee #AGBTph18 31 new syndromes defined. 37% led to 'changes in Dx testing'. WES/WGS powering a 'genotype first approach'.
2:43pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 Analysis of applicants (NEJM in press), 40% applicants accepted; 35% Dx yield, 11% based on clin revi… https://t.co/I8uJ5nIi31
2:42pm September 7th 2018 via Twitter Web Client
Lee #AGBTph18 Rare and unique variants in cases or families? UDN https://t.co/C0UiaQQZlb
2:41pm September 7th 2018 via Twitter Web Client
Brendan Lee (Baylor Coll Medicine) #AGBTph18 Multi-omic approach to undiagnosed diseases
2:38pm September 7th 2018 via Twitter Web Client
Q: Cost a barrier? Kingsmore #AGBTph18 Of n=42, save $82K per baby net (for payor). Cost of WGS fairly trivial cp to daily cost of NICU care
2:37pm September 7th 2018 via Twitter Web Client
A2 Kingsmore #AGBTph18 Heart reconstruction, intubation, etc. choices also affected
2:34pm September 7th 2018 via Twitter Web Client
Eric Green: 70% of clin mgmt changed of Dx. Examples? Kingsmore #AGBTph18 Many cases medications stopped. Rx interv… https://t.co/5Dwl6qN7mS
2:33pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 Goal is to re-educate workforce, and a large database of 10,000 NICU genomes to improve Rx, inform surgical mgmt
2:31pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 Implementing a more shallow learning curve - learning from peers, and put to use quickly. VT-Oxford network - VON-RCIGM.
2:30pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 Autoclinician: Precision 99%, recall 95% n=84, 86 Dx. 19h TAT. Expert manual: Precisoin 98%, recall 98%
2:28pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 (NB - here's a frontline piece on use of Diploid Moon software and Rady breaking a 'world recor… https://t.co/XxIx2O82Pc
2:26pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 shows complex path: rWGS (rapid), EHR, NLP of doctor notes, HPO phenotypes to sample metadata,… https://t.co/JOb9PPqQGT
2:25pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 Given computation on phenotypes, 75% of 95 pts matched the correct disease within 552 ranks
2:24pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 Cp OMIM versus expert manual review vs cNLP (automated). 5x increase of 101 children, 105 genet diseases
2:22pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 EHR updated with structured phenotyping info. Looking at their data - derived a PPV of cNLP= 0.74, sens 0.93
2:20pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 Blood culture: Pseudomonas aeruginosa. Immune deficient - due to IgG, IgA, IgM.
2:17pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 ER workup - lots of data. Req's intubation, broad antibiotics, 'one of the 16% that has imminent risk of death'
2:14pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 Cases: automated supervised 19h clinical WGS. 17m old healthy boy: 3d fever, vomiting, diarrhea… https://t.co/yJ6hGJDp4W
2:13pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 Informatics costs at hospitals 'skyrocketing'. Impact on healthcare economics 'non-incremental'… https://t.co/5GgmSg5LLM
2:12pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 Genomic Health has 115 experts involved in interpretation. "Not scalable nationally". Hospital margins are 1-2%
2:11pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 Impediments: untrained workforce 'expert labor shortage'; labor intensity of CLIA/CAP rapid gen… https://t.co/HtAApQr5qF
2:10pm September 7th 2018 via Twitter Web Client
Kingsmore #AGBTph18 48% of neonates in regional NICUs: unknown etiology; 2-7 days; 33-57% Genetic Dx; 23-37% precision Rx
Stephen Kingsmore (Rady Children's CA) #AGBTph18 Implementation of genomic medicine in the NICU and PICU by rapid w… https://t.co/QOXWgvUaOv
2:09pm September 7th 2018 via Twitter Web Client
Mardis: Seq all newborns long-term benefit? #AGBTph18 Green: need to continue to validate at larger and larger scal… https://t.co/CFOBoixwRt
1:39pm September 7th 2018 via Twitter Web Client
Green #AGBTph18 Can make the case for more pop'ln based WGS; "not for marketing" (or selling more sequencing) but f… https://t.co/XIHx1MgM6E
1:34pm September 7th 2018 via Twitter Web Client
Green #AGBTph18 Recent excitement on polygenic risk scores. What are reprod implications of recessive carrier states?
1:33pm September 7th 2018 via Twitter Web Client
Green #AGBTph18 Penetrance of Mendeliome may be higher than anticipated over a long time frame. EHR distorted by bi… https://t.co/6uHC2Xqv8p
1:32pm September 7th 2018 via Twitter Web Client
Green #AGBTph18 Substantial numbers in the population: no longer 'rare disease'. Downstream medical costs - 'may be… https://t.co/86N2e7bwTY
1:31pm September 7th 2018 via Twitter Web Client
Green #AGBTph18 Power of small data: don't want to be cavalier on people's reactions to genetic information. Monoge… https://t.co/BGEUrcHYMI
1:30pm September 7th 2018 via Twitter Web Client
