Zhao: Pursuing all 4 areas: early det, post-surgery/during trtmt, prostics, late-stage pts #TRICON
11:16am March 11th 2016 via Hootsuite
Zhao: For 6-12 copies, 80% detection, 10-20 copies 87%, >20 copies 100%. (6-10 copies is 0.1%) #TRICON
11:15am March 11th 2016 via Hootsuite
Zhao: Shows sens. down to 0.001 (unclear if this is %). At 2.5 copies, 47% detection rate, 0 false pos. Poisson pred: 60% #TRICON
11:14am March 11th 2016 via Hootsuite
Zhao: Detection by nt position for CYP2C19 SNV: showing 0.02% signal (2/10,000 sens) cp 'regular' method (noise from 0.05-1%) #TRICON
11:13am March 11th 2016 via Hootsuite
Zhao: Showing 0.1% - 1% range for KRAS of ddPCR against their NGS-method, good linearity #TRICON
11:11am March 11th 2016 via Hootsuite
Zhao: Points to M Snyder's 2016 Cell tissue-of-origin paper https://t.co/1xuScpWySw histogram of size #TRICON
Zhao: Compares read depth for 3K unique copies: 30K-60K depth vs 10K for their method #TRICON
11:09am March 11th 2016 via Hootsuite
Zhao: Ligation efficiency of 10ng cfDNA is 10-30%; since circularization is intramolecular, efficiency >90% #TRICON
11:08am March 11th 2016 via Hootsuite
Zhao: (NB: what she calls concatenation is actually circularization then rolling-circle amplification.) Cp typical ligation: 10-30% #TRICON
11:07am March 11th 2016 via Hootsuite
Zhao: Concatemer error correction: as tandem repeats. Repetitive variation in the tandem seq's. (Circligation + RCA) #TRICON
Zhao: Concatenates cfDNA, uses NGS-based detection w/0.02% sens, applies error correction, 0.0001% spec (1/1M) 2 copies / 10K copies #TRICON
11:05am March 11th 2016 via Hootsuite
Zhao: challenges: ng qty, low signal/noise, and error rates of both seq and enzymes. AccuraGen's Firefly approach #TRICON
11:04am March 11th 2016 via Hootsuite
Zhao: Starts by review of adv: diverse clinical utility. Screening, treatment selection / prognosis, MRD, evaluation/monitoring #TRICON
11:02am March 11th 2016 via Hootsuite
Grace Zhao (AccuraGen) An ultra-accurate system for cancer mutation detection in circulating cell-free DNA from plasma #TRICON
10:58am March 11th 2016 via Hootsuite
Q: Reg strategy of equivalence; proving validity wrt CEA? Clin trial design? Krishnan :in brief, CEA doesn't cover 100% of CRC pts #TRICON
10:44am March 11th 2016 via Hootsuite
Krishnan: Bioanalyzer 'trailing peak' tends to smear, much lower in abundance, looking for signal there #TRICON
10:42am March 11th 2016 via Hootsuite
Krishnan: Isolates w/o dilution. First assay is treatment response. Claims at QIAGEN prep shears cp to theirs, seeing higher MW DNA #TRICON
Krishnan: Sample prep for exosomes, compared to original Nature ref (a few hours instead of 2d) https://t.co/spKbRsMie4 #TRICON
10:39am March 11th 2016 via Hootsuite
Krishnan: Able to pick up Glypican-1 from cancer exosomes, data from Panc ca +, Colon ca neg; both CD63+ #TRICON
10:37am March 11th 2016 via Hootsuite
Raj Krishnan (Biological Dynamics) Tracking of circulating cfDNA from plasma for treatment response monitoring #TRICON
10:36am March 11th 2016 via Hootsuite
Study Shows Oncotype DX and PAM50 Breast Cancer Tests Disagree on Intermediate Risk Group | GenomeWeb ($) https://t.co/Ug5E66B4Xt
10:30am March 11th 2016 via Hootsuite
Genetic Counselor Highlights Importance of Ongoing Variant Classification Review at ACMG | GenomeWeb https://t.co/SLF9yjEWB3
9:18am March 11th 2016 via Hootsuite
RT @moorejh: #PrecisionMedicine requires reliable genome sequencing https://t.co/cz2mdGaSuk #genomics
8:25am March 11th 2016 via Hootsuite
RT @carlzimmer: Gleevec: miracle drug, economic nightmare. https://t.co/LXQci4FQc5
10:00pm March 10th 2016 via Hootsuite
Impending Actions on Laboratory Developed Tests (LDTs) Webinar - YouTube courtesy ACMG https://t.co/ts4uN0PgEf
9:05pm March 10th 2016 via Hootsuite
Grosu:Organ-spec isolation of cfDNA as markers? Future? Paweletz: Blood samples come in from cancer pts. 1 case: may have helped #TRICON
7:38pm March 10th 2016 via Hootsuite
Sanker: Offer focused panel of ddPCR approach; also MALDI prognostic. NGS reflex to go onto clinical trial #TRICON
7:37pm March 10th 2016 via Hootsuite
Grosu:Q:Will tech co-exist or NGS rule all? Patel:Applications for both; following known mut over time, PCR adequate, sens, fast #TRICON
7:36pm March 10th 2016 via Hootsuite
Q:What's the ideal volume? Patel: 5-10mL Metastatic pts will have enough where only 1mL plasma #TRICON
7:33pm March 10th 2016 via Hootsuite
Q:Report of absolute copies? Paweletz: Field is going back-and-forth. AF vs copies/mL still unsettled. #TRICON
7:32pm March 10th 2016 via Hootsuite
Grosu: Std of sample collection comes from NIPT, well-established processes for plasma collection #TRICON
7:30pm March 10th 2016 via Hootsuite
Q: Cp serum to plasma? Patel:Some release of DNA during clotting, higher background, any analysis sensitivity suffers #TRICON
7:26pm March 10th 2016 via Hootsuite
@crankyNGS This was a paper of another barcoding method I wasn't aware of, to suppress errors from NGS for ctDNA detection.
7:22pm March 10th 2016 via Hootsuite in reply to crankyNGS
Paweletz: For prospective trials, what is the spec/sens, but also what is the outcome? The gold std - going for all mutations #TRICON
7:15pm March 10th 2016 via Hootsuite
Paweletz:EGFR is reimbursed, others not. Q:T790M? A:Risk of false-positive, unclear benefits (studies ongoing) #TRICON
7:12pm March 10th 2016 via Hootsuite
Where are we today? Patel: Resistance mon. has clear adv.; Paweletz:used to guide clinical decisions, first prospective publ coming #TRICON
7:08pm March 10th 2016 via Hootsuite
Clinical implementation of ctDNA (Panel) including Dr. Patel (Yale), Dr. Paweletz (Dana Farber), Dr. Sabita Sankar (Biodesix) #TRICON
7:05pm March 10th 2016 via Hootsuite
Harkins: Data shows cfDNA with MAF 1% - 14%. #TRICON
7:01pm March 10th 2016 via Hootsuite
Harkins: 10mL draw, ave plasma 3.5mL, ave cfDNA 3.45 ng/mL #TRICON
7:00pm March 10th 2016 via Hootsuite
Harkins: Only 5ng input; not all 'healthy' controls are healthy for methylation (obesity, other conditions) #TRICON
6:59pm March 10th 2016 via Hootsuite
Harkins:GC% coverage plots are clearly better with single-stranded method. Highlights Dennis Lo's PNAS methylation paper #TRICON
Harkins: Using methylation: they use single-strand technology, shows trad method and random primer causing loss and bias #TRICON
6:57pm March 10th 2016 via Hootsuite
Harkins: And correlation to survival: freq down to 0.1%; looked specifically for point mutations (manual inspection w matched tumor) #TRICON
6:56pm March 10th 2016 via Hootsuite
Harkins:Mt Sinai data of tumor-normal pairs of ctDNA; table of time-course tumor vs cfDNA: some neg, others drop, others show up #TRICON
6:55pm March 10th 2016 via Hootsuite
Harkins: All at 10ng, single-tube format. Key metric: coverage uniformity; theirs is >95%. Shows favorably against AmpliSeq #TRICON
6:52pm March 10th 2016 via Hootsuite
Harkins: All included (except SPRY beads), many diff panels. TP53, 56G oncology, Sample_ID (for fingerprinting), BRCA1/2, CFTR, PGx #TRICON
6:51pm March 10th 2016 via Hootsuite
Harkins: Point mutations in cfDNA: Accel-Amplicon tech. gDNA, FF, FFPE, cfDNA - very similar profiles of % amplicons coverage #TRICON
6:50pm March 10th 2016 via Hootsuite
Harkins: Duplicated at Baylor - high duplication rate of 20%, they can see down to 5% (conservative in their calling) #TRICON
6:49pm March 10th 2016 via Hootsuite
Harkins: For 1% cfDNA for WES, controls for point mutations won't help. 1% titration of 3 different ethnicities - 0.5%-1.5% detect #TRICON
6:48pm March 10th 2016 via Hootsuite
Harkins: Illustrates GC% by coverage of cfDNA - PCR-free shows much better. Shows insert size histogram, 170 and 340bp minor peak #TRICON
6:46pm March 10th 2016 via Hootsuite
