Only 18% benefited RT @bbchealth: Cancer Drugs Fund 'huge waste of money' https://t.co/zWtgY0L5Qd

9:20am April 28th 2017 via Hootsuite

RT @Medscape: News Alert: FDA approves first new liver #cancer drug in a decade. Fully story here: https://t.co/OHifMorZbT

8:20am April 28th 2017 via Hootsuite

RT @NatureNews: Kasparov's account of the chess match that changed the world makes the ultimate distinction between man and machine: https:…

7:12am April 28th 2017 via Hootsuite

RT @aphillippy: Fun class assignment from @mike_schatz. Very similar workflow to real microbial forensics! https://t.co/WfoIltEIMs https://…

7:08am April 28th 2017 via Hootsuite

Lung Cancer Studies Yield Insight Into Tumor Evolution, Support Liquid Biopsy Potential | GenomeWeb https://t.co/WpdDGBKRW4

7:10pm April 27th 2017 via Hootsuite

RT @conradhackett: 1 in 4 Americans did not read or listen to a single book in the last year https://t.co/MGbBgeHso8 https://t.co/5PCNnnIrc3

5:10pm April 27th 2017 via Hootsuite

RT @mason_lab: @ewanbirney @mucociliary But I still like epitranscriptome for all the: mods, processes, regulation, detection, dynamics, as…

4:28pm April 27th 2017 via Hootsuite

Immunotherapy Pioneer James Allison Has Unfinished Business with Cancer - Technology Review https://t.co/iTVcclDckv

4:04pm April 27th 2017 via Hootsuite

RNA Is About to Make Personalized Medicine a Reality - Cofactor Genomics Blog https://t.co/LVEimtP0IH

3:47pm April 27th 2017 via Hootsuite

NSA Looked for 'Nefarious' Genetics Projects | GenomeWeb https://t.co/C2vRE5eTgT

2:25pm April 27th 2017 via Hootsuite

CSHL to boost sharing of global scientific research in collaboration with the Chan Zuckerberg Initiative https://t.co/U1TvivMXfv

12:05pm April 27th 2017 via Hootsuite

Garlick: Also getting digital PCR down to 0.1%, a challenge, also in a patient-like format. Info: https://t.co/RqBHXojGZU #genomewebinar

11:57am April 27th 2017 via Hootsuite

Q: What about liquid biopsy controls at low AF? Garlick:Approach is to develop DNA at the same size and AF, also encapsulated #genomewebinar

11:54am April 27th 2017 via Hootsuite

Q: Adequacy of MolDx stds? Daber: We continue to evolve in our understanding of req'ments. Want tests appropriate for pt care #genomewebinar

11:52am April 27th 2017 via Hootsuite

Q: Range of AFs may vary as much as 10%, does it range from 1-11%? Daber: 1 sample went from 4% then to 14% in a separate run #genomewebinar

11:51am April 27th 2017 via Hootsuite

Q: After validated a solid tumor test. How often to run? Daber: NYS requires controls; rec'd by others. Exome $ #genomewebinar

11:50am April 27th 2017 via Hootsuite

Garlick: Shows Levey-Jennings control plots across 4 SNVs, as well as read depth over time. #genomewebinar

11:48am April 27th 2017 via Hootsuite

Garlick: QC software focuses on the data. All the NGS data and parameters in 1 place. Details here: https://t.co/5LDTpoN60A #genomewebinar

11:45am April 27th 2017 via Hootsuite

Garlick: ctDNA and NIPT full-process formats; just launched an inherited cancer on indels in BRCA1/2, MSH2, MSH6, MLH1, PMS2 #genomewebinar

11:43am April 27th 2017 via Hootsuite

Garlick: @SeraCare has many product offerings: cancer, NIPT, germline, inf disease, Lab QC software #genomewebinar

11:42am April 27th 2017 via Hootsuite

Russell Garlick (CSO SeraCare) Reference materials and QC management software #genomewebinar

11:41am April 27th 2017 via Hootsuite

Daber: It is critical to provide highest level of test management #genomewebinar

11:40am April 27th 2017 via Hootsuite

Daber: Concludes: QC is critical throughout: build a truth set of RW and commercial samples for consistency in measuring perf #genomewebinar

11:40am April 27th 2017 via Hootsuite

Daber: Also new technician training - how many samples, neg sample, NTC. Thus control materials are needed to monitor #genomewebinar

11:39am April 27th 2017 via Hootsuite

Daber:New lot, new shipments; 6 mo machine comparison; post maintenance; new inst validations; chemistry upgrades #genomewebinar

11:38am April 27th 2017 via Hootsuite

Daber: Decided: Look at 5 critical variants (i.e. EGFR L858R, T790M) and variatnce allowed for +/- 5% allele burden #genomewebinar

11:38am April 27th 2017 via Hootsuite

Daber: Can see 0.5% variation in germline homozyghous; much higher for germline heterozyghous 3-5%. Somatic 1.5%-4% variation #genomewebinar

11:37am April 27th 2017 via Hootsuite

Daber:Shows data from a manuscript under review, an inter-lab study looking at variation of AF over time. Can plot a range #genomewebinar

11:36am April 27th 2017 via Hootsuite

Daber: Shows different precision from 20ng vs 0.5ng input. Next: ongoing 'truth controls': AF10 across time #genomewebinar

11:35am April 27th 2017 via Hootsuite

Daber: NYS was asking for acceptable ranges:hi, lo input; accuracy data in validation; new or changed instrumentation #genomewebinar

11:34am April 27th 2017 via Hootsuite

Daber: Thus a third tech may be needed. Read depth - 2000x vs 3500x? What is acceptable for changes in AFs? #genomewebinar

11:34am April 27th 2017 via Hootsuite

Daber: More complicated comparisons: PGM vs MiSeq, what variance will be allowed between technologies? What is truth? #genomewebinar

11:33am April 27th 2017 via Hootsuite

Daber: Accuracy in PCR days: a binary yes/no. In NGS - how does it perform at a lower input? What's acceptable AF variation? #genomewebinar

11:32am April 27th 2017 via Hootsuite

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

11:27am April 27th 2017 via Hootsuite

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

11:23am April 27th 2017 via Hootsuite

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

11:20am April 27th 2017 via Hootsuite

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