Tweets from web

Q: Take into acct strand bias? #ampeurope2018 Bonnert: Many automatically removed but for one mutation in question a manual component

6:29am May 2nd 2018 via Twitter Web Client

Q: Does their literature citations get weighted? #ampeurope2018 Bonnert: Yes they do weight and other factors (drug approval)

6:27am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Bonnert: Standards for minimum thresholds, and what rules to establish. Working w/data impt, assessing real/not real

6:24am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Bonnert: Battle4 TERT in context of NSCLC pathogenic in this context. Battle5: have TP53 that is called germline

6:22am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Bonnert: And their local re-alignment of reads, not seen in population databases.

6:16am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Bonnert: Actionability, pathogenicity. Goes through each sample. Battle1: Tier 2C. Battle2: CDKN2A del was not in aligned BAM

6:16am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Bonnert: There is a need for standards: like min depth, target region vs reportable regions.

6:12am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Bonnert: Imported FASTQ, align, call, filter <5% VAF. After QCI: added sample Dx, tumor cell %

6:10am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Bonnert: HGMD, and Ingenuity Pathway Analysis. QCI works on ACGM/AMP, AMP/ASCO/CAP guidelines/Rx

6:09am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Bonnert: The goal is a clear report. Reality: is complex pipeline scripts, datasources, dataformats.

6:07am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Tim Bonnert QIAGEN - not a clinical geneticist as a disclaimer. QCI interpret 'for illustration and educational use'

6:06am May 2nd 2018 via Twitter Web Client

Hage #ampeurope2018 If known data comes back; if unknown will be manually curated and come back in. A partnership with N-of-One

6:04am May 2nd 2018 via Twitter Web Client

Q: Report doesn't show FDA trials? Import back in? #ampeurope2018 Hage: that is the plan, to get an xml file back to add in.

6:03am May 2nd 2018 via Twitter Web Client

#ampeurope2018 If you use Agilent panels, aligner/caller pushes directly in. "Is it free to use? (no answer)"

6:02am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Marked CE-IVD, Class I exempt in US, Class I in AUS

5:56am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Shows summary table of all 5 Battle samples; sample 4 has potential signficance. N-of-One partnership: manually curated vars

5:56am May 2nd 2018 via Twitter Web Client

#ampeurope2018 'all-in' approach to calling, or 'consensus calls between aligners' more restrictive.

5:54am May 2nd 2018 via Twitter Web Client

#ampeurope2018 COSMIC, CIViC, ClinVar, their own MVL database. Check for coding effect (stop loss/gain), or splice site mut

5:49am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Called 221 vars, narrowed to 18; then took 500x readdepth and quality threhshold. Can change reference.

5:47am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Any kind of VCF, platform agnostic. Can use various callers. Interprets SNV, CNV, indels, SVs.

5:44am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Decision support across applications (from inh, carrier screen, germline cancer, somatic cancer). Across assay types

5:44am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Agilent to start: Elias Hage: Alissa Interpret is the newest Cartagenia Workbench. A reporting tool.

5:43am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Battle1/5 labeled datasets: .bed, 5 FASTQ, 5 BAMs. Sr tech Ron van Marion, bioinformatics Niels Krol.

5:41am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Asked for var's, annotation, AF, interpret of vars/pathogenicity on 5 tiers, and whether clonal or subclonal

5:38am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Aimed at clonal/subclonal mutations (not on low level <5% VAF), data generated by Ion Torrent 5XL platform

5:38am May 2nd 2018 via Twitter Web Client

#ampeurope2018 5 indep tumor samples, routine FFPE 'nothing special', analyzed conventionally. Tumor type, and tumor cell %

5:37am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Elias Hage Agilent, Tim Bonnert QIAGEN, Greg Tyrelle @gtyrelle from Thermo Fisher are the participants.

5:36am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Battle of the Bioinformatics Pipeline: background is managing, filtering, reporting data. Asked companies to help

5:35am May 2nd 2018 via Twitter Web Client

A2 Figdor: #ampeurope2018 We still don't know at what point T790M level in ctDNA would be the right time to switch.

5:24am May 2nd 2018 via Twitter Web Client

Q: Best time to change Rx? Lemoine: #ampeurope2018 Critical questions - if ctDNA rises, is it relevant? Doing CT imaging, T790M to change Rx

5:24am May 2nd 2018 via Twitter Web Client

Lemoine: #ampeurope2018 50ng input, multplex in 40 PCR/well. Metastatic lung, 100 consecutive plasma at progression.

5:10am May 2nd 2018 via Twitter Web Client

Lemoine: #ampeurope2018 Using tiled probes along ALK and EML4; only products ID'd by size and MSpec and shows result

5:07am May 2nd 2018 via Twitter Web Client

Lemoine: #ampeurope2018 Wanted daily practice: at Dx, at tumor progression, to monitor. Unpredictable breakpts, 150bp amplicons

5:04am May 2nd 2018 via Twitter Web Client

Lemoine: #ampeurope2018 RT-PCR not practical - 30% FN. RNA-Seq: large panels that needs high cost, expertise, large amt of input

5:02am May 2nd 2018 via Twitter Web Client

Lemoine: #ampeurope2018 No info on variants, unable to analyse all vars. IHC is the protein, deps on Ab, and results variable

5:00am May 2nd 2018 via Twitter Web Client

Lemoine: #ampeurope2018 Gold std is FISH: but laborious, not suitable to volume; no automation; consumes expertise

4:59am May 2nd 2018 via Twitter Web Client

Lemoine: #ampeurope2018 Prop of ALK vars could dep on ethnicity: few studies on non Asiatic cohorts. https://t.co/5mm9z4Qx9h

4:58am May 2nd 2018 via Twitter Web Client

Lemoine: #ampeurope2018 Gene fusion biomarkers have analytical difficuties; many new gene fusions like TMPRESS2. Few targeted.

4:55am May 2nd 2018 via Twitter Web Client

Lemoine: #ampeurope2018 Shows workflow - Stg IV NSCLC, if ALK-EML4, if EGFR, or PDL1. Either FFPE tissue or cfDNA

4:52am May 2nd 2018 via Twitter Web Client

Lemoine: #ampeurope2018 Shows effect of 3rd-gen TKI's; shows OS fig from '16 https://t.co/vprtqXnGVy

4:50am May 2nd 2018 via Twitter Web Client

#ampeurope2018 Antoinette Lemoine (APHP Univ Paris INSERM) ALK-EML4 fusions in ctDNA in lung cancer patients in the clinical practice

4:49am May 2nd 2018 via Twitter Web Client

van Schaik: #ampeurope2018 '17 a nat'l 'cell-free DNA day'. Will do another one in Utrecht, 14 June '18. https://t.co/mTjcQeoDUB website

4:45am May 2nd 2018 via Twitter Web Client

van Schaik: AR-V7 and PCa resp to hormone trtmt: PFS exosomes may be more sens than cfDNA #ampeurope2018

4:43am May 2nd 2018 via Twitter Web Client