April 2018

Palma: #ampeurope2018 Precision med today: genetic research and testing is the gateway to its promise; NGS is all about results in time.

9:44am April 30th 2018 via Twitter Web Client

Palma: #ampeurope2018 Shows K-M curves from publ. like this one https://t.co/FFnXbKRmqh of NSCLC and effectiveness

9:42am April 30th 2018 via Twitter Web Client

John Palma (Roche): #ampeurope2018 Clinical research applications in CRC. Will have more data at upcoming #ASCO18

9:41am April 30th 2018 via Twitter Web Client

Droege: #ampeurope2018 Oct '18 for tumor tissue with same genes for matched tissue / ctDNA analysis. 5-day workflow, 'end-to-end'

9:40am April 30th 2018 via Twitter Web Client

Droege: #ampeurope2018 SW does clustering and database integration w/COSMIC, TCGA db's.

9:39am April 30th 2018 via Twitter Web Client

Droege: #ampeurope2018 Soes very good sens at 20M reads at 0.5% AF across 3 products, 30ng or 50ng inputs

9:38am April 30th 2018 via Twitter Web Client

Great to find at #ampeurope2018 the first https://t.co/ugGjrmD6Mf commercial presence - real-time PCR and NGS for clinical, research markets

9:37am April 30th 2018 via Twitter Web Client

Droege: #ampeurope2018 Expanded: for progression; targeted for profiling pre-Rx. Shows integrated Digital Error Suppression (iDES)

9:36am April 30th 2018 via Twitter Web Client

Droege: #ampeurope2018 3 panels: Targeted 17 genes 81kb; Expanded 17 + 60 = 77 192kb; Surveillance 180+17 = 197 genes

9:36am April 30th 2018 via Twitter Web Client

Droege: #ampeurope2018 Optimized for NextSeq 500; coming up with analysis pipeline, spec report.

9:35am April 30th 2018 via Twitter Web Client

Droege: #ampeurope2018 Intended RUO, 4mL plasma, research subjects lung, CRC. All 4 mut classes in one panel; can do 16-plex on ILMN

9:34am April 30th 2018 via Twitter Web Client

Droege: #ampeurope2018 Limited input molecules in ctDNA; background reduction (they use error suppression), coverage - they have 3 designs

9:33am April 30th 2018 via Twitter Web Client

Marcus Droege (Roche) Technical overview of Avenio ctDNA analysis RUO #ampeurope2018

9:32am April 30th 2018 via Twitter Web Client

Greenawalt: #ampeurope2018 ID'd 4/40 JAK1 LoF muts w/previously-treated pts.

8:50am April 30th 2018 via Twitter Web Client

Greenawalt: #ampeurope2018 Shows results presented at #AACR18 (online https://t.co/roRLSiUyaj )

8:49am April 30th 2018 via Twitter Web Client

Greenawalt: #ampeurope2018 40 pts, WES, RNA-seq; muts called in paired T/N samples. Response was similar.

8:48am April 30th 2018 via Twitter Web Client

Greenawalt: #ampeurope2018 JAS1/2 LoF in preRx samples from CheckMate-142. PhII, non-randomized, mCRC or recurrCRC. dMMR/MSI-H >1 prior R

8:46am April 30th 2018 via Twitter Web Client

Roberts: #ampeurope2018 Increased LAG-3 mRNA exp post-Rx. Co-localization of LAG-3 w/MHC II may serve as checkpoint activation mechanism

8:42am April 30th 2018 via Twitter Web Client

Roberts: #ampeurope2018 '16 PNAS https://t.co/TaBWliRzwm

8:42am April 30th 2018 via Twitter Web Client

Roberts: #ampeurope2018 IgG4 Reltinimab is against LAG-3. Expression: correlated w/immune, inflamm markers by TCGA

8:41am April 30th 2018 via Twitter Web Client

Q: Why only missense for ML? Roepman: #ampeurope2018 Fixed for the trial, now want to include indels, fusions too.

8:34am April 30th 2018 via Twitter Web Client

Q: How did they validate tumor content? Roepman: #ampeurope2018 GIAB cell line mixed, but still more work to do on their method.

8:33am April 30th 2018 via Twitter Web Client

Roepman: #ampeurope2018 Can weed out structural variants in BRCA1; a clear benefit to their approach.

8:32am April 30th 2018 via Twitter Web Client

Roepman: #ampeurope2018 No more Rx option, >200pt receive 'off-label' to-date in DRUP. Large coverage, Barcode for Life, SUTC credits

8:30am April 30th 2018 via Twitter Web Client

Roepman: #ampeurope2018 Info about DRUP >500 pts enrolled (NB https://t.co/dvCbprZ5vi ) 30-35% benefit

8:29am April 30th 2018 via Twitter Web Client

Roepman: #ampeurope2018 DRUP - off-label study, showed ex of prostate ca after 7 lines of Rx! WGS shows high ML -> I-O in DRUP

8:28am April 30th 2018 via Twitter Web Client

Roepman: #ampeurope2018 They call TMB Mutational Load: used for eligability in 'DRUP' study ML >140

8:27am April 30th 2018 via Twitter Web Client

Roepman: #ampeurope2018 Then derive a Tuor-Adjusted Variant Freq (TAF). Have also derived MSI and TMB almost 100% concord shown

8:25am April 30th 2018 via Twitter Web Client

Roepman: #ampeurope2018 Report CNV, copy-gain and loss, SVs (NB: Hartwig dataset here: https://t.co/UVZbT46Pbh apply for access)

8:23am April 30th 2018 via Twitter Web Client

Roepman: #ampeurope2018 Has ~2,800 metastatic pt data, pan-cancer, uniform processing from biopsy to database

8:21am April 30th 2018 via Twitter Web Client

Roepman: #ampeurope2018 Hartwig Medical Found. - WGS-based pt report, database for learning healthcare system.

8:21am April 30th 2018 via Twitter Web Client

Paul Roepman (Amsterdam, The Netherlands) #ampeurope2018 Comp. Molecular Char of Metastatic Cancer Using WGS – a Dutch National Initiative

8:20am April 30th 2018 via Twitter Web Client

Q: Newer content helpful? de Voer: #ampeurope2018 Only V5 mapping to compare, haven't looked at it.

7:03am April 30th 2018 via Twitter Web Client

Q: NTHL1 recessive, what about carriers? de Voer: #ampeurope2018 Tumors are analyzed from biallelic, now looking. But low #'s, further study

7:01am April 30th 2018 via Twitter Web Client

de Voer: #ampeurope2018 Want more accurate var detection from FFPE; would like strand-spec capture of FFPE to remove artifacts

6:59am April 30th 2018 via Twitter Web Client

de Voer: #ampeurope2018 Concludes: FFPE WES feasible; helps in their NTHL1 work on signatures, mutation evolution.

6:58am April 30th 2018 via Twitter Web Client

de Voer: #ampeurope2018 Onto NTHL1 deficiency, and mutational processes in extracolonic tumors. Going after mutational signatures

6:57am April 30th 2018 via Twitter Web Client

de Voer: #ampeurope2018 Shows surprising lack of concordance between XT HS and V5 SureSelect; but high stringency helps explain (!)

6:54am April 30th 2018 via Twitter Web Client

de Voer: #ampeurope2018 Var absent from in-house DB, or <0.01% in ExAC or gnomAD; <20% or >80% VAF excluded. QC>200

6:52am April 30th 2018 via Twitter Web Client

de Voer: #ampeurope2018 Now doing WES at 80x coverage; compares regular FFPE to HS XS FFPE to germline.

6:51am April 30th 2018 via Twitter Web Client

de Voer: #ampeurope2018 UMI-labeled input - median 244bp; library median insert about 290bp. First 16 sample results reported

6:48am April 30th 2018 via Twitter Web Client

de Voer: #ampeurope2018 Extended to do SureSelect WES on FFPE. Before lib prep, add UMIs and PCR amplify. DIN scored, 10-200ng input

6:46am April 30th 2018 via Twitter Web Client

de Voer: #ampeurope2018 They study familiar, rare cancers and predisp. NTHL1 suspected. '16 ref https://t.co/S6v5mIPzg6

6:44am April 30th 2018 via Twitter Web Client

de Voer: #ampeurope2018 Shows fig from '15 ref https://t.co/3feWMDeVt9 on types of FFPE damage

6:42am April 30th 2018 via Twitter Web Client