Schroth #AGBT19 6.5h to pooled library; flexible to panel options and your own too. Points out Rady world record 19… https://t.co/9RBP86UCtU
12:20pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 Now no index repeated. Nextera Flex compared to XT in terms of GC coverage; compared to microbiome mock mixture.
12:15pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 Robust to DNA input - bead-based normalization. No need for library quant. Revamping indexing strat… https://t.co/RO7PYeyrSc
12:12pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 7y ago Epicentre purchased; Nextera XT best-selling; attached to beads gives control.
12:10pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 In Q3 of 2018 the amount of capacity shipped was the entire year's of 2016.
12:09pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 Sequencing capacity shipped by Illumina https://t.co/1m2PIXNS9W
12:08pm March 2nd 2019 via Twitter for iPhone
Gary Schroth (Illumina) Transforming the future of genomics, together @Genomics_Guy #AGBT19
12:07pm March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 Targeted long-read for 1MB would be great... Openly released just now: https://t.co/pXVKpqdgII Com… https://t.co/yC5K9Jh7CK
11:46am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 Is it correct? Showed some validation data via BstEII southern blot and other data. T2T assembly o… https://t.co/mTx6qzXOg2
11:45am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 The last gap: chrX. Found unique structural vars from PacBio reads, then unique k-mers confirmed v… https://t.co/slbGVR7Lqh
11:43am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 55x copies (165kb array) DXZ4 gene family, quantified with ddPCR.
11:41am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 First complete chromosome - manual gap closure, correct repeat collapse. Bionano map showed missing repeat units.
Phillippy #AGB19 Shows bands of contigs, and then '19 the contrast. Contigs in '02 was 0.15MB (?) now 75MB. Chose chrX
11:39am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 Continual sampling to high coverage: enough sampling will cover the repeat in question. CHM13 from… https://t.co/cCPH37hi0g
11:38am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 Shows read-length distribution - 50% of bases for ONT and BioNano are >100Kb. Nanopore UL read length is long-tailed.
11:37am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 30x nanopore ultra-long, 60x Pacbio for polishing, 50x 10X Genomics polishing, BioNano structural var.
11:36am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 @pathogenomenick and @mattloose have a Long Read Club (shirts!). Karen and Adam have formed a T2T consortium.
Phillippy #AGB19 Read coverage and accuracy matter too. MinION device - now readlengths >1 Mbp possible. If 8cm fis… https://t.co/JSXW65Z
11:34am March 2nd 2019 via Twitter Web Client
RT @aphillippy: Presenting "Telomere-to-telomere assembly of a complete human X chromosome" today at 11:30am #AGBT19. Slides: https://t.co/…
11:33am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 AGBT 2012: closed bacterial genomes with the help of long reads. (7kb rDNA repeats in microbes). S… https://t.co/Zo2ohDUALO
Phillippy #AGB19 Collaboration with Karen Miga (UCSC); @khmiga @aphillippy Repeats are long, reads are short. Stade… https://t.co/fsmMVQFhX2
11:32am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 The human reference genome is incomplete. 368 unresolved issues, 102 gaps. Gaps have impt info; mi… https://t.co/Wczilgvwmd
11:30am March 2nd 2019 via Twitter Web Client
Adam Phillippy (NHGRI) #AGBT19 Telomere-to-telomere assembly of a complete human X chromosome
11:29am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 The preprint of this work presented this AM https://t.co/s0cXj4FaJ4
11:27am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 Transformed metric LOEUF decile - constraint merics for protein-protein interactions, gene expression, disease assoc
11:23am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 Testing the model for severe ID - obs vs expected freq, LoF are strongly depleted. Perhaps embryonic lethal gene.
11:20am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 Dev tool called LOFTEE - variant-effect predictor not using freq. https://t.co/SAoYf53TUm Varian… https://t.co/sJjND8RrMc
11:17am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 'Staggering amounts of variation' - 250M vars in 15.7 WGS; 15M vars in 125.7M WES. And predict some 513K LoF variants.
11:16am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 Sub-continental ancestry. https://t.co/n73T95B4U3
11:15am March 2nd 2019 via Twitter for iPhone
Karczewski #AGBT19 Novel QC pipeline https://t.co/d6Ubr2deHk Shows plot of representation
11:15am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 New framework called https://t.co/vZpDeV60VH scaling to 1000's of CPUs. gnomAD site: https://t.co/esVGgeGtCn
11:13am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 However ID true LoF is hard: rarity, and enriched for artifacts. Catalogues - gnomAD 125.7K WES… https://t.co/7PMtY84GY6
11:12am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 Range of LoF impact - from embryonic lethal, haploinsuff, recessive, complex disease, nonessenti… https://t.co/7F10ecFoFq
11:11am March 2nd 2019 via Twitter Web Client
Konrad Karczewski (Broad Inst) #AGB19 Variation across 141,456 human exomes and genomes reveals the spectrum of los… https://t.co/YBngeigF59
11:10am March 2nd 2019 via Twitter Web Client
RT @TPU_ICR: AM. A higher proportion of HIV+ patients have higher tumour grade. Seq used - using WGS, WES, panel, mRNA seq, ChIP and Array…
11:01am March 2nd 2019 via Hootsuite Inc.
Hey #AGBT19 I just do what Eva tells me to - come down to @QIAGENscience to take the challenge in Seagrape1. https://t.co/h6NAkZ6JhG
10:46am March 2nd 2019 via Twitter for iPhone
Lincoln #AGBT19 Table 2: whole list of recommendations. https://t.co/mjrmvr0QzL
10:23am March 2nd 2019 via Twitter Web Client
Lincoln #AGBT19 Lays out how they tried to reduce overfitting.
10:21am March 2nd 2019 via Twitter Web Client
Lincoln #AGBT19 Imbalanced dataset: TPs vastly outnumber FPs. Many low-qual calls are TPs. The cost of a missed TP is great.
10:18am March 2nd 2019 via Twitter Web Client
Lincoln #AGBT19 Qual metrics, allele balance, read depth, content, etc. Many FP's have 'good' allele balance (!) Ma… https://t.co/P8abDNM8gW
Lincoln #AGBT19 Clin confirmation data from 80K pts, all five NIST samples, on- and off-target var calls, two labs.… https://t.co/0Dx9fKwWDy
10:17am March 2nd 2019 via Twitter Web Client
Lincoln #AGBT19 Data sets ize and diversity matters. Mu et al - >100x and AF >40%. The new study: 29 FP indels and 7 FP SNVs !
10:16am March 2nd 2019 via Twitter Web Client
Lincoln #AGBT19 How to rigorously est upper criteria? Many papers '15 ref https://t.co/L8JIIogluR
10:14am March 2nd 2019 via Twitter Web Client
Lincoln #AGBT19 Low thresholds for sensitivity, and a high threshold for high specficity. Collab with Matt Levo Har… https://t.co/86zibx3VBy
10:13am March 2nd 2019 via Twitter Web Client
Lincoln #AGBT19 Six different platforms! PacBio, short amplicon, LR-PCR, Sanger. Variants called from NGS - the one… https://t.co/ZNAlDMjtRZ
10:12am March 2nd 2019 via Twitter Web Client
Lincoln #AGBT19 Optimize for sens, enforce spec by an orthogonal method. and then clinical reporting, pt mgmt. Addi… https://t.co/1qw9aid9Qx
10:11am March 2nd 2019 via Twitter Web Client
Lincoln #AGBT19 Challenges - large % (9-19%) are technically challenging for NGS (large indels, single-exon CNVs, S… https://t.co/TLQUbJgssT
10:10am March 2nd 2019 via Twitter Web Client
Lincoln #AGBT19 Just published in J Mol Diag https://t.co/O4U6hsi4OX
10:09am March 2nd 2019 via Twitter Web Client
Stephen Lincoln (Invitae) #AGBT19 A rigorous study of the need for Sanger confirmation in clinical genetic testing
Q: Using blood - how often will it work or not? Montgomery #AGBT19 A bonus slide: about 66%-70% all known disease g… https://t.co/m8jWoOltdH
10:08am March 2nd 2019 via Twitter Web Client
