Daber: Intra- and Inter- also look at barcode contam; add'l runs on each NGS platform; also PhiX spike-ins #genomewebinar
11:31am April 27th 2017 via Hootsuite
Daber: Also batch 2 has a no-template control (NTC), add'l accuracy smpls. Batch 3 has inter repleciates, accuracy, NTC. #genomewebinar
11:30am April 27th 2017 via Hootsuite
Daber:Shows batch 1/2/3: Intra replictes (x3, AF10, AF20, GIAB, 3 clin DNAs near LOD); Batch 2 has inter replicates, low inpt #genomewebinar
11:29am April 27th 2017 via Hootsuite
Daber: Once AF, mut type, input: then precision and reproducibility run on top of those. How can enough samples be obtained? #genomewebinar
11:28am April 27th 2017 via Hootsuite
Daber: Also what about mutation type? Sens/Spec numbers may change. And input DNA? Another sens/spec dependency #genomewebinar
11:27am April 27th 2017 via Hootsuite
Daber: Validation of a somatic cancer panel - but are interdependent. For AF of sens/spec; some % will not detect #genomewebinar
Daber: Shows busy slide of FDA, CAP, ACMG, NYS DOH. Shows busy chart listing somatic and germline assays '12-'17 UPenn #genomewebinar
11:26am April 27th 2017 via Hootsuite
Daber: Validation: what is challenging is not knowing how many samples need to be run, what types, what steps to validate... #genomewebinar
11:25am April 27th 2017 via Hootsuite
Daber: They can thus show a certain algorithm just doesn't work; shows deletion sens by size and allele freq from '13 ref #genomewebinar
11:24am April 27th 2017 via Hootsuite
Daber: With an artificial dataset, can follow each read and see where they end up. And then iterate their informatics #genomewebinar
11:23am April 27th 2017 via Hootsuite
Daber: Wet-lab library prep, sequencing, bioinformatics: w/EGFR the bioinformatics was the problem. https://t.co/dcuUb2vPEt #genomewebinar
Daber: For the NCCN list, shows many genes where indels are not seen. (Open question - do they exist? Or just not detected?) #genomewebinar
11:21am April 27th 2017 via Hootsuite
Daber: The 15bp EGFR deletion was put into the unaligned 'trash' - never seen the mutation in the first place. #genomewebinar
11:20am April 27th 2017 via Hootsuite
Daber: Shows an IGV plot w/a missing EGFR indel. Normal control had 27K read depth, the sample had only 8K. Unmapped reads... #genomewebinar
Daber: Optimization involes tweaks to increase overall performance; easiest when a truth set of samples is held constant #genomewebinar
11:19am April 27th 2017 via Hootsuite
Daber: Technology eval requires abundant in nature and affordable. Biggest challenge: lack of control material (highlighted) #genomewebinar
11:18am April 27th 2017 via Hootsuite
Daber: Synthetic controls have most common and most complicated. Also normal - Genome in a Bottle NIST samples #genomewebinar
11:17am April 27th 2017 via Hootsuite
Daber: tech dev is 10s to 100's of real-world (RW) samples. Can also use synthetic controls as they are 'unlimited' in nature #genomewebinar
Daber: Tech eval: asking sensitivity, specificity, uniformity of coverage, how easy the workflow is, what it costs #genomewebinar
11:15am April 27th 2017 via Hootsuite
Daber: Establishing req's: what genes, targets, source material, mutation types, limit of detection, cost, TAT #genomewebinar
Daber: Add'l QC along LDT dev: tech eval (10's-100's); optimization (100's-1000's samples); analytical validation (10'-100's) #genomewebinar
11:14am April 27th 2017 via Hootsuite
Daber: Every test has its indications, its own uniqueness and needs be validated accordingly. #genomewebinar
11:13am April 27th 2017 via Hootsuite
Daber: Another (false) assumption: "RUO kit is fully dev and optimized for clinical use"; "someone has a magic checklist" #genomewebinar
Daber: But LDT's need validation. Only a handful of NGS tests are FDA cleared. Assumptions: "everything I need is in an RUO" #genomewebinar
11:12am April 27th 2017 via Hootsuite
Daber: For new labs: big difference between an FDA-cleared assay and an LDT; cleared ones only need verification. #genomewebinar
11:11am April 27th 2017 via Hootsuite
Daber: Control samples (i.e. from @SeraCare ) are 'of great value'. E.g. Tumor Mutation DNA Mix v2 AF4 LC #genomewebinar
11:10am April 27th 2017 via Hootsuite
Daber: In an ideal world - known mutations with well known and most complicated. Problem: hard to come by, esp w/new labs #genomewebinar
11:09am April 27th 2017 via Hootsuite
Daber: System 1: a truth set; if the output deviates, can look into this. Input are real-world samples, approp tissue types #genomewebinar
11:08am April 27th 2017 via Hootsuite
Daber: Starts with Wikipedia def'n of a system: connected processes leveraged to assess initial and ongoing performance #genomewebinar
Daber: Points to ENDEAR spinal muscular atrophy study, where Biogen's Ph 3 results PR here: https://t.co/RFJjrRDh0e #genomewebinar
11:07am April 27th 2017 via Hootsuite
Daber: But give different Rx depending on molecular traits (i.e. EGFR status, ALK-fusion present) #genomewebinar
11:05am April 27th 2017 via Hootsuite
RT @edyong209: Google's anti-ageing venture, Calico, is a black box @juliaoftoronto reports. https://t.co/MjEgsAr4ZC https://t.co/nUnVBDJxcv
Daber: "At the heart of precision medicine is precision diagnostics". ID of biomarkers - diverse indivs w/a phenotype... #genomewebinar
11:04am April 27th 2017 via Hootsuite
Daber: Keeping the patient in mind: LDT commercial, going through dev, validation, then launch. QC validation - other stps #genomewebinar
11:03am April 27th 2017 via Hootsuite
#genomewebinar archived here: https://t.co/fYkpKDiPmc Catalyzing Implementation of NGS-Based Tests Case Study
11:02am April 27th 2017 via Hootsuite
Bob Daber (Gnosity Consults; BioReference Labs) QC Systems to Comply with CAP, CLIA, & State Regulatory Guidelines #genomewebinar
11:01am April 27th 2017 via Hootsuite
GenomeWebinar at 11am ET Apr 27: QC Systems to Comply with CAP, CLIA, & State Regulatory Guidelines https://t.co/BHupboo3sP
10:46am April 27th 2017 via Hootsuite
NovaSeq Orders Bring Pleasant Surprises, Says deSouza - Bio-IT World https://t.co/KxcomysDhU
9:25pm April 26th 2017 via Hootsuite
The Scientists Who Tweet | GenomeWeb https://t.co/SXGthKwyzF
6:50pm April 26th 2017 via Hootsuite
This is depressing. "Parents Are Drowning in College-Loan Debt" - WSJ https://t.co/bRDymzvB6O Easy money = not good.
6:25pm April 26th 2017 via Hootsuite
Large Genomic Profiling Study Sees Mutation-Rich Tumors From Many Cancer Types | GenomeWeb https://t.co/l5uWxMoNdB
5:50pm April 26th 2017 via Hootsuite
RT @NatureNews: Reviewers' reliance on bibliometrics is resulting in risk-averse science: https://t.co/AnFvuh8lg9 https://t.co/mSqUzXTt5q
4:40pm April 26th 2017 via Hootsuite
Massive Virus Found in Sewage Plunges Biologists into Debate — NOVA Next | PBS https://t.co/yXUyONduWf
3:59pm April 26th 2017 via iOS
RT @drbachinsky: New genetic variants associated with extreme old age | Science Daily https://t.co/cwIIbYR0Zl
3:35pm April 26th 2017 via Hootsuite
Thermo Fisher Scientific Posts 11 Percent Growth in Q1 Revenues, Raises Guidance for 2017 | GenomeWeb https://t.co/E9QXyuIFDp
1:50pm April 26th 2017 via Hootsuite
How Elon Musk learns faster and better than everyone else — Quartz https://t.co/5J7YfVmAfr
12:20pm April 26th 2017 via Hootsuite
GenomeWebinar: QC Systems to comply with CAP, CLIA April 27 11am ET w/Bob Daber https://t.co/tVBBySr4gf
11:40am April 26th 2017 via Hootsuite
RT @gregsramblings: I just discovered a cool Google account feature - Assign a trustee to access to your Google account if you go dark - ht…
10:18am April 26th 2017 via Twitter Web Client
RT @spwells: Primitive human 'lived much more recently' https://t.co/48rmUjAjhf
9:25am April 26th 2017 via Hootsuite
RT @DrKhouryCDC: “I had no idea I carried a potentially fatal genetic mutation because we never talked about our family history.” https://t…
8:16am April 26th 2017 via Hootsuite
