SK:Q:Navigating LDT? A:A research test, Sanger confirmed. Only needed to report back 1x in 35 cases before confirmation (FDA OK'd) #AGBT15
11:20am February 27th 2015 via Hootsuite
SK:Q(Plon):Unusual presentation of HLH - something add'l? A:Addressed the acute, could be add'l conditions #AGBT15
11:19am February 27th 2015 via Hootsuite
SK:NSIGHT = NGHRI's Newbork Sequencing In Genomic Medicine and Public Health for prospective work http://t.co/U549af5phJ #AGBT15
11:18am February 27th 2015 via Hootsuite
RT @bioinformer: SK: drilling down and tying phenome to genome in under 50h for #wgs #neonatal #genomics #AGBT15 http://t.co/IXHfBWC2Nf
11:15am February 27th 2015 via Hootsuite
SK:Nov 11 to Oct 14 shows unpubl data, will stop tweeting now.
11:14am February 27th 2015 via Hootsuite
SK: Sanger confirmation. Clin picture - change in medication, high dose Ig/steriods. Now healthy w/normal liver fn #AGBT15
SK: From 341 possible diseases, matches to 2 symptoms. PRF1 cmpd heterozygous. Dx: hemophagocytoic lymphohistiocytosis type 2 #AGBT15
11:13am February 27th 2015 via Hootsuite
SK: 913 ID ACMG var's cat 1-3. EMR has unstructured text; symptoms entered; automated OMIM/EntreGene differential dx gives 341 #AGBT15
11:12am February 27th 2015 via Hootsuite
SK: Uncommon, likely pathogenic vars in known disease w/high penetrance. E.g. sickle-cell SNV w/300K affected/y #AGBT15
11:10am February 27th 2015 via Hootsuite
SK: 28h var called and annotated. 1.6TByte DNA sequence (120Gbase), 2.8B genotypes. 4.8M var's. 1.085M <1% AF left #AGBT15
11:09am February 27th 2015 via Hootsuite
SK: (He's admits he's at risk for losing his @illumina t-shirt by saying the 18h figure.) #AGBT15
11:07am February 27th 2015 via Hootsuite
SK: Acute situation; organs not completely formed; difficult group. After ID an emergency: 26-34h turnaround time 2x100 in 18h poss #AGBT15
11:06am February 27th 2015 via Hootsuite
SK:23 deaths / 563 adm. in their institution. Infant monogenic diseases: 4.4K known, 20 discovered/month. Affect 4-8% of children #AGBT15
11:04am February 27th 2015 via Hootsuite
SK: Starts with NICU: 71d old w/acute liver failure. 14.4% of newborns in LII-LIV admissions in US; 49% preterm; 13.2d; $76K cost #AGBT15
11:03am February 27th 2015 via Hootsuite
Stephen Kingsmore, Children’s Mercy Kansas City. Newborn Sequencing: Rapid Genome Sequencing for Genetic Disease Dx in NICU” #AGBT15
11:01am February 27th 2015 via Hootsuite
LG:Q:Single-cell CN from RNA data? A:Largely not somatically seen. #AGBT15
10:35am February 27th 2015 via Hootsuite
LG:Q:WES vs WGS:we looking wide enough? A:Material is a limitation; targeted fits into clinical workflow, timeframe #AGBT15
10:34am February 27th 2015 via Hootsuite
LG: Clear there remain 'significant discovery opportunities' in clin cancer genomics. Response, resistance to therapy #AGBT15
10:31am February 27th 2015 via Hootsuite
LG: final point - key component is computational analysis geared toward questions asked in the clinic. #AGBT15
LG: Distinguishing from CNV's in tumor against TIL's. Further, subdividing T-cell subtypes, look at T-cell 'exhaustion' via profile #AGBT15
10:30am February 27th 2015 via Hootsuite
LG: An alternate transcr. profile: can tell a substantial subset that will be indifferent to targeted therapy. #AGBT15
10:29am February 27th 2015 via Hootsuite
LG: Does FNAs, pleural effusions, other biopsies: can cluster T-cells and tumors cells. Aviv Regev's group - distinct transc. states #AGBT15
10:28am February 27th 2015 via Hootsuite
LG: Other factors than mutations and their frequency - want single-cell RNA-seq for subsets of tumor cells; see predictive markers #AGBT15
10:27am February 27th 2015 via Hootsuite
LG: Some respond, others don't: 'the mother of all biomarker projects' Shows Lawrence mut freq plot #AGBT15
10:26am February 27th 2015 via Hootsuite
LG: DNA/RNA: of particular interest due to immunotherapy. Shows melanoma tumor; interior region of clearing #AGBT15
10:25am February 27th 2015 via Hootsuite
LG: Shows nice WES-only signal - but does the fusion occur via chromoplexy? Redid analysis on both sides, found ERG cognates #AGBT15
10:24am February 27th 2015 via Hootsuite
LG: To assess - mentions Kristina Giorda and Mirna Jarosz from 10x - WGS vs WES TMPRSS2-ERG fusion from VCaP Prostate line #AGBT15
10:22am February 27th 2015 via Hootsuite
LG: Of interest - pull down exonic DNA w/phasing into surrounding introns; thus rearrangements easily pulled. #AGBT15
10:21am February 27th 2015 via Hootsuite
LG: Puts up a 10X Genomics slide - 100kb region from 1ng DNA; linked exonic reads. Random priming w/barcodes in pL volumes #AGBT15
LG: No obv. way to do this other than WES; already targeted is difficult enough to interpret. #AGBT15
10:20am February 27th 2015 via Hootsuite
LG: PTEN observed 10/60 freq; disrupted by chromoplexy, invisible to current panels. What implications for #precisionmedicine? #AGBT15
10:19am February 27th 2015 via Hootsuite
LG:Busy slide from Baca et al Cell 2013 http://t.co/kEg0N5IEnw Cancer genes often disrupted by chromoplexy #AGBT15
10:18am February 27th 2015 via Hootsuite
LG: DNA and RNA; pharmacodynamics, splice and fusion isoforms, and accout for tumor heterogeneity #AGBT15
10:17am February 27th 2015 via Hootsuite
LG: Next: 'ideal' profiling, ID all major categories of somatic var: incl. complex rearrangements. 'Beyond targeted but not WGS' #AGBT15
10:16am February 27th 2015 via Hootsuite
LG: Application of state-of-the art tech: targeted panels, CanSeq (CSER grant) for WES to oncologists #AGBT15
10:15am February 27th 2015 via Hootsuite
LG: Another example - response/resistance determinants may be hetergeneous. (same Wagel paper) #AGBT15
10:14am February 27th 2015 via Hootsuite
LG: A case of resistance to combined RAF/MEK inh - Wagel Cancer Disc '14 http://t.co/5NVjQ4FJVr #AGBT15
10:13am February 27th 2015 via Hootsuite
LG: RAF/MEK inh - the long tail of drivers detailed here in Nature Med '14 http://t.co/tXE2TtM6Gl #AGBT15
10:12am February 27th 2015 via Hootsuite
LG: Idea of liquid biopsy (Note: Cynvenio liquid biopsy blog http://t.co/MYOMToe0s5 ) #AGBT15
10:10am February 27th 2015 via Hootsuite
LG: Exceptional responders - goal is new therapeutics and combinations agains molecularly defined tumors #AGBT15
10:08am February 27th 2015 via Hootsuite
LG: Future trials can be designed; some still aspirational, others in place now. Genotype to Phenotype; reversed too #AGBT15
LG: Shares a figure "Engine of Cancer Precision Medicine" from his 2013 JCO review http://t.co/TYmfweUJqy #AGBT15
10:07am February 27th 2015 via Hootsuite
.@CIgenomics "And this is not a joke."
10:05am February 27th 2015 via Hootsuite in reply to
LG:Shares story of last year he shared a joke. Twitter sent it worldwide, of course he heard about it later. (No jokes today.) #AGBT15
10:05am February 27th 2015 via Hootsuite
Levi Garraway, Dana Farber. Genomic Frontiers in Cancer Precision Medicine #AGBT15
10:04am February 27th 2015 via Hootsuite
EA:Q:NLP for EHR's? A:Emerging technology, yet a degree of manual curation is req'd. #AGBT15
EA: From the HGP to 1M genomes: the end of the beginning. Precision oncology, PGx, inf disease. "Boundless possibilities" #AGBT15
9:59am February 27th 2015 via Hootsuite
EA:His own work - MyoKardia, Gilead for longQT syndrome. Feb 28 Rare Disease day, collab w/Bill Gahl NHGRI http://t.co/JUuv8ftTws #AGBT15
9:57am February 27th 2015 via Hootsuite
EA:'Practice precision medicine' - presidential reference to this CFTR paper NEJM 2011 http://t.co/4zwxV5rDNP #AGBT15
9:56am February 27th 2015 via Hootsuite
EA: 'we need to share and connect': Phenotips, GenomeConnect, Matchmaker Exchange, Rare Genomics Inst #AGBT15
9:54am February 27th 2015 via Hootsuite
