Pfeifer: We worry a lot about cellularity. And library complexity. #FDANGSWorkshop
10:00am February 25th 2016 via Twitter Web Client
Schetter: Topic 2: What specific concerns around sample processing of FFPE? What level of validation? Isolation methods? #FDANGSWorkshop
9:57am February 25th 2016 via Twitter Web Client
Schetter: For vendors, what metrics are needed? Berger: coverage, yet terminology may cause confusion #FDANGSWorkshop
9:55am February 25th 2016 via Twitter Web Client
Pfeifer: May not necessarily be an extra step, could be add'l analysis #FDANGSWorkshop
9:54am February 25th 2016 via Twitter Web Client
Pfeifer: Contamination an impt point - haplotype analysis. At NIH trials - genotyping needed (a 'provenance step') #FDANGSWorkshop
Berger: They look at tumor-normal pairs, look for sources of contamination; it's 'not all artifact' #FDANGSWorkshop
9:53am February 25th 2016 via Twitter Web Client
Berger: Enrichment technologies (hyb vs amplicon) have different nomenclature ('duplicates') need to consider #FDANGSWorkshop
9:51am February 25th 2016 via Twitter Web Client
Michael Rossi (Emory U): Discussion has been DNA-centric. Assessment of RNA too; hard cutoffs are not practical #FDANGSWorkshop
Aisner: Situations w/poor prob. of library success - hard decision to go to lower-complexity test. Many times: in parallel #FDANGSWorkshop
9:49am February 25th 2016 via Twitter Web Client
Luthra: With limited sample, they will try. Have to look at the 'beginning to end' product #FDANGSWorkshop
9:48am February 25th 2016 via Twitter Web Client
Raja Luthra (MD Anderson): 15% of cases used fail due to DNA conc input requirement; relaxing it they go down to 5%. #FDANGSWorkshop
9:46am February 25th 2016 via Twitter Web Client
Berger: Because the data could be beneficial to the patient. #FDANGSWorkshop
9:45am February 25th 2016 via Twitter Web Client
Berger: They move forward even if after pre-analtyical QC, they will still sequence. If LOD is only 15%, still get data #FDANGSWorkshop
Michael Berger (MSKCC): they run a 400-gene panel (10K samples); all around post-seq QC. Assay shown to be robust #FDANGSWorkshop
9:44am February 25th 2016 via Twitter Web Client
Pfeifer: The library complexity metric - addresses complexity of the sample. But still doesn't capture upstream var #FDANGSWorkshop
9:42am February 25th 2016 via Twitter Web Client
Pfeifer: They (WashU) look at % reads mapped, % reads on-target, % unique reads (library complexity measurement) #FDANGSWorkshop
9:41am February 25th 2016 via Twitter Web Client
Panel discussion: Pfeifer: 'We take a "proof in the pudding approach" - look at the sequence metrics after the input' #FDANGSWorkshop
9:39am February 25th 2016 via Twitter Web Client
Aaron Schetter: What pre-analytical QC to eval DNA/RNA prior for NGS oncology panels? QC metrics? When not needed? #FDANGSWorkshop
9:38am February 25th 2016 via Twitter Web Client
Aisner: Points out the weakness of macrodissection, risk of false negatives, unless careful microdissection occured #FDANGSWorkshop
9:29am February 25th 2016 via Twitter Web Client
Aisner: 'This should not be over-prescribed' - shows slides of melanoma, difference between resolutions #FDANGSWorkshop
Aisner: Enrichment commentary: will vary widely. Microdissection, 'this is the practice of medicine'. #FDANGSWorkshop
9:28am February 25th 2016 via Twitter Web Client
Aisner: Organ tissue: Is skin and lung really that different? May look at core tissue, and ECM / other var's separately #FDANGSWorkshop
9:25am February 25th 2016 via Twitter Web Client
Aisner: For ERBB2 to stipulate cold ischemic time - has caused a 'lot of tumult' in the medical practice context #FDANGSWorkshop
9:23am February 25th 2016 via Twitter Web Client
Aisner: Transfer media, temp, cold ischemic time, target organ, procurement method: FDA may not be able to stipulate #FDANGSWorkshop
9:22am February 25th 2016 via Twitter Web Client
Dara Aisner (U CO) #FDANGSWorkshop From tissue acquisition - how assessed, enriched, extracted, assessed, and quantified
9:21am February 25th 2016 via Twitter Web Client
Pfeifer:Bioinformatic approaches? in-silico datasets to evaluate pipelines. #FDANGSWorkshop
9:20am February 25th 2016 via Twitter Web Client
Pfeifer: How to look at different VAFs, sequence artifacts possible, but still not comprehensive. #FDANGSWorkshop
9:19am February 25th 2016 via Twitter Web Client
Pfeifer: Brings up constructs / cell lines - what's the appropriate mix of mutations? (@SeraCare's approach) #FDANGSWorkshop
9:18am February 25th 2016 via Twitter Web Client
Pfeifer: Points to Boland's '13 WES cross-platform comparisons Venn diagam #FDANGSWorkshop
Pfeifer: DNA quality https://t.co/LYdMwlkCnc #FDANGSWorkshop measuring complexity as a fn of input amounts. 10ng - may have lost info
9:17am February 25th 2016 via Twitter Web Client
Pfeifer: Assessment of tumor cellularity. 2 labs, same specimens, but different results b/c of enrichment (microdissection) #FDANGSWorkshop
9:15am February 25th 2016 via Twitter Web Client
Pfeifer: The DNA you do get - lower (usable) quanity. What people don't look at: Add'l cytology specimens (FNAs) #FDANGSWorkshop
9:14am February 25th 2016 via Twitter Web Client
Pfeifer: 1 week of fixation: no 'major difference' in % of mapped reads. Increased coverage var, lower unique reads #FDANGSWorkshop
9:13am February 25th 2016 via Twitter Web Client
Pfeifer: The reality: high concordance, only 1/10kb differences; but 100x higher depending inter-tumor heterogeneity #FDANGSWorkshop
9:12am February 25th 2016 via Twitter Web Client
Pfeifer: Also chemical artifacts, transitions (C -> U) rate of 0.0015 and 4x more common than fresh #FDANGSWorkshop
9:11am February 25th 2016 via Twitter Web Client
Pfeifer: Clinical FFPE tissue: Formalin fixation #FDANGSWorkshop https://t.co/oK0Q0CLWuT and looking at GC content
9:10am February 25th 2016 via Twitter Web Client
Pfeifer: #FDANGSWorkshop Points to this 2010 Nature fig https://t.co/cmT9as4zoE on heterogeneity and sampling
9:08am February 25th 2016 via Twitter Web Client
Pfeifer: Not only quant and qual of DNA, but 'something small called library complexity' #FDANGSWorkshop
9:06am February 25th 2016 via Twitter Web Client
Pfeifer: Starts on pre-analytical steps 'before step 1' of NGS. Gross processing, tissue proc, histopath review; DNA pur #FDANGSWorkshop
Schetter: Intro panelists John Pfeifer (WashU), Dara Aisner (U CO) M. Berger (MSK), R Luthra (MDA), M.Rossi (Emory U) #FDANGSWorkshop
9:05am February 25th 2016 via Twitter Web Client
RT @FDADeviceInfo: Public Workshop - Next Gen Sequencing-Based Oncology Panels, 2/25/16 https://t.co/6Or0w4Hxc4 #fda #medicaldevice
6:55am February 25th 2016 via Twitter Web Client
RT @SeraCare: #IT staffing considerations for the #NGS #laboratory https://t.co/Cjkjr423qL https://t.co/lpQZhjqlXU
6:08am February 23rd 2016 via Twitter Web Client
RT @SeraCare: Going to @TriConference in SF? We'll meet you there! Click here for more info: https://t.co/S0TfL1DSOb https://t.co/CMeqwyQI…
5:43am February 23rd 2016 via Twitter Web Client
RT @SeraCare: #BRCA mutation testing increasing in younger women https://t.co/Xsss1UPHLK https://t.co/cns7WhfMej
5:38pm February 17th 2016 via Twitter Web Client
RT @OmicsOmicsBlog: How could I have possibly thought I'd have resolve to put off summarizing ILMN CEO Jay Flatley's #agbt16 talk? https://…
9:24am February 16th 2016 via Twitter Web Client
RT @Jason_Gammack: "One of these kids is doing his own thing..." #AGBT16 https://t.co/g686PWtIXo
4:08pm February 13th 2016 via Twitter Web Client
RT @jgreid: Impressive new balloon-based sequencing technology from inGen is really a game changer here in Orlando #AGBT16 https://t.co/zcp…
3:26pm February 13th 2016 via Twitter Web Client
RT @SeraCare: First #MERS autopsy reveals critical information https://t.co/9kQyg2XYd8 https://t.co/a6PLibU7k9
11:17am February 8th 2016 via Twitter Web Client
RT @BookOfTamara: The Klementinum (Prague) https://t.co/z3oc7QhpnG
3:51pm February 6th 2016 via Twitter Web Client
RT @BookOfTamara: George Peaboby Library, at @JohnsHopkins https://t.co/38R0r5kvJ0
