Bijwaard #NGDx18 Pre-analytical is part of the assay. Assay selects target population. Analytical perf: contrived samples, factors, etc.
12:15pm August 22nd 2018 via Twitter Web Client
Bijwaard #NGDx18 Pre-analytical factors 'are key that will kill an application'. Representative variant approach, s… https://t.co/v45kXw3J7T
12:13pm August 22nd 2018 via Twitter Web Client
Bijwaard #NGDx18 liquid biopsy intended to drive Rx. Analytical validation, under challenging conditions, clin vali… https://t.co/7gQbdfpCRv
Bijwaard #NGDx18 Only 2 approved to-date - EXACT for CRC in stool, and cobas EGFR Mutation Test v2.
12:12pm August 22nd 2018 via Twitter Web Client
Bijwaard #NGDx18 She works mainly with companion Dx. '14 guidance https://t.co/6SWJacBvzf
12:11pm August 22nd 2018 via Twitter Web Client
Karen Bijwaard (FDA) #NGDx18 Considerations with liquid biopsy in vitro diagnostic tests
12:09pm August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 Refers to Newman et al https://t.co/4AyY0oBuA7 probably this reference to CAPP-Seq, and monitor multiple variants
12:05pm August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 Describes monitoring post-Rx as the 'killer app' for ctDNA analyses. Only need to see some vars, not all
12:03pm August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 Illustrates graphically the scale of signal to noise - very effective. (a tiny dot). Shows data for… https://t.co/mL0MK6DLTA
12:01pm August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 chart / data for this 0.1% AF data available here: https://t.co/OUR9CrZOwH
12:00pm August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 Titrating the input mass and detecting 0.05% - 50 ng at 200M reads gets near 100% sens. 30ng only 70% sens at 200M reads
11:58am August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 Shows 100% sens at 0.5% AF and 'strong sensitivity' for 0.1% AF
11:57am August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 Assay conversion: of course higher is better; want at least 3 copies to reliably detect.
Lovejoy #NGDx18 Input: 30ng has 9K GEq from a 4mL plasma draw. At 0.1% AF, 9 mutant copies. 10 ng is only 3 copies, 1 ng is only 0.3 copies
11:55am August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 AVENIO cfDNA: problems of limited input, background noise, different mutations.
11:54am August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 Shows SNV, indel, fusion (all 5% VAF) and CNV (down to 5 copies) PPV >99%.
11:53am August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 Can adjust input mass as a function of quality. 99% of sampls have >90% of positions with LOD of 5%.
11:52am August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 Their quality check: real-time qPCR w/2 different sizes, on ratio correlates w/increase depth, and decreasing error rate
11:51am August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 Shows 12 different substitution, spike of C-T and G-A, before/after damage repair. About 2-fold reduction in error
11:50am August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 Their sample prep- 2h, no Xylene, bead-based cleanup. These tumor tissue kits 'currently under dev'… https://t.co/Ib7M3rkRle
11:49am August 22nd 2018 via Twitter Web Client
Lovejoy #NGDx18 Reviews the three different panels, challenges w/FFPE; they include DNA repair, and offer a quality check.
11:48am August 22nd 2018 via Twitter Web Client
Alex Lovejoy (Roche) #NGDx18 Complementary detection of somatic variants from tumor tissue and plasma samples using AVENIO analysis kits
Papadopoulos #NGDx18 May include add'l markers - methylation, other NAs, metabolites, add'l proteins.
11:45am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 Shares limitations - controls were healthy individs, further validation of algorithms needed,… https://t.co/6xaXqq9DgL
Papadopoulos #NGDx18 8 cancer types, increasing target size reach a plateau. So about 55 amplicons, w/high protein… https://t.co/dH5gxRJEC1
11:44am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 But combined with ctDA, Stg I-II, doubled the sens. CancerSEEK: '18 Science https://t.co/UHbX6MNxqB
11:39am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 KRAS in ctDNA: 30% sens (66/221) <2 molecules / mL in 15/66 (23%) Thus include proteins - even… https://t.co/iu0s972
11:38am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 Now to include protein biomarkers: a multi-analyte test. '17 PNAS https://t.co/rLsYE6JFl3
11:37am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 Lays out rationale of Safe-SeqS along with BEAMing '14 ref https://t.co/vWHFySH2FD Not every c… https://t.co/q9WTo4tsyZ
11:35am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 '100% of Stg IV cancers start out as Stg I' Rx work better in early cancers.
11:32am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 Early detection: they know 'it works' 5y survival - 91% localized vs distant (~20%). Even for… https://t.co/IDFL6WH5nX
Papadopoulos #NGDx18 Now a NZ / AU interventional study called Dynamic n=450, stg II colo-rectal cancer, ongoing
11:31am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 Shows data of ctDNA as a maker for recurr after surgery. Post-chemo (elective) also ctDNA posi… https://t.co/9JT1cNxUdp
11:30am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 ctDNA is a dynamic biomarker. https://t.co/PwcllFFYdl https://t.co/rTXnVPsGfd
11:28am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 Shows difference between seq error (artifact) vs 'supermutant' (consisten mutation signal per barcode).
11:26am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 Lays out Safe-SeqS, using UID and can detect a 0.01% MAF '11 ref https://t.co/0EHBeNpmTM
11:24am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 somatic muts (SNV and indels); illustrates needle in haystack w/digital PCR in '99 (Vogelstein… https://t.co/GEYWiOpb0y
11:21am August 22nd 2018 via Twitter Web Client
Papadopoulos #NGDx18 Earlier detection MRD and screening: reviews need that vast majority of DNA is not tumor DNA;… https://t.co/4BEBsxETaW
11:19am August 22nd 2018 via Twitter Web Client
Nick Papadopoulos (Hopkins) #NGDx18 Non-invasive early detection of cancer
11:18am August 22nd 2018 via Twitter Web Client
Q: Different types of FFPE? Amts? Montagna #NGDx18 Not different tumor types yet, 1-3 curls.
10:13am August 22nd 2018 via Twitter Web Client
Montagna #NGDx18 Acknowledges Julie La Liberte of Takara. Q: Have done AmpliSeq? A: Next up.
10:12am August 22nd 2018 via Twitter Web Client
Montagna #NGDx18 200uL whole blood data, buccal swab, library efficiency shown. Takara's Thru-Plex (Rubicon) also tested from FFPE
10:07am August 22nd 2018 via Twitter Web Client
Montagna #NGDx18 Rheonix: 4.5h, have magnets, no difference between autom and manual methods. Nextera DNA Flex - no normalization, adapted.
10:05am August 22nd 2018 via Twitter Web Client
Montagna #NGDx18 Selling to food and beverage markets, and working with Illumina library prep. Univ Buffalo, using… https://t.co/9rb3yetshq
10:01am August 22nd 2018 via Twitter Web Client
Montagna #NGDx18 Liquid handler, reagent carts, tips. Cartridge reagents driven by pumps underneath. Have CMOS dete… https://t.co/Z3WUuejwvh
10:00am August 22nd 2018 via Twitter Web Client
Montagna #NGDx18 Orig dev for sample-to-answer with PCR. They dev a CARD cartridge technology. 22 targets, 24 sampl… https://t.co/lMe0d2XwNM
9:58am August 22nd 2018 via Twitter Web Client
Richard Montagna (Rheonix) #NGDx18 Combined and fully automated DNA isolation and NGS library prep
9:57am August 22nd 2018 via Twitter Web Client
Q: What protocol for automated purification? Tsui #NGDx18 QIAsymphony, 2x Streck, typically 10 mL plasma. Evaluatin… https://t.co/fW8VrGWknz
9:55am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 Explains integration with OncoKB, explains EDRN, SPDIA, CANCER-ID ongoing efforts w/standardization
9:53am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 Any change to the protocol they have to validate, positive controls across extraction runs. MSK-ACCESS… https://t.co/eSmEXV7s6J
9:50am August 22nd 2018 via Twitter Web Client
