Gore #ASHG18 Targeted methylation method that maximizes yield; also unique analysis of haplotypes. Mixture of tumor and wt molecules.
12:55pm October 18th 2018 via Hootsuite Inc.
Gore #ASHG18 676 healthy: matched by age, sex, followed up for 5y. 1,193 samples analyzed by PanSeer assay. Paper c… https://t.co/neNcsrRLlJ
12:54pm October 18th 2018 via Hootsuite Inc.
Gore #ASHG18 The 358 post-dx were from biobanked samples, same collection and storage.
12:53pm October 18th 2018 via Hootsuite Inc.
Gore #ASHG18 Given physicals, 575 were dx w/cancer within 4y of first sample collection. 358 post-dx; 159 pre-dx; 676 healthy
12:52pm October 18th 2018 via Hootsuite Inc.
Gore #ASHG18 Case control studies won't do it. Wang et al 09 https://t.co/pdLcnfWhLS 120K people, monitored for 10y… https://t.co/0WxR49GzNB
12:51pm October 18th 2018 via Hootsuite Inc.
Gore #ASHG18 But a longitudinal study is needed to show early detection. The real way to change mortality. Move the time point forward
12:50pm October 18th 2018 via Hootsuite Inc.
Gore #ASHG18 Tumor-like behavior - a similar methylation profile. Shows JHU, GRAIL results: participants were already diagnosed.
Gore #ASHG18 ctDNA methylation 'is a promising marker'. Looking at the epigenome downstream of DNA mutation: not on… https://t.co/Ub9Lib1bkc
12:49pm October 18th 2018 via Hootsuite Inc.
Gore #ASHG18 Early detection of cancer 'incredibly impt' - 9/10 pts survive CRC 5y. Late - only 2/10 make it 5. Nov… https://t.co/XubpXhbFqr
12:47pm October 18th 2018 via Hootsuite Inc.
Athurva Gore (Singlera Genomics) #ASHG18 Circulating tumor DNA methylation haplotypes in plasma can detect cancer f… https://t.co/os66vjwYRA
12:45pm October 18th 2018 via Hootsuite Inc.
LaCroix #ASHG18 Method STRetch '18 https://t.co/7xKzlGqIlX decoy repeat sequence to help analysis
12:39pm October 18th 2018 via Hootsuite Inc.
LaCroix #ASHG18 300 to 2500 larger than wt size bands: next whether it was a (GGC)-repeat.
12:38pm October 18th 2018 via Hootsuite Inc.
LaCroix #ASHG18 'We traveled back in time a few decades and did Southern Blot analysis' - due to repeat expansion s… https://t.co/d71mCmfvyu
12:37pm October 18th 2018 via Hootsuite Inc.
LaCroix #ASHG18 Suspected Exon 1 aberrant methylation. Explains bisulfite seq; found 48 CpG sites in Exon 1 were hy… https://t.co/mHplMpsZin
12:34pm October 18th 2018 via Hootsuite Inc.
LaCroix #ASHG18 A rare disorder, applied WES, targeted, microarray for CNA, Sanger. 2 probands, 2 vars; 1 proband w… https://t.co/9QlwirHTTe
12:33pm October 18th 2018 via Hootsuite Inc.
Amy LaCroix (Univ WA) #ASHG18 Promoter GGX repeat expansion and exon 1 methyl of XYLT1 in Baratela-Scott syndrome
12:31pm October 18th 2018 via Hootsuite Inc.
van den Oord #ASHG18 Pts with BK virus and UTI have varying white cell content. Different bacterial cell types can… https://t.co/BI1F5CvUog
12:26pm October 18th 2018 via Hootsuite Inc.
Cheng #ASHG18 Shows PCA overlaid with tissue clusters. Kidney contribution correlate w/donor fraction. '17 ref https://t.co/b6bKUh7E43
12:24pm October 18th 2018 via Hootsuite Inc.
Cheng #ASHG18 did ss WGBS (2-5x coverage) from kidney transplant pts. n= ~50. ssDNA: urinary cfDNA is short, degraded, damaged.
12:21pm October 18th 2018 via Hootsuite Inc.
Cheng #ASHG18 Now WGBS on urinary cfDNA; 19K kidney transplants/y; 30% dev BK polyomavirus reactivation; 75% dev UTIs.
Cheng #ASHG18 Shows results from 110 ref materials, and PCA plots showing grouping at organ and cell-type levels.
12:20pm October 18th 2018 via Hootsuite Inc.
Cheng #ASHG18 Metagenomic assay informing host response - tissue-spec methylation markers, to help det where infectious site occurs
12:19pm October 18th 2018 via Hootsuite Inc.
Cheng #ASHG18 Half-life of cfDNA is ~30min. Using urinary cfDNA to look for UTI. '18 ref https://t.co/8fi9bekhqZ 'A versatile analyte'
12:18pm October 18th 2018 via Hootsuite Inc.
Alex Cheng (Cornell) #ASHG18 Distinguishing inf from inf disease using methylation marks comprised within cell-free DNA
12:17pm October 18th 2018 via Hootsuite Inc.
van den Oord #ASHG18 Different mech - current vs cumulative; substantial overlap with WAS, other MWAS of health outcomes
12:15pm October 18th 2018 via Hootsuite Inc.
van den Oord #ASHG18 Method used when many more predictors than effects. Concl: T-cells, granulocytes methylome 'substantial impact'.
van den Oord #ASHG18 Many findings 'significant' - their approach for methylation biomarkers and prediction algorit… https://t.co/RkfypoVBOc
12:13pm October 18th 2018 via Hootsuite Inc.
van den Oord #ASHG18 Have to look at spec celltypes in blood; Tool RaMWAS '18 ref https://t.co/KMy6BULHoE
12:07pm October 18th 2018 via Hootsuite Inc.
van den Oord #ASHG18 Covers ~94% of WGS. Only 5-10% of reagent cost, 15x faster, methylome-wide at cost of arrays.
12:06pm October 18th 2018 via Hootsuite Inc.
van den Oord #ASHG18 Method - optimized MBD-seq (methyl-binding protein). Shows chart w/comparison with WG-Bisulfite seq.
12:05pm October 18th 2018 via Hootsuite Inc.
van den Oord #ASHG18 Longitudinal study for 25y, from childhood on. The methylome - trauma in past 3 mos. Cumulativ… https://t.co/6Ph5kcyQPc
12:03pm October 18th 2018 via Hootsuite Inc.
#ASHG18 Edwin van den Oord (VCU) Dev methylomics of childhood trauma and its health consequences
12:02pm October 18th 2018 via Hootsuite Inc.
For those at #ASHG18, this will be presented at 945am today in Room 6C https://t.co/xdNb3Rg4RW
11:57am October 18th 2018 via Hootsuite Inc.
RT @ceccerslike: "Detecting cancer four years before conventional diagnosis" https://t.co/KisKfFL5Ye by @DaleYuzuki on @LinkedIn
11:56am October 18th 2018 via Hootsuite Inc.
@cathcoste Thank you for the kind mention!
11:56am October 18th 2018 via Hootsuite Inc. in reply to cathcoste
RT @nabsys: Simple, sleek, and powerful - introducing the new @Nabsys HD-Mapping system. Come to booth 1342 to learn how electronic detecti…
9:43am October 18th 2018 via Buffer
RT @girlscientist: Well, if there were ever a piece to get you to come to my 12pm talk on genetic literacy and the public #ASHG18, this mig…
7:41am October 18th 2018 via Twitter Web Client
If you are attending #ASHG18 at 9:45am in Room 6C Dr. Athurva Gore from @singlerainc will present "Circulating tumo… https://t.co/EkQjWjelPD
Konigshofer #ASHG18 About 1/2 are around 5%; about another half in the 3% range.
4:39pm October 17th 2018 via Hootsuite Inc.
Konigshofer #ASHG18 Presents variants in 'ctDNA Complete' material from a synthetic data example. With 'real' SureS… https://t.co/zzOmdM6itd
4:38pm October 17th 2018 via Hootsuite Inc.
Hi #ASHG18 take a look at an interesting methylation haplotyping poster from cell-free DNA #2793 - early detection of CRC
4:36pm October 17th 2018 via Hootsuite Inc.
Konigshofer #ASHG18 Shows interesting representation of interlab study results - for their AF10 and AF20 somatic mutation products.
4:34pm October 17th 2018 via Hootsuite Inc.
Konigshofer #ASHG18 Now doing WES at 1000x coverage; but use of UMIs need 10x to 10K fold coverage of WES. Does the… https://t.co/Al6lJQT4tQ
4:32pm October 17th 2018 via Hootsuite Inc.
Konigshofer #ASHG18 Also notes 'ref sequence info provided by a vendor is acceptable'. NGS for GM24395 (NIST GIAB materials) wasn't >500x
4:30pm October 17th 2018 via Hootsuite Inc.
Konigshofer #ASHG18 But: sequencing errors in the barcodes, that may inflate the counts (!) Quotes Palmetto GBA's '… https://t.co/bKxANE9qLx
4:29pm October 17th 2018 via Hootsuite Inc.
Konigshofer #ASHG18 UMI tech can be used, i5 or i7 indexes used in SureSelectXT/HS; NEBNext Direct, IDT. First base… https://t.co/aiZvIWQEpg
4:28pm October 17th 2018 via Hootsuite Inc.
Konigshofer #ASHG18 Within the assay - heating, sonication, pol errors, even BSA may have bovine DNA in it (!)
4:27pm October 17th 2018 via Hootsuite Inc.
Konigshofer #ASHG18 FFPE causes muts; dividing cells will accumulate muts; clonal hematopoeisis. NIST HG002 has hig… https://t.co/YgaMNktbf4
4:26pm October 17th 2018 via Hootsuite Inc.
Konigshofer #ASHG18 Has an interesting plot with limit of blank (LOB). 95% of noise may not be sufficient; may want… https://t.co/Kp23cqzM7v
4:24pm October 17th 2018 via Hootsuite Inc.
Konigshofer #ASHG18 cfDNA is 165-170bp; typically thought around nucleosome wrapping. Fits 150-200bp desired size f… https://t.co/AcNDYrvjZQ
4:21pm October 17th 2018 via Hootsuite Inc.
