August 2017

A pathology atlas of the human cancer transcriptome | Science https://t.co/b39utc9c3b

6:20pm August 17th 2017 via Hootsuite

Corcoran: Seeing 'convergent inhibition' to overcome diversity of resistance. fig from '15 Cancer Disc https://t.co/OU2YNgl4Qj #NGDx17

3:41pm August 17th 2017 via Hootsuite

Corcoran: Resistance may be target alteration, adaptation via feedback mechanism, or another pathway. Understanding mechanism impt #NGDx17

3:37pm August 17th 2017 via Hootsuite

Corcoran: Drug resistance remains a major clinical obstacle. '12 NEJM https://t.co/0tzbqyo1Hp #NGDx17

3:34pm August 17th 2017 via Hootsuite

Ryan Corcoran (Massachusetts General Hospital): Insights into drug resistance and tumor heterogeneity through liquid biopsy #NGDx17

3:32pm August 17th 2017 via Hootsuite

Speicher: #NGDx17 By nucleosome occupancy can determine what genes expressed '16 Nature Gen https://t.co/rN212uWYHP

3:21pm August 17th 2017 via Hootsuite

Speicher: Goes back to basic biology: plasma DNA is protected by nucleosomes. 166bp size. MNase-digested allows precise mapping #NGDx17

3:19pm August 17th 2017 via Hootsuite

Speicher: Shows data where CNV changed in 25% of pts in 6 months over course of Rx '16 Nature Comm https://t.co/2DQOhouODl #NGDx17

3:16pm August 17th 2017 via Hootsuite

Speicher: Uses TruSight rapid capture, able to detect CNV. Show responders and non-responders based upon CNV changes #NGDx17

3:13pm August 17th 2017 via Hootsuite

Speicher: Then you can find under- or over-represented tumor DNA. Inexpensive #NGDx17

3:09pm August 17th 2017 via Hootsuite

Speicher: If low - <1% ctDNA, use dPCR, Tam-Seq, CAPP-Seq. If 5-10%, use WGS. Screen is fast aneuploid screening. PCr of 20K LINE-1 #NGDx

3:08pm August 17th 2017 via Hootsuite

Speicher: Graz is famous - where Arnold Schwartznegger is from. 900 pts, over 2K samples, across cancer types. First relative ctDNA #NGDx17

3:07pm August 17th 2017 via Hootsuite

Michael Speicher (Med Univ Graz): Inferring expressed genes by whole-genome sequencing of plasma DNA #NGDx17

3:05pm August 17th 2017 via Hootsuite

Q: TAT for Avenio ctDNA assay? Diehn: 5 days. #NGDx17

3:02pm August 17th 2017 via Hootsuite

Diehn (in concluding) "detection of MRD may allow personalization of adjuvant therapy #NGDx1

3:01pm August 17th 2017 via Hootsuite

Kudlow: Est their ligation efficiency to be on the order of 90% #NGDx17

1:08pm August 17th 2017 via Hootsuite

Kudlow: Can go down as low as 1ng input. ‘Sensitive car detection to well below 1%’ #NGDx17

1:05pm August 17th 2017 via Hootsuite

Kudloq: Able to adjust calling thresholds individually on a per-mutation basis after error-correction. #NGDx17

1:04pm August 17th 2017 via Hootsuite

Kudloq: Showed SeraCare data at 1% and 0.25% with only one FP out of >200 possible calls. #NGDx17

1:03pm August 17th 2017 via Hootsuite

Kudlow: Shows systematic noise from NGS with biological noise, and after error correction. (Still lots of noise remains at 0.1%) #NGDx17

12:58pm August 17th 2017 via Hootsuite

Kudlow: Archer method measured AF's a few percentage points higher in each mutation. (i.e. PCR method 'undermeasured' low VAF) #NGDx17

12:55pm August 17th 2017 via Hootsuite

Kudlow: Took HD780 from Horizon, diluted 5% down to 1%. showed comparison to 4 KIT mutations, amplicon vs Archer methods from 15ng #NGDx17

12:54pm August 17th 2017 via Hootsuite

Kudlow: At 100bp, you go down to 21% of fragments that contain the variant of interest #NGDx17

12:51pm August 17th 2017 via Hootsuite

Kudlow: Can easily add/subtract additional genes. If ave size is 125bp, 60bp amplicon is only 53% of variant-containing fx #NGDx17

12:50pm August 17th 2017 via Hootsuite

Kudlow: Shows error correction. <1h hands-on time, libraries in less than 1d, no mastermixes (all reagent in one tube). 28 genes #NGDx17

12:48pm August 17th 2017 via Hootsuite

KudlowL Polish ctDNA ends, dA-tail, random 8mer used for error correction and mutants. Use nested PCR, symmetrical both-strand #NGDx17

12:46pm August 17th 2017 via Hootsuite

Kudlow: Often low input, high dilution of wt background. Showed figure from Bettegowda, mutation fragments per 5mL plasma #NGDx17

12:44pm August 17th 2017 via Hootsuite

Kudlow: Known for Fusion RNA assays, moved into immune repertoire and ctDNA. Short fragments resist capture by opposing primers #NGDx17

12:43pm August 17th 2017 via Hootsuite

Kudlow: ArcherDx aims to democratize NGS testing, easy-to-use kits and powerful data analysis for labs of all sizes. #NGDx17

12:42pm August 17th 2017 via Hootsuite

Brian Kudlow (ArcherDx) Increasing target spec to Reveal ctDNA from liquid biopsies by NGS #NGDx17

12:41pm August 17th 2017 via Hootsuite

Casdin: LabCorp - largest revenue, lowest multiple. Exact highest multiple due to growth. FMI high multiple. Enterprise value/Rev #NGDx17

12:28pm August 17th 2017 via Hootsuite

Casdin: Starting to see Dx industry 'swim back to the FDA first'. Exact first to do it via dual-path, now FMI #NGDx17

12:25pm August 17th 2017 via Hootsuite

Casdin: Four parts - product (support clinicians), service (drug industry enablement), approved (FA on-board), reimbursed (CMS) #NGDx17

12:24pm August 17th 2017 via Hootsuite

Casdin: LabCorp - from Covance purchase. Exact - highest valued pure Dx, serving exclusively physicians #NGDx17

12:23pm August 17th 2017 via Hootsuite

Casdin: Where is Dx/Rx today? LabCorp 30%, Invitae 10%, Exact 0%, FMI 66% (percent as biopharma revenues) #NGDx17

12:22pm August 17th 2017 via Hootsuite

Casdin: Whoa re your customers? What kind of business: lab, service, informatics? There are two markets - Rx and Dx, but one product #NGDx17

12:21pm August 17th 2017 via Hootsuite

Casdin: Shows the value is in therapeutics given the Dx part of that pie is miniscule. 'What business are you in?' #NGDx17

12:21pm August 17th 2017 via Hootsuite

Messner: When payers feel more pressure to act, they will. #NGDx17

12:18pm August 17th 2017 via Hootsuite

Messner: Big private payers are 'hanging back a little bit', closely watching Palmetto and Guardant. "I thought it a smart thing" #NGDx17

12:17pm August 17th 2017 via Hootsuite

Gandera: Feels that NGS ctDNA is ready. Kopetz: Where tissue not available; sufficient to move forward. #NGDx17

12:16pm August 17th 2017 via Hootsuite

Moderator: ctDNA ready for prime-time in NSCLC? Gandera: Approved in the US in EGFR-mut for 2y in US/EU. Q is if NGS is preferable #NGDx17

12:14pm August 17th 2017 via Hootsuite

Eli Casdin (Casdin Capital) Investment perspective #NGDx17 What's the business behind the technology? How value is viewed, product strategy

12:11pm August 17th 2017 via Hootsuite

Kopetz: At MDACC ctDNA is used where no tissue avail, before and after hi-risk surgery for MRD, before and on trtmtn with chemo resp #NGDx17

12:09pm August 17th 2017 via Hootsuite

Kopetz: ASCO17 they reported tissue and ctDNA in mCRC at 93% accuracy. 92% sens, 94% spec #NGDx17

12:02pm August 17th 2017 via Hootsuite

Kopetz: Another gap: test needed vs tissue available. For CRC: NGS of 180 genes, RNA fusion, MSI by IHC, MSI by PCR, HER IHC #NGDx17

12:01pm August 17th 2017 via Hootsuite

Kopetz: Also tumor heterogeneity. Access: 23% at MDACC for lung QNS. For mCRC, 70% chemo and surgery are different locations #NGDx17

12:00pm August 17th 2017 via Hootsuite

Kopetz: Screening, recurrence detection, metastatic disease. Utility: access to tumor, speed, rapid dynamics, resistance assessment #NGDx17

11:58am August 17th 2017 via Hootsuite

Scott Kopetz (MDACC TX) Value from the perspective of a GI oncologist #NGDx17

11:57am August 17th 2017 via Hootsuite

Gandara: Shows an example of chasing mutations in ctDNA in course of trtmt. "Plasma First" method. #NGDx17

11:57am August 17th 2017 via Hootsuite