Nusbaum: Not one quest - proposing five quests: cost, length, accuracy, speed, speed, detecting base modifications #AGBT17
12:50pm February 15th 2017 via Hootsuite
Nusbaum: "We are living in the golden age of sequencing". But he is nervous . '03 Collins paper calling for the $1K genome #AGBT17
12:49pm February 15th 2017 via Hootsuite
Chad Nusbaum (Dir Broad Technology MA) The future-history of NGS #AGBT17
12:47pm February 15th 2017 via Hootsuite
Beechem: switch to live feed #AGBT17 and shows sample, and flow cell https://t.co/kRShNoA6fs
12:46pm February 15th 2017 via Hootsuite
Q: Homopolymers? Beechem: For targeted, know what the regions are. Can use blocking oligos to cover these areas. And can stack deck #AGBT17
12:44pm February 15th 2017 via Hootsuite
Beechem: They've been able to do DNA, RNA, short, long-reads, cancer panel, FFPE, no amp, tissue. #AGBT17
12:42pm February 15th 2017 via Hootsuite
Beechem: "I call this fast forwarding" (This is way cool!) Will be talking later with more on the chemistry. #AGBT17
12:40pm February 15th 2017 via Hootsuite
Beechem: Targeted phased long reads: you 'control the cards' - you can look at specific regions that are blocked via hyb to probe #AGBT17
12:39pm February 15th 2017 via Hootsuite
Beechem: Shows ordered reads (simultaneous labels on the same molecule). Able to look at phased results, w/3kb spacing #AGBT17
12:38pm February 15th 2017 via Hootsuite
Beechem: With repeat hexamers, can go to two locations; able to compare DNA and RNA efficiency (very close, RNA is slightly better) #AGBT17
12:36pm February 15th 2017 via Hootsuite
Beechem: Shows data down to 1ng of RNA input. #AGBT17
Beechem: Can sequence RNA and DNA simultaneously (!) Shows DNA and RNA spots. #AGBT17
12:35pm February 15th 2017 via Hootsuite
Beechem: Notes there is no enzymology or polymerase error. The final floor 'may be lower'. Shows RNA direct seq #AGBT17
Beechem: 400 cycles, QV14 at 1-pass, QV22 at 2, QV27 at 3, QV31 at 4-pass, QV 40 at 5-pass. #AGBT17
12:34pm February 15th 2017 via Hootsuite
Beechem: Shows majority vote consensus calling. Shows error statistics - 150K molecules of KRAS, 425 seq probes, 11-plex #AGBT17
12:32pm February 15th 2017 via Hootsuite
RT @ScienceJill: Live-stream of @coregenomics doing full Nanostring seq workflow starting with a single FFPE curl. #agbt17 #thisisreallycool
Beechem: Wrote their own assembler, Pavel Pevzner also wrote one, gets same answers for de-novo 6-mer assembly. #AGBT17
12:31pm February 15th 2017 via Hootsuite
Beechem: #AGBT17 photo of their sequencing Hyb & Seq https://t.co/keAYUFPLuX
12:30pm February 15th 2017 via Hootsuite
Beechem: 512 cards on R1: green-yellow is 'GC'. Next deck is red-red 'TG'. Next is green yellow, 'GC'. 30sec = 'GCTGGC' x 20 million #AGBT17
12:29pm February 15th 2017 via Hootsuite
Beechem: Uniform coverage: want deep, accurate coverage in regions of clinical interest. Thus: can 'stack the deck' to get hi cov #AGBT17
12:28pm February 15th 2017 via Hootsuite
Beechem: "I make the cards, and make up the deck any way I want." Came up with eight decks of cards, 512 reporters at a time #AGBT17
12:27pm February 15th 2017 via Hootsuite
Beechem: Show raw seq images (spots with different colors). With 4096 'cards'; unique hexamers needs to separate out complementaries #AGBT17
12:26pm February 15th 2017 via Hootsuite
Beechem: Hyb of six-base probe, add collection of different probes each with 2-colors, and cycle through the 3 reporters R1-R3 #AGBT17
Beechem: Reading two bases for R1, then two more bases for R2, then two more for R3. Six bases read per cycle. Shows busy slide #AGBT17
12:24pm February 15th 2017 via Hootsuite
Beechem: 4^6 combination of six bases; need 4096 with every base combination. Encode ID of each di-base 'pair'. Two color reporter #AGBT17
12:23pm February 15th 2017 via Hootsuite
Beechem: Reading six bases; last year reported at #AGBT16. Now doing <100bp probes. Detail on bases 1-6, connected to R1-R3 #AGBT17
12:22pm February 15th 2017 via Hootsuite
Beechem: 2000nm large nCounter barcodes; shrunk to 20-50nm in size, cycling reactions 'in seconds' #AGBT17
Beechem: Capture is 5' and 3' bound to flow-cell. Biotinylated on one end, second probe also brought down via Strepavidin/biotin #AGBT17
12:21pm February 15th 2017 via Hootsuite
Beechem: For clinical sequencing: FFPE melting, remove particulates via filter, then apply to sequencer. #AGBT17
12:20pm February 15th 2017 via Hootsuite
Beechem: No enzymology: no library amplification, cluster generation. Can use FFPE, lysates, blood, tissue sample types #AGBT17
12:19pm February 15th 2017 via Hootsuite
Beechem: Wanted to go from FFPE to targeted sequencing to <1h w/<15min hands-on time. Enables long- and short-reads simultaneously #AG
12:18pm February 15th 2017 via Hootsuite
Beechem: Will talk about the why, how and what next. His own history - before NanoString in '12 was at Life Tech '00-'12. #AGBT17
12:17pm February 15th 2017 via Hootsuite
@coregenomics and Michael Rhodes of @nanostringtech showing live video starting an FFPE prep at #agbt17 https://t.co/C7B4BbEpXj
12:16pm February 15th 2017 via Hootsuite
Beechem: He too James Hadfield @coregenomics and will show a live feed (!) of him sequencing. Shows a slide of the workflow #AGBT17
12:14pm February 15th 2017 via Hootsuite
Beechem: "We're going to do a crazy thing. I've done a lot of PCR etc., and we've erased all that stuff" #AGBT17
12:12pm February 15th 2017 via Hootsuite
NanoString Workshop:Joe Beechem (R&D) Hyb & Seq technology: a no amp, no library, single molecule sequencer designed for the clinic
Levin: PTCHD1 muts found in humans w/autism, attn deficit, similar to mice KO. '16 ref https://t.co/6mSzSYtOk2 #AGBT17
10:09am February 15th 2017 via Hootsuite
Levin: Shows role of TRN between cortex and thalamus - attention, sensory processing, sleep. All disrupted in psych disorders #AGBT17
10:08am February 15th 2017 via Hootsuite
Joshua Levin (Broad MA) Single cell profiling the thalamic and reticular nucleus (TRN) implicated in schizophrenia and autism #AGBT17
10:07am February 15th 2017 via Hootsuite
(Many Q's relate to how work can be expanded, no further data.) #AGBT17
10:06am February 15th 2017 via Hootsuite
RT @ScienceJill: Emma Teeling of @BatLabUCD - Pretty sure this is the best Twitter avatar ever! #agbt17 https://t.co/PUbdtqY98c
RT @timp0: "Bonferroni correction, the murderer of all decent data" - ET about gene evolution in bats for telomere maintenance #agbt17
10:01am February 15th 2017 via Hootsuite
Teeling: Next looking at 50+ samples for whole transcriptome from 0-5 years. Acknowledges groups in Germany, France, Portugal #AGBT17
10:00am February 15th 2017 via Hootsuite
Teeling: Looked at other telomere-assoc'd genes. didn't find any genes evolving under positive selection. Divergence: ATM, SETX #AGBT17
9:55am February 15th 2017 via Hootsuite
Teeling: Telomerase expression in bats? Why don't bats get cancer? Looked for TERT expression via RNA-Seq, undetected #AGBT17
9:53am February 15th 2017 via Hootsuite
Teeling: Humans, badgers, seals, chimps: telomeres all shorten w/age. Found populations - 60y of data on bats, studied smpls #AGBT17
9:52am February 15th 2017 via Hootsuite
Teeling: Uses qPCR for long and short telomeres, related to cT. Age and length ' in 45 individuals 'do not shorten w/age' #AGBT17
9:50am February 15th 2017 via Hootsuite
Teeling: Looking at telomeres, and blood transcriptome. Telomere analogy - a shoelace aglet as it wears down... #AGBT17
9:49am February 15th 2017 via Hootsuite
Teeling: Fed mealworms, wing membrane regenerates quickly. Have 3K wing punctures. Able to do population pedigree #AGBT17
9:48am February 15th 2017 via Hootsuite
Teeling: Know locations, catch same individuals, a big 'sock' to have the fly down (i the castle), moved to boxes. Wing membrane #AGBT17
9:47am February 15th 2017 via Hootsuite
