.@gedankenstuecke Ah, overlooked your inclusion in the program! Will be sure to hop over from the cancer session.
11:13pm October 23rd 2015 via Hootsuite in reply to gedankenstuecke
Dean #icg10 Few somatic muts inCLL; driven by Chr copy number and RNA expression. Shows 2D illustration by a tool called Monocle
11:11pm October 23rd 2015 via Hootsuite
Dean #icg10 chr13q14 deletions shown. Single-cell RNA-Seq over time shown. https://t.co/gvn43BNGIR
11:09pm October 23rd 2015 via Hootsuite
Dean #icg10 Showed effect of therapy. Single-cell WGS shows distribution of karyotypes. Trisomy 12 major cell type at time of death
11:07pm October 23rd 2015 via Hootsuite
Dean #icg10 For single cells: CLL’s Dx but took 22y before treatment. Monitored over time. Showed aCGH data over 20y https://t.co/kb7938EBnZ
11:05pm October 23rd 2015 via Hootsuite
Dean #icg10 Normal stem cells migrate, differentiate, resistant to radiation and toxins; cancer SC’s are very similar
11:04pm October 23rd 2015 via Hootsuite
Mike Dean (NCI) Single cell genomics and cancer evolution #icg10
Pan #icg10 MRE- using restriction enzymes, or Me-DIP not applied to single cells. He dev. new method: Sc-mmCpG-seq, 72% coverage of CpGs
10:41pm October 23rd 2015 via Hootsuite
Pan #icg10 Bisulphite: problem is low, inconsistent coverage, esp. for CpG islands. 16 cells, only 1.12% consistent! RRBS - 9%.
10:38pm October 23rd 2015 via Hootsuite
Pan #icg10 Sci Reports 2014 pub doing RNA and DNA from single cell. Onto methylation: can do BS, Methyl-RE, and differential binding
10:36pm October 23rd 2015 via Hootsuite
Pan #icg10 SCT-pqPCR is the telomere method. Data from oocytes and polar bodies.
10:35pm October 23rd 2015 via Hootsuite
Pan #icg10 Able to get alt splicing and allele-spec expression from these single-cell RNA Seq methods. Now telomere length from single cells
10:34pm October 23rd 2015 via Hootsuite
Pan #icg10 PMA and SMA methods for full-length RNA-Seq.
10:32pm October 23rd 2015 via Hootsuite
Pan #icg10 Full-length RNA-Seq, methylation. He worked at Molecular Staging and dev. repli-g, now QIAGEN. MDA, MALBAC, PCR...
10:31pm October 23rd 2015 via Hootsuite
Pan #icg10 Science 6 Mar 2015 ref with mouse hippocampus cells.
10:30pm October 23rd 2015 via Hootsuite
Pan #icg10 Heterogeneity and oscillation will be impossible with average-based methods.
10:29pm October 23rd 2015 via Hootsuite
Pan #icg10 Single cell historically has only been one gene. Now WGS from single cells: sensitivity is the most impt motivation
10:27pm October 23rd 2015 via Hootsuite
Xinghua Pan (Yale Univ) Single cell sequencing from bench to clinic #icg10
10:26pm October 23rd 2015 via Hootsuite
@gedankenstuecke Hi Bastian, would like to meet you sometime here at ICG10 - I’ll be at the SeraCare booth when not in sessions... Dale
10:26pm October 23rd 2015 via Hootsuite in reply to gedankenstuecke
Helleday #icg10 PolK resp. for 8-oxodG incorporation and MTH1-inhibitor sensitivity.
10:10pm October 23rd 2015 via Hootsuite
Helleday #icg10 MHT1-inhibitor may also be useful for autoimmune diseases (overly activated T-cells)
10:08pm October 23rd 2015 via Hootsuite
Helleday #icg10 Shows nice movie of the replication fork and fn of MTH1. May be essential for activated T-cells. https://t.co/QEhI8NgUby
10:07pm October 23rd 2015 via Hootsuite
Helleday #icg10 An MTH1 inhibitor targets a ca phenotype. Effective against cisolatin-resistant cells; induces apoptosis
10:04pm October 23rd 2015 via Hootsuite
Helleday #icg10 MTH1 sanitizes oxidated NTPs to prevent DNA damage. siRNA knock-down shows MTH1 req’d for survival. ID’d a small molecule...
10:02pm October 23rd 2015 via Hootsuite
Helleday #icg10 Can’t predict phenotype from genotype. So is personalized genomics the answer? His ideal: working for all and all cancers
9:58pm October 23rd 2015 via Hootsuite
Helleday #icg10 Story of one pt with multi-resistant ca. now cancer-free. Variable response to PARP-inh, lots of heterogeneity.
9:56pm October 23rd 2015 via Hootsuite
Helleday #icg10 Have been studying the replication fork for 20y. BRCA2-deficient cells are killed by PARP inhibitors.
9:53pm October 23rd 2015 via Hootsuite
Helleday #icg10 Cancer cells have a lot of DNA damage; they can handle high damage load. https://t.co/5IYFucMR0N
9:52pm October 23rd 2015 via Hootsuite
Helleday #icg10 How can all this sequencing help us in treating cancer? ‘We don’t know.’ Radiation, mustard gas, Chinese medicine.
9:50pm October 23rd 2015 via Hootsuite
Thomas Helleday (Karolinska Inst Sweden) Targeting DNA repair in cancer treatments #icg10
9:48pm October 23rd 2015 via Hootsuite
Bond #icg10 Concl: many genes in the p53 pathway are highly sensitive to both heritable and somatic genetic variants
9:44pm October 23rd 2015 via Hootsuite
Bond #icg10 Diving into GWAS susceptibility: cancer suscept. genes are enriched for p53 pathway genes.
9:39pm October 23rd 2015 via Hootsuite
Bond #icg10 Zeron-Medina 2013 Cell paper: validated in cell lines with allele-spec ChIP; reporter-based assays in enhancer-trap assay
9:33pm October 23rd 2015 via Hootsuite
Bond #icg10 p53 enhancer polymorphism a probed with ChIP-Seq; 17K peaks. Found one - KITLG gene, strong OR of 2.7
9:31pm October 23rd 2015 via Hootsuite
Bond #icg10 GWAS can now be mined for Tumor Suppressor genes. Reasoned that p53 response elements may appear in GWAS data
9:29pm October 23rd 2015 via Hootsuite
Bond #icg10 p53 normal fn inhibits DNA damage - via cell cycle arrest or apoptosis. Studied for a long time. But what about broad population
9:27pm October 23rd 2015 via Hootsuite
Bond #icg10 >50% mutated gene in tumors; rare highly penetrant (Li-Fraumeni) in families. Many #TCGA papers - a network of mutations.
9:25pm October 23rd 2015 via Hootsuite
Gareth Bond (Oxford) The roles of SNPs in the p53 pathway in human cancer and evolution #icg10
9:23pm October 23rd 2015 via Hootsuite
Jiang #icg10 570 samples from multi-center cohort, shown here. https://t.co/vAVZmQyenx
9:18pm October 23rd 2015 via Hootsuite
Jiang #icg10 Validated in 71 samples; had aCGH data; ID’d 42 constitutional pCMVs from 1.3MB to 69.1MB in prenatal group
9:16pm October 23rd 2015 via Hootsuite
Jiang #icg10 CNV detection, long list of criteria for pathogenicity.
9:14pm October 23rd 2015 via Hootsuite
Jiang #icg10 Able to show balanced translocation w/mate-pairs and 30M reads. Ding 2014 Hum Mutation ref
9:12pm October 23rd 2015 via Hootsuite
Jiang #icg10 Showing CNV data 99.7% sens 100% spec for aneuploidy. Mate-pair for balanced translocation 30M reads enough. Dong 2014 Hum Mut
9:11pm October 23rd 2015 via Hootsuite
Jiang #icg10 Microdeletions / duplications can account for as much as 300MB. Example DiGeorge Syndrome
9:05pm October 23rd 2015 via Hootsuite
Hui Jiang (BGI) Inplementation of NGS for CNV detection in routine clinical practice #icg10
8:57pm October 23rd 2015 via Hootsuite
Vajta #icg10 Implantation rates are higher w/vitrification. NGS for PGS is most suitable; CNV, aneuploidy.
8:55pm October 23rd 2015 via Hootsuite
Vajta #icg10 He showed his OPS method of vitrification with a plastic straw; $7. First paper cited over 1200x’s
8:54pm October 23rd 2015 via Hootsuite
Vajta #icg10 Shows nice video of removal of single cell from trophoblast, with a laser shot to cut cell away.
Vajta #icg10 Shows how simple it can be to get 5% O2 in a heat-sealed bag for embryo culture.
8:48pm October 23rd 2015 via Hootsuite
Vajta #icg10 Some photos of BGI’s existing and future facilities.
8:44pm October 23rd 2015 via Hootsuite
