.@mason_lab Chris Mason (Columbia): 'Targeted RNA sequencing, urban metagenomics, and astronaut genetics" #AGBT16
12:25pm February 11th 2016 via Hootsuite
Gammack: Mentions their recent collab w/ @10Xgenomics to drive 'unique insights' #AGBT16
12:24pm February 11th 2016 via Hootsuite
Gammack: They ahve 120K users of their bioinformatics products; >420K sequenced samples uploeaded to Ingenuity cloud #AGBT16
12:23pm February 11th 2016 via Hootsuite
Gammack:Introduces GeneReader, #AGBT16 BTW I wrote it up here: https://t.co/TrJKYPFcHj
12:21pm February 11th 2016 via Hootsuite
Gammack: Mentions QIAseq, their new name for targeted sequencing enrichment; both for targeted RNA-Seq as well as gene panels #AGBT16
12:19pm February 11th 2016 via Hootsuite
Jason Gammack of @QIAGEN introducing their lunchtime workshop at #AGBT16 https://t.co/Zl0GeM0gUK
Sol-Church: One a genetic mutation, another an epigenetic phenomenon: everyone is accounted for in pedigree #AGBT16
12:02pm February 11th 2016 via Hootsuite
Sol-Church: No maternal SNPs were transmitted to offspring.BsrF1 digestion uncovers 'hidden allele'. Turned out to be methyl-sens! #AGBT16
12:00pm February 11th 2016 via Hootsuite
For those listening to #AGBT16 wondering about stats, here's the @symplur analysis https://t.co/L62eiJy13W
11:56am February 11th 2016 via Hootsuite
.@CIgenomics I was told that @nanostringtech will have cool USB light-bulbs ronight (to match the cool batteries in our #AGBT16 backpacks
11:54am February 11th 2016 via Hootsuite in reply to CIgenomics
Sol-Church: XYLT1 - fn is first step in glysosaminoglycan (GAG) chain elongation; affecting ECM and cartilage formation #AGBT16
11:52am February 11th 2016 via Hootsuite
Sol-Church: Went from SOLiD to ILMN but it wasn't the technology; one had splice var XYLT1. Looked for CNV: found 3MB del in 3/7 #AGBT16
11:50am February 11th 2016 via Hootsuite
Sol-Church: Flattened mid-face, broad nasal bridge, cleft palate, dev delay. Resembles Desbuquois (CANT1) #AGBT16
11:49am February 11th 2016 via Hootsuite
Sol-Church: Baratela Scott Syndr. rare recessive, mental disability well-hidden by children, 7 boys from 6 families, not X-linked #AGBT16
Sol-Church: Their work acknowledges the Center for Mendelian Genomics (UW and JHU); researchers, clinicians, community #AGBT16
11:45am February 11th 2016 via Hootsuite
Katia Sol-Church (duPont Hospital for Children) Baratela Scott Syndrome is a rare recessive skeletal dysplasia #AGBT16
11:43am February 11th 2016 via Hootsuite
Martignetti: Acknowledges Cassie Schumacher of Swift Biosciences for a lot of hard work #AGBT16
11:41am February 11th 2016 via Hootsuite
Martignetti:Showing Swift data of genes' overlap between cell pellet lavage and cell-free DNA. Strong overlap shown #AGBT16
11:39am February 11th 2016 via Hootsuite
Martignetti: Screening - a saline uterine lavage. Collection of cell-free, cell pellet. 'Swift has worked incredibly well for us' #AGBT16
11:38am February 11th 2016 via Hootsuite
Martignetti: With 5 gene panel, can do ctDNA. Published last month, showing PFS and OS differences PLoS One https://t.co/1jvUOw6g03 #AGBT16
11:36am February 11th 2016 via Hootsuite
Martignetti: The Accel-Amplicon 56G Oncology panel, validated using orthogonal technology, retrain and showed 5 genes, 82% #AGBT16
11:32am February 11th 2016 via Hootsuite
Martignetti: And from only 4 genes, used TCGA data as a training set. Predicted 86% into type1/2. Then went to SwiftBio 56G #AGBT16
11:31am February 11th 2016 via Hootsuite
Martignetti: Developed a tool MutationAssessor https://t.co/dA7W2n36ob came up with 15 gene AmpliSeq panel #AGBT16
11:30am February 11th 2016 via Hootsuite
Martignetti: In-revision paper Rykunov D NAR 2016, can look at Molecular Signature Method with a weighting scale #AGBT16
11:29am February 11th 2016 via Hootsuite
Martignetti: From this '13 @TCGAupdates paper: https://t.co/O6V2PTKfVP supports classic distinctions by grade by OS #AGBT16
11:27am February 11th 2016 via Hootsuite
Martignetti: Three points where change can be made: in the office, at surgery, and quarterly followup #AGBT16
11:26am February 11th 2016 via Hootsuite
Martignetti: From symptoms, to D&C in the office, pathology H&E grading, affecting surgical choice, another set of grading #AGBT16
11:24am February 11th 2016 via Hootsuite
Martignetti: Classification based on histology; problem is judgement of % in grade 1/2/3. Most reliable: 2 groups. #AGBT16
11:23am February 11th 2016 via Hootsuite
Martignetti: Lists symptoms, diagnosis (pelvic exam, pap smear, biopsy, D&C). No clinically useful mol markers / diagnostics #AGBT16
11:22am February 11th 2016 via Hootsuite
Martignetti: Endomet ca is 55K new cases, >10K deaths, incidence increasing due to obesity, increase in menarche #AGBT16
11:21am February 11th 2016 via Hootsuite
John Martignetti (Mount Sinai): A pre-operative, diagnostic gene panel for guiding primary treatment choices in endometrial cancer #AGBT16
11:20am February 11th 2016 via Hootsuite
Rapaport: Conclude - combination of RNA and DNA ID's a complex landscape of events, with prognostic and therapeutic impact #AGBT16
11:19am February 11th 2016 via Hootsuite
Rapaport: Second most common was MLL fusion. Goes on to subdivide by type of accompanying mutation by type (cell cycle etc.) #AGBT16
11:11am February 11th 2016 via Hootsuite
Rapaport: Showed samples on x-axis, genes on y-axis, shrt event, rearr, gain, loss: 36% BCR-ABL1. #AGBT16
11:10am February 11th 2016 via Hootsuite
Rapaport: Used FoundationOne Heme, 405 gene exons, 265 RNA fusions, 189 samples, 435x DNA coverage #AGBT16
11:09am February 11th 2016 via Hootsuite
Rapaport: The adult form is only deduced from the pediatric form (survival rate 80%, but in adults 30-40%). Higher BCR-ABL fusion #AGBT16
11:06am February 11th 2016 via Hootsuite
Franck Rapaport (Memorial Sloan Kettering) “Integrated DNA/RNA profiling for somatic alterations in adult B-cell ALL” #AGBT16
11:05am February 11th 2016 via Hootsuite
Diaz: Showed OS and PFS clear difference in MMR-def CRC. 1700 mut/genome in responders, few in non-responders #AGBT16
10:28am February 11th 2016 via Hootsuite
Diaz: After getting support,designed study of CRC and nonCRC with mismatch repair deficiency. Showed clear difference in response #AGBT16
10:27am February 11th 2016 via Hootsuite
Diaz: Explosion of immunotherapy: PD-1 pathway, spec for melanoma, lung ca. May be helpful in mismatch-repair tumors #AGBT16
10:24am February 11th 2016 via Hootsuite
Diaz: Need high-impact studies to drive overall survival. #AGBT16
10:23am February 11th 2016 via Hootsuite
Diaz:Limited more by 'biology rather than technology' in the future - need the clinical utility to move things forward #AGBT16
10:22am February 11th 2016 via Hootsuite
Diaz: Only about 12 mutations with targeted cancer therapies. MRD, early detection, or novel applications of Rx #AGBT16
Diaz: Not for every type of tumor - due to anatomic barriers (i.e. gliomas). Challenges: not all clonal events are cancer #AGBT16
10:21am February 11th 2016 via Hootsuite
Diaz: For liquid pap-smear specimens - able to get 100% sens for cervical, 41% for ovarian cancer. Up to 10% mutant fraction #AGBT16
10:19am February 11th 2016 via Hootsuite
Diaz: False-positive issues are minimized - due to nature of genomic rearrangement data in ctDNA #AGBT16
10:17am February 11th 2016 via Hootsuite
Diaz: From NIPT data: testing from 10's of thousands, found a total of 38 cases of CNV from cfDNA #AGBT16
Diaz: Another high-impact area for ctDNA: early detection. 1600 pts, 40% in stage I '14 ref https://t.co/iBSZZPQx48 #AGBT16
10:16am February 11th 2016 via Hootsuite
Diaz: Wrapping up a study, stage II CRC ctDNA measured 6-8 weeks post-op. Showing clear data for Br cancer https://t.co/m717UOwnkP #AGBT16
10:14am February 11th 2016 via Hootsuite
Diaz:Show BEAMing data from '08 Nature Med paper: https://t.co/NOyFZ74A4d Evidence of whether all of the tumor has been removed #AGBT16
10:12am February 11th 2016 via Hootsuite
