Gary Schroth (Illumina CA) The next era of sequencing starts now #AGBT17
4:23pm February 14th 2017 via Hootsuite
Hoischen: "Few answers... more questions..." Clone dynamics, and also role in disease or perhaps normal aging phenomena #AGBT17
4:05pm February 14th 2017 via Hootsuite
Hoischen: Clonal hematopoeis can be detected as sensitivity is driven down. Observed as early as 21y of age. #AGBT17
4:04pm February 14th 2017 via Hootsuite
Hoischen: 196/225 were missense, 21 indels. Shows # by age, steady exponential w/age #AGBT17
4:03pm February 14th 2017 via Hootsuite
Hoischen: Shows IGV plot of DNMT3A R326C mut in 25yo woman; seq coverage was 4,000x, 1% AF. Of 225: only 8 synonymous, 217 known CH #AGBT17
4:00pm February 14th 2017 via Hootsuite
Hoischen: Plot of mut by age, 225 somatic SNVs and indels. From 0.08% to 30% Allele Fraction. #AGBT17
3:58pm February 14th 2017 via Hootsuite
Hoischen: Able to sequence both directions. Able to use Poisson for error distribution on a per-base basis, multiple test correction#AGBT17
Hoischen:Had 400 samples for every decade 20-29, etc through 60-69 from healthy blood donors. Screened for 131 hotspots common to CH #AGBT17
3:56pm February 14th 2017 via Hootsuite
Hoischen: #AGBT17 Quickly reviews the method described here '13 Genome res https://t.co/oh8yrYCQYK
3:55pm February 14th 2017 via Hootsuite
Hoischen: Another '15 ref https://t.co/cJIKa7fwtb Working with Ashley (Stanford) and Shendure (U Wash) and smMIPs #AGBT17
3:54pm February 14th 2017 via Hootsuite
Hoischen: 'New insights into age-related clonal hematopoiesis': Landmark papers, of which is '14 Nat Med https://t.co/coUo3JudD9 #AGBT17
3:53pm February 14th 2017 via Hootsuite
Alex Hoischen (Radboud Univ Med Ctr Netherlands) Ultra-sensitive mosaic mutation detection in blood DNA of healthy individuals #AGBT17
3:51pm February 14th 2017 via Hootsuite
Cuppen: In intestine, 3/14 small deletions at fragile sites. Colon: large chromosomal events 5/15 #AGBT17
3:42pm February 14th 2017 via Hootsuite
Cuppen: Showing chromosomal segregation errors may play a role in driving colon ca. 1/9 livers dupl. w/microhomology... #AGBT17
Cuppen: Regional biases in mutation patterns may be explained by MMR; by doing CRSPR MMR-deficient, demonstrated this #AGBT17
3:40pm February 14th 2017 via Hootsuite
Cuppen: First is cell-cycle tissue-indep, next is cell cycle-, and tissued dependent, third may be culture assoc'd #AGBT17
3:38pm February 14th 2017 via Hootsuite
Cuppen: Looking at signatures, determined three: Unknown proc, deamination-induced, oxidative stress-induced. #AGBT17
3:37pm February 14th 2017 via Hootsuite
Cuppen: Across abt 30 donors, seeing about 40 mutations/year in these cells. Shows chart of type of mut across colon, gut, liver #AGBT17
3:36pm February 14th 2017 via Hootsuite
Cuppen:. Culture is 7-14d, to single ASCs, do clonal organoid culture 6w. Only 200 - 2K mutations/cell #AGBT17
3:34pm February 14th 2017 via Hootsuite
Cuppen: They use 3D organoid cultures to grow '13 Science ref https://t.co/NSu5wxZc2R #AGBT17
3:33pm February 14th 2017 via Hootsuite
Cuppen: ASCs (adult stem cells) rare, no markers/Abs available, mutation rate is low, may not be non-random, need scWGS w/low error #AGBT17
3:32pm February 14th 2017 via Hootsuite
Cuppen: Adult stem cells have impt role in tissue homeostasis, aging and cancer. Present, multipotent, long-lived. #AGBT17
3:31pm February 14th 2017 via Hootsuite
Edwin Cuppen (Univ Med Ctr Utrecht) Tissue-specific mutation accumulation in human adult stem cells during life #AGBT17
@Invitae Steve Lincoln presenting a poster with some @SeraCare reference materials #AGBT17 https://t.co/4wvHABqP0W
2:18pm February 14th 2017 via Hootsuite
RT @nebiolabs: Wondering where everyone at #agbt17 is getting these awesome t-shirts? Visit Suite 216 and find out! https://t.co/3lt3X4Oyd7
1:05pm February 14th 2017 via Hootsuite
Blaesius: Goes onto describe their Cellular Research Precise Assays, avoiding PCR bias with molecular indexing #AGBT17
12:40pm February 14th 2017 via Hootsuite
Blaesius: Closes with FACSMelody, 9-color, 3 lasers. scRNA-Seq - capture on size, phenotype, discriminate live/dead cells #AGBT17
12:38pm February 14th 2017 via Hootsuite
Blaesius: Shows experiment with bulk, dissociated, and dissociated and sorted and comparing RNAseq data #AGBT17
12:34pm February 14th 2017 via Hootsuite
Blaesius: Does sample handing affect gene expression? '15 ref (microarray data) https://t.co/UGQ0mR3pSC #AGBT17
12:33pm February 14th 2017 via Hootsuite
Blaesius: Cp RNA seq heatmaps of TCGA and their sorted cells; distinct phenotype maps in sorted cell subpopulations #AGBT17
12:29pm February 14th 2017 via Hootsuite
Blaesius: NGS of sorted cells at 98% purity; used CD184 as a br ca marker for cancer stem cells, RNASeq had clear differentiation #AGBT17
12:27pm February 14th 2017 via Hootsuite
Blaesius: Within mouse, consistent marker quantitation; across PDXs, wide variation. PDX from br ca, shows relatedness #AGBT17
12:22pm February 14th 2017 via Hootsuite
Blaesius: Their PDXs, can look at 10 human-spec markers (CD90, CD194 etc) across 13 PDX individuals #AGBT17
12:21pm February 14th 2017 via Hootsuite
Blaesius: Going from Pt-derived Xenografts (PDX), using tumor-dissociation reagents, with filtration, washing, RBC removal, FACS #AGBT17
12:19pm February 14th 2017 via Hootsuite
At the @BDBiosciences #AGBT17 workshop Rainer Blaesius (R&D, BD) Single-cell Proteogenomics integrating cell sorting and sequencing
12:18pm February 14th 2017 via Hootsuite
This billionaire's cancer moonshot is falling far short of the hype | StatNews https://t.co/qaP1Fkahfi Update on Soon-Shiong’s effort
12:10pm February 14th 2017 via Hootsuite
Colwell: Hospital biofilms in sink drains - tracked to bacteria at strain-level, showed antibiotic resist transmission via plasmids #AGBT17
11:40am February 14th 2017 via Hootsuite
Colwell: Four strains ID'd, only one strain migrated to internal organs. Strains interacted, produced Pseudomonas-like toxin #AGBT17
11:39am February 14th 2017 via Hootsuite
Colwell: Necrotizing fascitis from a zip-line incident '16 Cell https://t.co/lRmbCNBJce Both legs, arms needed amputation (!) #AGBT17
11:38am February 14th 2017 via Hootsuite
Colwell: Can monitor antibiotic resistance genes; also can look at gene abundance related to carbohydrate metabolism #AGBT17
11:35am February 14th 2017 via Hootsuite
Colwell: History: infectious disease and microbial ecology. Cholera affects 7M people/year. 7th pandemic started in '60's #AGBT17
Colwell: Probiotic bacteria likely came from yogurt, buttermilk in diet. A bioforensic tool is the healthy metabiota of the gut #AGBT17
11:34am February 14th 2017 via Hootsuite
Colwell: In the healthy controls: much larger numbers of pathogens. These would make us ill. Colored area in pie chart:protective #AGBT17
11:33am February 14th 2017 via Hootsuite
Colwell: Between 4 and 10 pathogens were present in stool; 50% had Giardia. Unknown etiology: mixture of enteropathic E.coli #AGBT17
11:32am February 14th 2017 via Hootsuite
Colwell: They test for 9 bacteria, 4 parasites, 5 viruses (from Vibrio to Campylobacter, to Cryptosporidium etc) #AGBT17
11:31am February 14th 2017 via Hootsuite
Colwell: Working with a center in Calcutta, provided 74 NICED samples, healthy controls, sick with known and unknown etiology #AGBT17
11:30am February 14th 2017 via Hootsuite
Colwell: Culture diagnostics - time-consuming, now can use MAb's, M-S. to dx in minutes #AGBT17
11:29am February 14th 2017 via Hootsuite
Colwell: Bengal delta is known as 'native homeland' of cholera. Exist naturally; 'highly unlikely cholera will be eradicated' #AGBT17
11:27am February 14th 2017 via Hootsuite
Rita Colwell (Univ MD, CosmosID MD) Metagenomics of hospitalized diarrheal patients and healthy individuals in Kolkata, India #AGBT17
11:24am February 14th 2017 via Hootsuite
Q:Animal-to-human, can that be followed? Rubin: We don't have this data, and are starting to generate it. #AGBT17
11:22am February 14th 2017 via Hootsuite
