Precision Health: wanted to not squeeze out the genomic tech focus; still want to seed the Sept mtg, but a focus on medical apps #AGBT16
4:20pm February 13th 2016 via Hootsuite
#AGBT16 AGBT Precision Health will continue the same theme, closer to the clinic. Sept 22-24 Committed for several years.
4:19pm February 13th 2016 via Hootsuite
My three #AGBT16 blog posts: https://t.co/3KTWbncPfs https://t.co/2yK3qkDGmy and https://t.co/VLGk0caIWq Thank you everyone!
4:13pm February 13th 2016 via Hootsuite
Hill: 86% of indels (>50bp) variants were not previously observed. Shows large 130kb inversion prev unknown #AGBT16
4:10pm February 13th 2016 via Hootsuite
RT @Jason_Gammack: "One of these kids is doing his own thing..." #AGBT16 https://t.co/g686PWtIXo
4:08pm February 13th 2016 via Twitter Web Client
Hill: Added megabases of missing exon and regulatory data. #AGBT16
4:07pm February 13th 2016 via Hootsuite
Hill:Susie3 closes 94% of gorGor3 gaps. Added 164MB of euchromatic sequence. #AGBT16
Hill: Detecting mis-assemblies: looking for spikes in depth of coverage. BAC and fosmids coverage is the back-up supporting info #AGBT16
4:06pm February 13th 2016 via Hootsuite
Hill: New assembly: an 800-fold improvement in contig size. 23Mb N50 scaffold, 9.6Mb contig N50. Contigs reduced from 464K to 16K #AGBT16
4:04pm February 13th 2016 via Hootsuite
Hill: (Oops, meant he credited @infoecho ) #AGBT16
4:03pm February 13th 2016 via Hootsuite
Hill: Credits @igenomics Using BACs to scaffold contigs. The 12 prior assembly method reviewed https://t.co/9UCu95kPle #AGBT16
Hill: SMRT seq: error rate, long high-quality DNA needed. Goal to use PacBio. #AGBT16
4:01pm February 13th 2016 via Hootsuite
Hill: Problems: repetitive seq, SINEs and Alus, LINES, L1 and segmental duplications. Nice summary of Sanger and NGS #AGBT16
4:00pm February 13th 2016 via Hootsuite
Hill: (Thought he'd make a joke showing photo of Venter on the same slide as apes, but he didn't go there.) #AGBT16
3:59pm February 13th 2016 via Hootsuite
Hill: Showed great ape lineage tree and assemblies. Orangutan, gorilla, chimp, bonobo. #AGBT16
Hill: He has no disclosures. But is happy if you'd like to add to the list. (Showed a blank screen, then a tumbleweed.) #AGBT16
3:58pm February 13th 2016 via Hootsuite
Christopher Hill (Univ Washington) Long-read sequence assembly of the gorilla genome #AGBT16
3:57pm February 13th 2016 via Hootsuite
Biezuner: Case study in AML, work via prior platform. Ref '12 https://t.co/SFpFkEYp4L Showed prelim data to recapitulate #AGBT16
3:53pm February 13th 2016 via Hootsuite
Biezuner: Validated by DU145 cell-line (prostate ca), 15 divisions per clone; single cells and regrown; every time sampled cells #AGBT16
3:48pm February 13th 2016 via Hootsuite
Biezuner: Shows video of Tecan liquid handling automation; also uses Echo550 acoustic liquidhandler (inverted 1536-well plate) 2nL #AGBT16
3:46pm February 13th 2016 via Hootsuite
Biezuner: Single cell WGA, use 1st PCR on Access-array. 2nd PCR do barcoding of 48 cells; pool and sequence. #AGBT16
3:45pm February 13th 2016 via Hootsuite
Biezuner:Current methods - not cost-effective nor scalable (WES at low AF) They use microsatellites and get cost to $40/cell #AGBT16
3:44pm February 13th 2016 via Hootsuite
Biezuner: Can reconstruct phylogenetic tree as mutations occur during development. #AGBT16
3:42pm February 13th 2016 via Hootsuite
Biezuner: '03 Sulston cell lineage and beyond in c elegans https://t.co/NuJ1m37Pv4 but in human? #AGBT16
3:41pm February 13th 2016 via Hootsuite
Biezuner: Humans are 10^13 cells. But in development - what happened from one zygote to adult. '13 Nat Rev https://t.co/kohbBBcOru #AGBT16
3:39pm February 13th 2016 via Hootsuite
Tamir Biezuner (Weizmann Institute of Science) A generic, cost-effective and scalable cell lineage analysis platform #AGBT16
3:37pm February 13th 2016 via Hootsuite
Korlach:Q:Roadmap for chem improvement? A:Sample prep same; chemistry will both be supported, improving both, analysis same #AGBT16
3:36pm February 13th 2016 via Hootsuite
Korlach:Q:6x loading but library amt the same? A:Vol is little more, amt dep on insert size. At work on improving loading still #AGBT16
3:35pm February 13th 2016 via Hootsuite
Korlach: Showing many isoforms ID's from Sequel not in RSII (NB - unclear to me why Sequel better in this application) #AGBT16
3:34pm February 13th 2016 via Hootsuite
Korlach: CRC line SW480 before/after siRNA for splicing machinery - cp RSII and Sequel - about 4x higher detect. Ex of exon skipping #AGBT16
3:33pm February 13th 2016 via Hootsuite
Korlach:Iso-seq - using Univ Human Ref RNA (UHRR) showing transcript isoform detection on Sequel. 3 genes, only 2 were det on RSII #AGBT16
3:32pm February 13th 2016 via Hootsuite
Korlach: Structural var in Glioblastoma (GBM) - also from workshop yesterday. #AGBT16 video here: https://t.co/6cG0ABtCdF
3:31pm February 13th 2016 via Hootsuite
Korlach: Challenging C9orf72 ALS G4C2 repeat mentioned yesterday - very difficult >900 bases of G's and C's (!) #AGBT16
3:29pm February 13th 2016 via Hootsuite
Korlach: Direct comparison of bias fto '15 Nat Rev Genet figure https://t.co/T7pSrUdRVO striking comparison to ILMN data #AGBT16
3:28pm February 13th 2016 via Hootsuite
Korlach: K-12 de novo: 6kb library, 4-h acquisition, HGAP. 1 contig, 4.6MB, 9.9992% (QV51) Bias relative to GC content: nice! #AGBT16
3:27pm February 13th 2016 via Hootsuite
RT @jgreid: Impressive new balloon-based sequencing technology from inGen is really a game changer here in Orlando #AGBT16 https://t.co/zcp…
3:26pm February 13th 2016 via Twitter Web Client
Korlach: Poster that used Multiplicom Tumor Hotspot MASTR Plus: got to 1% sensitivity, and cp to MiSeq was more accurate #AGBT16
3:25pm February 13th 2016 via Hootsuite
Korlach: Of 215K reads, 160K QV30 reads, 101K QV40 reads. #AGBT16
3:24pm February 13th 2016 via Hootsuite
Korlach: Shows one of Sebra's slides from workshop: RET driver mutation, T>C and consistent RSII vs Sequel data. #AGBT16
Korlach: Points out ability to read mutations impt in cancer, but not accessible to ILMN chemistry. #AGBT16
3:23pm February 13th 2016 via Hootsuite
Korlach: Showed histogram of RL. Single-pass accuracy is 89% Mode) 84% (mean). #AGBT16 '15 ref https://t.co/xkHOUYI31e direct linked reads
3:22pm February 13th 2016 via Hootsuite
Korlach: Test template - 2kb amplicon; 4h acquisition; 5.1GB, 615K reads; N50 17.7kb; max RL 66kb #AGBT16
3:20pm February 13th 2016 via Hootsuite
Korlach: Sequel is about 6.5x the throughput; ave >10Kb, 99.999% consensus accuracy #AGBT16
3:19pm February 13th 2016 via Hootsuite
Jonas Korlach (Pacific Biosciences) Addressing complex diseases and hidden heritability with the sequel system #AGBT16
3:18pm February 13th 2016 via Hootsuite
Levy:Q:What about small vars? A:Looked at largest vars - 200-500bp. Still ongoing review #AGBT16
2:51pm February 13th 2016 via Hootsuite
Levy: But the other metrics 'are pretty impressive'. Insert size similar, mapping and duplication rates similar (except 1ng input) #AGBT16
2:40pm February 13th 2016 via Hootsuite
Levy: Patterned flowcells take a bit of a hit on higher noise - 'nothing terrible but worth noting'; the biggest negative #AGBT16
Levy: Changed title to 'Early access to 10X Genomics on Chromium'. Shows insert size distribution 350bp a bit wider on 10X #AGBT16
2:39pm February 13th 2016 via Hootsuite
Levy: Testing Chromium 10X Genomics v2: keeping sequencing costs 'manageable' 120Gb, 1ng input (vs 600ng) #AGBT16
2:37pm February 13th 2016 via Hootsuite
Levy: Many methods - LFR, CPT-seq, Moleculo - leverage MPS but get higher-resolution data. May '15 received @10Xgenomics instrument #AGBT16
2:34pm February 13th 2016 via Hootsuite
