@ShobaAnantha Sorry I missed this message! Was speaking with Anna C of Roche. Reach out again if you are at exhibit or in same session.
3:14pm October 8th 2015 via Hootsuite in reply to ShobaAnantha
Weitzel: Of the 26: 11 had 1st degree relative w/cancer. Went onto to look at individual cases. #ASHG15
3:12pm October 8th 2015 via Hootsuite
Weitzel: Of >50K NGS panel cases, TP53+, n=166. Of 166, n=26 abnormal NGS metrics and looking at these. mean age: 57y, #ASHG15
3:08pm October 8th 2015 via Hootsuite
Weitzel: Li-Fraumeni Syndrome - acknowledges Dr. Li's passing. LFS: needs >50x coverage, Sanger confirmed. #ASHG15
3:05pm October 8th 2015 via Hootsuite
Jeffrey Weitzel (City of Hope) Somatic TP53 mutations detected in germline testing: The importance of phenotypic correlations #ASHG15
3:02pm October 8th 2015 via Hootsuite
Raymond: Q:What about family members? A: Confirmed, returned to oncologist, discussed with family, before cascading #ASHG15
3:01pm October 8th 2015 via Hootsuite
Raymond: Q:How to guide Rx? A:One DICER1 did make that difference. #ASHG15
2:59pm October 8th 2015 via Hootsuite
Raymond: Of 1594 Cat 1/2, 24.8% werre VUS; of which 64.6% weren't reported before. Importance of data sharing, interpretation #ASHG15
2:58pm October 8th 2015 via Hootsuite
Raymond: 3.7 vars/individ. Majority benign. 3% pathogenic or likely. 20 pts/483. 23 categroy 2. One had both: MSH2, HOXB2 #ASHG15
2:55pm October 8th 2015 via Hootsuite
Raymond: 2011-14: 463/500 sequenced. median age of adults - 53y; median age of pediatric pts 11y #ASHG15
2:53pm October 8th 2015 via Hootsuite
Raymond: Berg method for categorization: 1-disclose (BRCA1); 2-case by case (ATM); 3-undiscl. pathogenic w/autsomal recessive FANCA #ASHG15
2:51pm October 8th 2015 via Hootsuite
Raymond: With germline - 161 genes involved with ca pathways. Genetic counseling at the outset. #ASHG15
2:50pm October 8th 2015 via Hootsuite
Raymond: @hail_CSER project, now open to both adult and pediatric arms. Therapeutic decision-making. Both germline & tumor samples #ASHG
2:49pm October 8th 2015 via Hootsuite
Victoria Raymond (U Mich) Germline variants in a tumor/normal cancer genomic sequencing project ID's a high % with inh. risk #ASHG15
2:48pm October 8th 2015 via Hootsuite
LaRochelle: Enrichment <8h (although no overall turnaround time). Up to 20K targets. Can pick up rearrangements. #ASHG15
2:22pm October 8th 2015 via Hootsuite
LaRochelle: Two oncology panels, full coding regions of 60 genes; another w/53 hotspots. Can do custom designs #ASHG15
2:20pm October 8th 2015 via Hootsuite
LaRochelle:Thanks to the UID barcode, can easily remove PCR duplicates Showing AF from 1% to 25% ]#ASHG15
2:19pm October 8th 2015 via Hootsuite
LaRochelle: Inversion probe extends and ligates increases specificity. Has barcoded tag, just inside universal primer binding sites #ASHG15
2:15pm October 8th 2015 via Hootsuite
LaRochelle:High Efficienty Amplification of Targets for Sequencing - MIPs, scales to whole-exome. Cancer first offering. #ASHG15
2:13pm October 8th 2015 via Hootsuite
LaRochelle: Roche RUO of PacBio Sequel '2nd half of next year' HEAT-Seq enrichment system product introduction #ASHG15
2:12pm October 8th 2015 via Hootsuite
Urban: Greally lab publication NAR '15 http://t.co/R1KUdhPNeD w/CpGiant. Several projects underway, including ASD, DNMT1 in iPSC #ASHG15
2:08pm October 8th 2015 via Hootsuite
Urban: Complements the 450K microaray, 84Mbp, >5.5M CpG sites. Conversion before capture. On-target ~50-70% #ASHG15
2:06pm October 8th 2015 via Hootsuite
Urban: 3rd:SeqCap Epi: probes designed for fully methylated, hemi and un-methylated. Custom or 'Cp-Giant' #ASHG15
2:05pm October 8th 2015 via Hootsuite
Urban: A 2012 ref for single neuron and L1 retrotransposition http://t.co/NVgdEqmI60 Data tends to be messy #ASHG15
2:01pm October 8th 2015 via Hootsuite
Urban: Topic 2 - locations of somatic retro-transposed elements in the human genome in the brain. Down to single-cell ASHG15
1:59pm October 8th 2015 via Hootsuite
.@GHRouth It was for the initial plenary, Neil Risch (UCSF) talking about diversity in the ASHG BOD composition over decades, then panel.
1:57pm October 8th 2015 via Hootsuite in reply to GHRouth
Urban:Also looking at other chr22 - Philadelphia chr cases, and they have add'l samples (t(10;22) etc) to still analyze #ASHG15
1:55pm October 8th 2015 via Hootsuite
Urban: Single MiSeq run got 170x seq. coverage of Chr22. (Actual, with mate-pair information). Showed mapping, where del occurred #ASHG15
1:52pm October 8th 2015 via Hootsuite
Urban: But exact breakpoint still unk. CLIP-Cap 35Mb target. 1 oligo/17bp, 21M oligos. Nextera MP library prep, 2-20kb size #ASHG15
1:51pm October 8th 2015 via Hootsuite
Urban:, with 70 clonal cultures: some with 3 copies, many with 1 (via dPCR). FISH indicated isodicentric centromeres in Chr22 #ASHG15
1:50pm October 8th 2015 via Hootsuite
Urban: By capture; used MLPA-PCR of 22q area; reanalyzed via SNP array and ddPCR - suspicious of complex deletion #ASHG15
1:48pm October 8th 2015 via Hootsuite
Urban: Poster at #ASHG15 1934T. Typical insert: 1kb - 15kb. '07 Science http://t.co/D4kMU7yOsT chr 22q13 Pheelan-McDermid syndrome
1:47pm October 8th 2015 via Hootsuite
Urban: CLIP-Cap - target capture plus mate-pair. 'Combined Long-Insert PE and Capture Seq'. Whole chromosome w/complex rearr. #ASHG15
1:46pm October 8th 2015 via Hootsuite
Alex Urban (Stanford): Analysis of complex genomic and epigenomic variation in humans using target-capture sequencing approaches #ASHG15
1:43pm October 8th 2015 via Hootsuite
Mane: Shares his long history with @rochesequencing from 2008. 2009 PNAS ref http://t.co/nFKtM2cC4b #ASHG15
1:40pm October 8th 2015 via Hootsuite
.@GHRouth Hi Geoff! (From the Roche workshop at ASHG).
1:37pm October 8th 2015 via Hootsuite in reply to GHRouth
Mane: Thanks to saving of sequencing amount, their cost per exome down from about $500 to $330 #ASHG15
1:36pm October 8th 2015 via Hootsuite
RT @GenomeWeb: Half of labs surveyed plan to adopt liquid biopsy in next 1-2 years: https://t.co/VvfMzxJ1UD
1:34pm October 8th 2015 via Hootsuite
Mane: Showed 96% coverage at >8x; only about 81% at >20x, FWIW. Data from NA12878 on 56 ACMG at 100% coverage next #ASHG15
1:33pm October 8th 2015 via Hootsuite
Mane: Clear improvement on read depth distribution. PCR duplicates relatively high (16.5%), function of HiSeq rather than enrichment #ASHG15
1:32pm October 8th 2015 via Hootsuite
Mane: "MedExome at 3.9GB has similar sens/spec at V2 at 5.1GB on V2" #ASHG15
1:30pm October 8th 2015 via Hootsuite
Mane: Cp to V2 (they've done 47K exomes with it), marked improvement of the >8x coverage metric. #ASHG15
1:29pm October 8th 2015 via Hootsuite
Mane: EZ MedExome: add'l coverage, 47MB target, enzymatic frag, GRCh38 ref, 16h hyb, 100 ng input #ASHG15
1:28pm October 8th 2015 via Hootsuite
Mane: V2, V3, VCRome exome captures compared at 8x or above: very similar results between the 3. #ASHG15
1:27pm October 8th 2015 via Hootsuite
Mane: Annotation via ANNOVAR and ExAC and other db's. Nice chart of sens., precision across SNV and Indels. Sens 98.7%, Spec 98.5% #ASHG15
1:26pm October 8th 2015 via Hootsuite
Mane: Their center has 6 HiSeqs, 1 PacBio, MiSeq, PGM. 63% of volume is for WES. Pipeline GATK3, BWAMEM, MuTect, Indelocator #ASHG15
1:25pm October 8th 2015 via Hootsuite
Shrikant Mane (Yale) Performance evaluation of Roche NimbleGen exome capture products #ASHG15
1:23pm October 8th 2015 via Hootsuite
LaRochelle: Also Bina with analysis - 'long-term commitment' to end-to-end. ASHG15
1:21pm October 8th 2015 via Hootsuite
LaRochelle: CAPP Medical explored a bit, and Ariosa's Harmony test. Stratos, Genia, PacBio platforms all described in brief #ASHG15
1:18pm October 8th 2015 via Hootsuite
Here at @RocheSequencing lunchtime #ASHG15 workshop, William LaRochelle (Roche) briefly reviews their whole NGS portfolio
1:17pm October 8th 2015 via Hootsuite
