August 2018

Garlick #NGDx18 FDA guidelines for germline testing; here's the document https://t.co/QjBAEYb0Rc from April 2018

3:03pm August 21st 2018 via Twitter Web Client

Russell Garlick (SeraCare) and Gayatry Mohapatra (UIC) #NGDx18 Achieving compliance w/ NG quality control for NGS

3:01pm August 21st 2018 via Twitter Web Client

Zook #NGDx18 Q: With long reads, any interesting new things? A: focus is on accuracy. 1/2 of SVs are in tandem repeats.

3:00pm August 21st 2018 via Twitter Web Client

Zook #NGDx18 Also representative examples (different variants in different genome contexts), and comprehensive evaluation.

2:39pm August 21st 2018 via Twitter Web Client

Zook #NGDx18 What does 'gold standard' mean? Accurate (high confidence - comparison is FP/FN in your method, not theirs).

2:39pm August 21st 2018 via Twitter Web Client

Jarosz #NGDx18 Lays out the signal spreading problem with cross-talk. Addressed and published '18 https://t.co/HEslDjnjMi

12:54pm August 21st 2018 via Twitter Web Client

Jarosz #NGDx18 Illumina has authorized IDT to offer 8- and 10bp indexes for 384-plex or 7000-plex sample indexing.

12:47pm August 21st 2018 via Twitter Web Client

Jarosz #NGDx18 Shows usefulness of Unique Dual Index (UDI) for germline; for low-level 1% AF, UDI+UMI. 0.1%: ds molecular barcode

12:45pm August 21st 2018 via Twitter Web Client

Jarosz #NGDx18 Shows P5 - i5 index - seq primer site - insert - seq primer site - i7 index - P7 illustration.

12:41pm August 21st 2018 via Twitter Web Client

Jarosz #NGDx18 200-600bp size fragments; need adapter 'handles'; illus 'Y' adapters, stub adapters w/transposase.

12:40pm August 21st 2018 via Twitter Web Client

Jarosz #NGDx18 Library prep to target enrichment (w/xGen universal blockers, xGen lockdown probes). Focus: universal adapters

12:38pm August 21st 2018 via Twitter Web Client

Mirna Jarosz (IDT) #NGDx18 High-performance NGS adapters for dual indexing and NGS workflow

12:37pm August 21st 2018 via Twitter Web Client

Ghazani #NGDx18 Of n=71 for PancSeq: 30% somatic contribution, 4% germline, 63% both germline and somatic.

12:30pm August 21st 2018 via Twitter Web Client

Ghazani #NGDx18 Germline: find aberrant mutations in ~20%. All have family history, all referred to high-risk genetics clinic.

12:23pm August 21st 2018 via Twitter Web Client

Ghazani #NGDx18 One case PDAC w/liver mets. Had BRAF in-frame del, Trametinib. cfDNA showed polyclonal resist, changed Rx, deceased.

12:21pm August 21st 2018 via Twitter Web Client

Ghazani #NGDx18 Their landscape: KRAS, TP53, CDKN2A, SMAD4 top 4. 92% clin relevant. n=70 '18 ref https://t.co/2EqCiiYyYE

12:19pm August 21st 2018 via Twitter Web Client

Ghazani #NGDx18 PancSeq: metastatic PDAC (pancreatic ductal adenocarcinoma). Look at CN, SNV, cfDNA. Look at both somatic and germline.

12:17pm August 21st 2018 via Twitter Web Client

Arezou Ghazani (Dana Farber) #NGDx18 The value of germline genome beyond cancer risk assessment

12:14pm August 21st 2018 via Twitter Web Client

Cristofanilli #NGDx18 I-CURE: PhII, single-arm Pembro + carboplatin in pts with CTCs >=5 and MBC. To provide the best possible treatment.

11:22am August 21st 2018 via Twitter Web Client

Cristofanilli #NGDx18 Defines Clinical Utility: a favorable balance of benefity to harm (DFS, PFS, OS)

11:10am August 21st 2018 via Twitter Web Client

Cristofanilli #NGDx18 CTCs <5 do 'well overall' '14 ref https://t.co/oi7n0kIosn

11:09am August 21st 2018 via Twitter Web Client

Cristofanilli #NGDx18 Shows MDA work fo rel's of CTCs to type of systemic Rx. Kaplan curves: CTCs <5 vs >=5: PFS and OS SWOG0500

11:09am August 21st 2018 via Twitter Web Client

Massimo Cristofanilli (Northwestern) #NGDx18 Dissectin liquid biopsy in MBC: CTCs, ctDNA and CAMLs to eval innate immunity

11:05am August 21st 2018 via Twitter Web Client

Clarke #NGDx18 Non-invasive tech: raman scattering, sweat test in '16 ref https://t.co/7QzxWFy12T

9:24am August 21st 2018 via Twitter Web Client

Clarke #NGDx18 Breath VOCs: molecularly imprinted polymer, binding event changes electrochem feedback

9:22am August 21st 2018 via Twitter Web Client

Clarke #NGDx18 SPR: label-free, an E-M wave at the surface. Sensitive to interface https://t.co/CawRi821BL

9:19am August 21st 2018 via Twitter Web Client

Clarke #NGDx18 Mass Spec at POC, via a paper-based system.: https://t.co/PFmysbTXsz Already in use for screening https://t.co/Ee5TS7ab5t

9:17am August 21st 2018 via Twitter Web Client

Clarke #NGDx18 Multiple waveguides, can do absorbance measurement in propagation loss. Also surface label detection

9:15am August 21st 2018 via Twitter Web Client

Clarke #NGDx18 What's next: Some may never work out. Maverick: waveguide w/evanescent tail; silicon photonics sensor chip.

9:12am August 21st 2018 via Twitter Web Client

Clarke #NGDx18 Disposability? Lenses, cartridges, dongles: can a swab be both collection and analytical?

9:10am August 21st 2018 via Twitter Web Client

Clarke #NGDx18 Capillary sampling: depending on the analyte, may or may not be the appropriate sample. Expectations of end-users as well.

9:09am August 21st 2018 via Twitter Web Client

Clarke #NGDx18 The smaller the device, the more rugged it needs to be. Specimen integrity: Quality, integrity checks for the sample.

9:07am August 21st 2018 via Twitter Web Client

William Clarke (Hopkins) NGDx18 New POCT devices in the near future: what will POCT look like?

9:06am August 21st 2018 via Twitter Web Client

Aurora-Garg #NGDx18 (NB - while the TMB is log-scale, the whisker plots show pretty wide spread, and a slight bump in mean TMB values.)

9:02am August 21st 2018 via Twitter Web Client

Aurora-Garg #NGDx18 Shows TMB between responders, non-responders, some signal between HPV+/-.

9:01am August 21st 2018 via Twitter Web Client

Aurora-Garg #NGDx18 TMB historically assessed via WES; 'a lot of effort going on with panels as surrogates' - FMB, TMO, PGDx

8:58am August 21st 2018 via Twitter Web Client

Aurora-Garg #NGDx18 18 gene sig '15 ref https://t.co/d80JIWrB6p

8:57am August 21st 2018 via Twitter Web Client

Aurora-Garg #NGDx18 n=255, 22C3 PD-L1 IHC; GEP score via NanoString n=237 of 18 genes; TMB via WES in blood/normal n=258. Eval HPV status

8:53am August 21st 2018 via Twitter Web Client

Aurora-Garg #NGDx18 MMR defect also leads to MSI. (Both approved for Keytruda).

8:52am August 21st 2018 via Twitter Web Client