Neumaier: #ampeu18 Could there be endogenous or exogenous decay markers, to track degradation? Nucleic acids, proteins?
5:58am April 30th 2018 via Twitter Web Client
Neumaier: #ampeu18 Shows funny result '06 paper: zero bases reported, 'sequence not in GenBank' (!!) (it was reported as complement seq)
5:57am April 30th 2018 via Twitter Web Client
Neumaier: #ampeu18 Shows results from this '06 https://t.co/76zrwzWjbH for Sanger Dx - both technical and medical interpretation scores
5:54am April 30th 2018 via Twitter Web Client
Neumaier: #ampeu18 RfB genotyping: cp labs from '02 to '15. Also case-based proficiency for sequencing, come up w/a report
5:52am April 30th 2018 via Twitter Web Client
Neumaier: #ampeu18 Shows gel across 40 labs '98 ref https://t.co/f7j7OCnGVw Just for pur, 2-plex PCR
5:49am April 30th 2018 via Twitter Web Client
Neumaier: #ampeu18 Ratio of 366 bp fragments: ratios from 0.1x to 1.4x. Five different methods used for purification. 366bp and 779bp 2-plex
5:48am April 30th 2018 via Twitter Web Client
Neumaier: #ampeu18 5 of 85 programs are molecular; molecular genetics groups 1/2. 40 labs w/EDTA plasma: very diff results
5:47am April 30th 2018 via Twitter Web Client
Michael Neumaier (Heidelberg Univ, Germany) #ampeu18 Improving the Proficiency of Molecular Diagnostics by External Quality Assessment (EQA)
5:44am April 30th 2018 via Twitter Web Client
Q: RNA? Deans: #ampeu18 Distribution on dry ice a challenge, on the list.
5:42am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 Consensus guidance for best practice cfDNA being prepared. 350 labs now involved, second pilot EQA in '18
5:39am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 Measurement of DNA yield 'all over the map'. Measurement of AF also plenty of variation there.
5:38am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 Shows of n=31 labs, plenty of FPs, FNs at 5%, 1% AF for RAS. For EGFR 1.79 ave score, better than RAS
5:37am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 Looked at EGFR in lu ca, KRAS/NRAS in CRC. Shows results of genotyping; 1.58 score w/2.00 possible 'considered low for EQA"
5:32am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 Collab in IQN Path: standard testing of ctDNA in plasma. 4 providers Italy (AIOM), EQMN, EQA and UK NEQAS. Det feasibility.
5:27am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 Pharma: only use commercial ref mats only when validating assays.
5:25am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 Engineered materials may introduce scars, endogenous underlying mutations, and cost. But fit for EQ… https://t.co/lSufqGoS9P
Deans: #ampeu18 Disadv: high-quality DNA doesn't reflect testing lab reality; low DNA recovery, fixation problems
5:24am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 And consistent levels of protein in samples. Also variety in samples: rare muts, different muts impt for Rx, scalability
5:22am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 Lays out adv of using ref materials: heterogneity (limitation of tissue, assurance of uniformity, tested&confirmed varia
5:21am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 Held a survey summer '17, examples of challenges w/obtaining and using ref materials for FFPE. Examples of EQA's materials
5:17am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 Reduce adverse events and costs incurred by errors or poor quality. Improve interaction between stakeholders.
5:14am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 Also control samples. EQA directly impacts quality of care; GT errors, analytical errors to improve quality
5:12am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 Scope: tissue-based dx, prog, predictive biomarkers in pathology. Publ, guidelines, training, best practices
Deans: #ampeu18 Improving quality of clin biomarker testing in pathology. China, CAP, Australia now members
5:10am April 30th 2018 via Twitter Web Client
Deans: #ampeu18 IQNpath is int'l quality network for Pathology. The problem of 'scheme-hopping' to get 'easy' EQAs
5:09am April 30th 2018 via Twitter Web Client
Sandi Deans (UK NEQAS Edinburgh) #ampeu18 The Role of Reference Materials for Improving Quality of Cancer Diagnosti… https://t.co/8QfAsB4uNE
5:08am April 30th 2018 via Twitter Web Client
Q: Amplification tech efficiency about 50%, can it be improved? Lin: #ampeu18 'Definitely'; enzymology, ligases use… https://t.co/evAIDWgmTq
4:44am April 30th 2018 via Twitter Web Client
Q: Vars enriched for indels, for low bckgnd? Lin: #ampeu18 Yes.
4:43am April 30th 2018 via Twitter Web Client
Q: WGS? Lin: #ampeu18 Haven't seen a lot of adv for what they want to do. They could use a broad panel, WES easy an… https://t.co/bcWz9URiz8
Lin: #ampeu18 And also unique difficulties with urine as a sample type, lots to consider there.
4:41am April 30th 2018 via Twitter Web Client
Q: Bladder ca:what about cfDNA in urine? Lin: #ampeu18 Think blood is one of many specimen types, even more impt in early-stg dis
4:40am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 A complementarity there. Able to personalize rapidly.
Q: Does WES biased against cancer? (They use ONCObeam 34-plex, EU900-EU1200 reimbursed soon) Lin: #ampeu18 Thinks BEAMing is excellent tech
4:38am April 30th 2018 via Twitter Web Client
Q: Value of larger panels? Lin: #ampeu18 Diff muts at different rates; mentioned BEAMing (sysmex-inostics), ddPCR valuable
4:36am April 30th 2018 via Twitter Web Client
Q: Cost of WES is part of that... Lin: #ampeu18 For TMB often up-front built-in. And WES is still cheaper as already enriched for tumor DNA
4:33am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Statistically: 8-plex to 10-plex needed. Need to predict clonality; 8-plex vs 16-plex similar cost.
4:32am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 It's in the sub-$1k test cost, compared to many thousands. 16-plex: want low freq muts due to stochastic, Poisson errors
4:31am April 30th 2018 via Twitter Web Client
Q: For lung, why 16 markers for lung? Cost? Lin: #ampeu18 Their test is designed to be 10-fold less cost. Amplicons, 3kb-5kb, at 100,000x
Lin: #ampeu18 Rethink the term as 'liquid biopsy' - monitoring in near-real-time, revolutionizing cancer care, and… https://t.co/fEzc9AhqR5
4:26am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 For br ca, neoadj Rx response w/UCSF, I-SPY, early det of recurr. w/Univ Leicester.
4:25am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Interesting, n=1 detected it later instead of earlier cp to imaging in CRC. Onto Breast ca: no results yet, descr approach
Lin: #ampeu18 For CRC, looked at ctDNA status after adjuvant Rx #AACR18 abs 1590 https://t.co/DT2xQuzHTx Also recur… https://t.co/lKkQvx1kuN
4:23am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 n=9 relapse, 100% sens, lead time median 128d; 0-265d range.
4:22am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Looking at ctDNA as a new way to look at bladder cancer staging. Not seen in lung or CRC.
4:16am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 n=50, 3y relapse post cystectomy clear. All the way back to Dx: pts w/o ctDNA at Dx for staging, at 800d.
4:15am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 With Aarhus, bladder cancer study reported at #AACR18 Abstr 3653 here: https://t.co/JSJKGynXnQ
4:13am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Shedding of cfDNA in lung ca - adeno much less than squamous; matters how active tumor is.
Lin: #ampeu18 Another example where 1y post-chemo relapse and mutation freq. 1 subclone Erlotinib disappeared. Other clones survived
4:09am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Shows another fig showing ctNDA analysis post-surgery, implying residual disease but clearing, no relapse 1.5y later
4:08am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Shows chart from '17 Nature https://t.co/haKNNXMMuv Can see rise of markers much earlier
4:07am April 30th 2018 via Twitter Web Client
