April 2018

de Voer: #ampeurope2018 Usually FFPE insuff; bigger challenge is fixation process damaging DNA. Deamination and crosslinking.

6:41am April 30th 2018 via Twitter Web Client

#ampeurope2018 Richarda de Voer (Radboud Univ Netherlands) Challenges with using FFPE samples for NGS

6:40am April 30th 2018 via Twitter Web Client

Bossuyt: #ampeu18 Reviews DAKO offering for IHC, and NGS from QC, library prep and automation.

6:36am April 30th 2018 via Twitter Web Client

Bossuyt: #ampeu18 Shows interesting FFPE vs HMW coverage between good and poor quality FFPE samples; amplifiability x amplicon size

6:35am April 30th 2018 via Twitter Web Client

Bossuyt: #ampeu18 FFPE considerations: need assay designed for it; 0.6 mm3, or 4-8 slices; >20 tumor cellularity; UNG removing deaminatio

6:32am April 30th 2018 via Twitter Web Client

Bossuyt: #ampeu18 Smaller panels have lower cost, fewer incidental findings, easier to implement.

6:31am April 30th 2018 via Twitter Web Client

Bossuyt: #ampeu18 AIO 'all in one' SureSelect-based. SNPs, indels, CNV and fusion from 1 sample. Using XTHS sample prep tech, UMI compat

6:27am April 30th 2018 via Twitter Web Client

Bossuyt: #ampeu18 Preferred markers KRAS, MET, BRAF not testd. Using MASTR Plus (Multiplicom). MASTR reporter software has a QC component

6:27am April 30th 2018 via Twitter Web Client

Bossuyt: #ampeu18 For NSCLC: EGFR testing, perhaps ALK/ROS fusion test w/FISH. Minimally-req'd markers: EGFR, ALK and ROS fusion, amplf.

6:25am April 30th 2018 via Twitter Web Client

Wouter Bossuyt (Agilent Product Manager, workshop) #ampeu18 Integrating NGS in a pathology workflow

6:22am April 30th 2018 via Twitter Web Client

Neumaier: #ampeu18 Shows heat-induced frag, duplex PCR w/a spec pyroseq G/A ratio (G larger, A smaller PCR prod) https://t.co/CaofWJcbUW

6:01am April 30th 2018 via Twitter Web Client

Neumaier: #ampeu18 Just measuring 260/280 w/same DNAs, and quant numbers: all over the place. Pyro seq: sensitive to amt, quality

5:59am April 30th 2018 via Twitter Web Client

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 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

5:12am April 30th 2018 via Twitter Web Client

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

Q: Vars enriched for indels, for low bckgnd? Lin: #ampeu18 Yes.

4:43am April 30th 2018 via Twitter Web Client

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.

4:40am April 30th 2018 via Twitter Web Client

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