May 2018

Figdor: #ampeurope2018 Points out in 1970 Morton described marked tumor regression, with BCG injection w/melanoma (https://t.co/zbnvcUg4yG)

2:10am May 2nd 2018 via Twitter Web Client

Figdor: #ampeurope2018 Illust the complexity of the innate and adaptive immune system: an ensemble, interactions, different in each pt

2:07am May 2nd 2018 via Twitter Web Client

Figdor: #ampeurope2018 Major difficulty: only a fx of pts respond. How will we predict who will respond - the challenge for the next decade

2:06am May 2nd 2018 via Twitter Web Client

Figdor: #ampeurope2018 Shows a K-M curve from people with lymphopenia: less immune cells, do worse '13 https://t.co/EcQH5g6Dcj

2:05am May 2nd 2018 via Twitter Web Client

Figdor: #ampeurope2018 As a novel treatment modality: Immune surveillance in '11 Science https://t.co/HsJtiD3qXR

2:04am May 2nd 2018 via Twitter Web Client

Carl Figdor (Nijmegen NE): #ampeurope2018 Immunotherapies in cancer, 21st century vaccines

2:03am May 2nd 2018 via Twitter Web Client

Nikiforova: #ampeurope2018 Credits @AMPath staff @Robyn_Temple and Mrudulla for all their hard work!

12:04pm May 1st 2018 via Twitter Web Client

Nikiforova: #ampeurope2018 '15 NEJM https://t.co/tFZsqYQ0gy

12:00pm May 1st 2018 via Twitter Web Client

Nikiforova: #ampeurope2018 WHO Grade I/II/III det by IDH1/2, then TP53 mut/loss and ATRX, then RB1. Shows K-M and difference in outcomes

11:59am May 1st 2018 via Twitter Web Client

Nikiforova: #ampeurope2018 Not only reporting vars but explanation to physician what it means.

11:41am May 1st 2018 via Twitter Web Client

Nikiforova: #ampeurope2018 Also gene exp, SNVs, indels. 112 genes, 12K hotspots, 120 gene fusion types, preoperative test.

11:41am May 1st 2018 via Twitter Web Client

Nikiforova: #ampeurope2018 PPA is % of known vars detected by NGS cp to orthogonal method. Worksheet: https://t.co/Ph28MLN7Ln

11:40am May 1st 2018 via Twitter Web Client

Nikiforova: #ampeurope2018 Est min read depth of >250 reads/amplicon or target for 5% MAF. Validation: using exact sample type.

11:33am May 1st 2018 via Twitter Web Client

Nikiforova: #ampeurope2018 Labs were all over, Larry Jennings proposed statistics (in paper), established distribution of TP, FP

11:32am May 1st 2018 via Twitter Web Client

Nikiforova: #ampeurope2018 Need to understand how the platform works, ref materials and standardizing methods. Depth for LoD determined.

11:31am May 1st 2018 via Twitter Web Client

Nikiforova: #ampeurope2018 Validation, it's long, will make highlights and observations. Majority of clin labs: targeted over WGS, WES, RNA

11:27am May 1st 2018 via Twitter Web Client

Nikiforova: #ampeurope2018 And a long process, 14-18 months. JMD Validation: https://t.co/siZw2tdgJn Reporting: https://t.co/G22oEoj6GC

11:25am May 1st 2018 via Twitter Web Client

Q: Can CITE-seq be only surface proteins? Pugh: #ampeurope2018 Currently, yes only surface to-date.

11:04am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 Concl with the Human Cell Atlas, the Chan Zuckerberg intitiative. https://t.co/Ts13bnB0gh

11:00am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 Upcoming methods - DroNc-Seq '17 Nature Methods https://t.co/x8EJboai7I And CITE-Seq https://t.co/LOmMoxTtHD

11:00am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 Combining cancer, healthy cell data highlights shared and private cellular populations.

10:52am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 Sees tumor cells, BTSC line, TIL immune cells. Treated each chr as a pathway. Inferred Chr 7, Chr 10 gain/loss

10:47am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 Large, freq loss of chr6 at scWGS, unexplained. Secret sauce is dissociation of brain tumor tissue. Shows tSNE1/2 plots

10:46am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 Glioblastomas have self-renewing cancer stem cells. Shows scRNA core set of genes, then tracked to chr6.

10:44am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 Gene sets, pathways. '17 https://t.co/LOmMoxTtHD But a lack of a reference standard set.

10:40am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 Review of challenges in scRNA analysis '15 Nat Rev Genetics https://t.co/x1z5y9TBad Many ways to readout PCA.

10:37am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 Full length can also find coding mutaitons. Baran-Gale ref compares methods. Shows fig: 3 exons vs end-reads.

10:35am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 Difference: transcript structure throughout mRNA in SmartSeq 2, only 10's of thousands. 10X does only end-reads.

10:34am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 SmartSeq2 https://t.co/sjwypWsLB2 Cheap. $2-4/cell https://t.co/lYl7UQTxWl

10:33am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 Rev on sc techniques in immunol https://t.co/STQmZGLeAE Talk only about 10X Genomics, SmartSeq2

10:32am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 Estimates of immune and stromal cell content, scored from bulk GEx data. Yoshihara et al '13 https://t.co/aV6EsrlwUx

10:26am May 1st 2018 via Twitter Web Client

Pugh: #ampeurope2018 '13 fig https://t.co/X3qRbM2NYM worked on infrastructure w/fresh biopsies with INSPIRE program, Pembro resp

10:25am May 1st 2018 via Twitter Web Client