Tweets from Hootsuite

Vasmatzis: About $3K per pt. Expects to be so much better than the current non-targeted Rx approach. Mate-Pair, WES, GEX #NGDx17

8:55am August 18th 2017 via Hootsuite

Vasmatzis: Combined w/genomic info, sounds like her2+ cancer, pt treated w/afatinib. Pt responded but had a brain met #NGDx17

8:53am August 18th 2017 via Hootsuite

Vasmatzis: RNAseq shows genes as log2 looking at set of BrCa genes. Also CD274 cp for I-O Rx. 3D model: showed afatinib strong resp #NGDx17

8:52am August 18th 2017 via Hootsuite

Vasmatzis: Did FOne test, showed rearr using their WES CNV analysis, found ERBB2 ampl. FISH showed her2 neg. #NGDx17

8:51am August 18th 2017 via Hootsuite

Vasmatzis: Starting with GBM in 4 days get 10K cells. Example of BC liver metastatic pt, started Dec '16 Feb 17 lot of data #NGDx17

8:50am August 18th 2017 via Hootsuite

Vasmatzis: Hanging drop is not an organoid, he calls it microcancer model in 3D. Lists advantages over 2D culture and mouse avatars #NGDx17

8:49am August 18th 2017 via Hootsuite

Vasmatzis: CNVs via whole exome, RNAseq for GEX. Proteomics not done now b/c it's 'too expensive'. insphero tech - 3D culture #NGDx17

8:48am August 18th 2017 via Hootsuite

Vasmatzis: Doing a lot of sequencing (mate pair, RNA, exome) will go into 3D models, avatars, isolate ctDNA, generate hypotheses #NGDx17

8:47am August 18th 2017 via Hootsuite

Vasmatzis: Could design primers, and then find the cDNA to confirm. Shows ERBB2 amplification - cholangiocarcinoma #NGDx17

8:44am August 18th 2017 via Hootsuite

Vasmatzis: '16 ref https://t.co/xXlhEqHegA shows chromoplexy. Shows ALK rearranged twice. RNASeq fusion not detected (on the 5' end) #NGDx17

8:43am August 18th 2017 via Hootsuite

Vasmatzis: Another PrCa chr 21 del, 'completely different pattern', many different examples #NGDx17

8:40am August 18th 2017 via Hootsuite

Vasmatzis: In PrCa, shows event in chr6; another w/5 different deletions across four chromosomes. Another with a huge AR gene ampl #NGDx17

8:40am August 18th 2017 via Hootsuite

Vasmatzis: Linear plot, lines show a balanced transloc between chr2/8. Red show deletions across chromosomes. #NGDx17

8:38am August 18th 2017 via Hootsuite

Vasmatzis: Shows read pileup ALK gene; 100kb windows showing copy loss/gain. Linear 2D lines vs Circos (but circos not as helpful) #NGDx17

8:37am August 18th 2017 via Hootsuite

Vasmatzis: Fusions and DNA rearr's: points to Chinnaiyan's ERG-TMPRSS2 fusions in prostate. Now uses Ion Ampliseq method #NGDx17

8:35am August 18th 2017 via Hootsuite

Vasmatzis: Shows microarray gene expression plot; heatmaps clusters GEX by tissue of origin easily. PCA separated out #NGDx17

8:33am August 18th 2017 via Hootsuite

Vasmatzis: "Is a cancer where it came from, or where it evolved to?" Path slides - recognizable to a pathologist immediately #NGDx17

8:31am August 18th 2017 via Hootsuite

George Vasmatzis (Mayo Clinic MN) Predictive biomarkers for targeted therapy #NGDx17

8:30am August 18th 2017 via Hootsuite

Blood Biopsy Reveals Unique, Targetable Genetic Alterations in Patients with Rare Cancer | Newswise https://t.co/j7zRxJKXIH

6:30am August 18th 2017 via Hootsuite

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