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
Lin: #ampeu18 Looking for 1 mut; a stochastic process. Shows chart from #AACR18 poster 4542 https://t.co/lTU9waP3Kp
4:06am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Can go down to 0.005% at SNV, at 7-10mL plasma. 0.01% for cfDNA VAF at 90% sens. Spec at >99.5%
4:04am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Uses Streck (glass) and extraction/library prep are proprietary. Effic. is critical.
4:03am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 choice of mutants - want low background rate, spec cancer types that make sense for the type of cancer.
4:02am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Muts that not necessarily actionable; but rather the first driver + passengers (a signature, clonal mutations, ('clonotype'?)
4:01am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Their workflow: collect tumor, do WES, custom indiv-spec assays. Collect blood at 0,3,6,9 mos, extract, seq
4:00am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 For metastatic Rx - measuring effect of drugs. Signatera: looking at MRD, recurr monitoring, and Rx response
3:59am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Another Q, can you predict resp to neoadjuvant Rx? For Surveillance - imaging, symptoms often too late.
3:56am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Question - for bladder cancer, can you avoid surgery, by detecting mutations that arise early during tumor evol?
Lin: #ampeu18 Their Signatera (RUO) focus on ctDNA for monitoring, not early detection or Rx selection.
3:55am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Did work with Swanton; recent bladder work reported #AACR18 GenomeWeb writeup ($) https://t.co/5OnMK857r7
3:52am April 30th 2018 via Twitter Web Client
Lin: #ampeu18 Done over 1M NIPT; >800 empl, shows fastest growth of any NGS-based test (by quarterly vol). Many labs in EU.
C. Jimmy Lin (CSO Natera) #ampeu18 Personalized Liquid Biopsy: Applications in Colorectal, Bladder, Breast, Lung and Beyond
3:50am April 30th 2018 via Twitter Web Client
Babayan: #ampeu18 Better selection, perhaps smaller fragments? Rosenfeld's work here at CRUK.
3:47am April 30th 2018 via Twitter Web Client
Q: Eval of preanalytic var's w/yield, high sensitivity? Babayan: #ampeu18 Cohen paper great step twrds screening; e… https://t.co/RNvtmptV4E
Q: Comment on CTC shedding? Babayan: #ampeu18 Theories around tissue of origin, less space from lung vs liver.
3:44am April 30th 2018 via Twitter Web Client
Q: Any rec's for collection variables for ctDNA? Babayan: #ampeu18 Goal is to come up with a std recommendation dep on the goal
Babayan: #ampeu18 CTCs for recurrence; they migrate to marrow, but what is the 'wake-up call'? Relapse may be many years later.
3:41am April 30th 2018 via Twitter Web Client
Q: Goals - what for detection? Monitoring? Resist? Babayan: #ampeu18 Depends. Early-stage: ctDNA makes sense, CTCs hard to detect.
Q: CTCs vs ctDNA? Babayan: #ampeu18 Depends on the question posed; complementary approaches.
3:38am April 30th 2018 via Twitter Web Client
Babayan: #ampeu18 Impt, intensive collaboration. Founded, organizing the European Liquid Biopsy Society. Also May 3… https://t.co/uQukitP9aR
3:36am April 30th 2018 via Twitter Web Client
Babayan: #ampeu18 MicroRNAs fig from https://t.co/QhyVvD6WcQ Many kits - QIAseq, NanoString, TaqMan, Toray 3D, miRNA-Seq, miRCURY
3:34am April 30th 2018 via Twitter Web Client
Babayan: #ampeu18 Transfix unpubl data on 50 spiked SK-MEL26 cells - good for 3 days, cp to EDTA for CTCs.
3:32am April 30th 2018 via Twitter Web Client
Babayan: #ampeu18 Evidence: to use of CellSave for both cfDNA and CTCs. Shows unpubl data cp EDTA vs Transfix
3:31am April 30th 2018 via Twitter Web Client
Babayan: #ampeu18 EDTA vs. CellSave: blood cells preserved up to 96h. Dive's work '16 https://t.co/9rNrtzkL1w shows… https://t.co/CgfrA8dcMh
3:30am April 30th 2018 via Twitter Web Client
Babayan: #ampeu18 Another set of difficulties: how about collection, preservation? PaxGene, Streck, CellSave, EDTA, Norgen, Roche...
3:29am April 30th 2018 via Twitter Web Client
Babayan: #ampeu18 Cp Cellsearch and see results and variability. Used for std of analysis. Can use 1 sample, sep both MNC and plasma
3:28am April 30th 2018 via Twitter Web Client
Babayan: #ampeu18 Doing diagnostic leukopheresis (DLA) for CTC enrichment. Shows ex of ring trial: DLA product div, dist.
3:27am April 30th 2018 via Twitter Web Client
Babayan: #ampeu18 Shows side-by-side chart from '16 ref https://t.co/pFoX7ieCcA Cp Cellsearch and Parsortix
3:26am April 30th 2018 via Twitter Web Client
Babayan: #ampeu18 CellSearch: CD45 exclusion marker. Independent of marker: size, or deformability: Parsortix (mis-spoke on prior tweet)
3:25am April 30th 2018 via Twitter Web Client
Babyan: #ampeu18 Lots of methods for CTC - Parsortix, Siemens, ClearCell, CellSieve are several of label-dep ones
3:24am April 30th 2018 via Twitter Web Client
Babyan: #ampeu18 40 partners; 3 working groups (CTCs, ctDNA, miRNA). https://t.co/fiWOZGnBRD Ring trials: diff comparisons
Babayan: #ampeu18 CANCER-ID - technical eval of methods, SOP est, clinical validation for NSCLC and HER2res mBC
3:22am April 30th 2018 via Twitter Web Client
Babayan: #ampeu18 Preanalytical variables that affect results https://t.co/ZLawV7lsgA
3:22am April 30th 2018 via Twitter for iPhone
Babyan: #ampeu18 Advances - points to CancerSEEK from Hopkins Almost 100% detection in Ov, https://t.co/UHbX6MNxqB
3:21am April 30th 2018 via Twitter Web Client
