MH: N5010.4Mb; N90 1.3Mb. Showed large-scale heterozygous variation in HLA-DQA1/DQB1 (151kb region) phased automatically #AGBT15
12:16pm February 27th 2015 via Hootsuite
MH:Took HuRef-1 sample, did PacBio reads. Constructed diploid-aware contig represention ("FALCON"). DALIGNER (Myers), FALCON (chin) #AGBT15
12:14pm February 27th 2015 via Hootsuite
MH: Quotes @deannachurch in this '13 Bio-IT World http://t.co/yy11TgYzBR 'we have to have de novo assy' #AGBT15
12:11pm February 27th 2015 via Hootsuite
MH:Non-SNP variation is 22%; 35% of genes are encompassed by CNV's; less than 1% of var's present in CHM1 in newer assemblies #AGBT15
12:10pm February 27th 2015 via Hootsuite
Mike Hunkapiller @PacBio workshop: compares human de novo assemblies - N50 contig of 7.7kb for CHM1 far longer than rest #AGBT15
12:08pm February 27th 2015 via Hootsuite
RT @mike_schatz: Today at noon: @PacBio Sequencing and Structural Analysis of a Breast Cancer Cell Line. #AGBT15
11:53am February 27th 2015 via Twitter Web Client
RT @mike_schatz: @mike_schatz damn repeats. Wishing we had some long reads http://t.co/C7f90BWWCM
MG:Q:How much sample for library prep? A:AML has almost unlimited amts of DNA/RNA ddPCR 'uses a ton' - a few ug #AGBT15
11:52am February 27th 2015 via Hootsuite
MG:Q:RNA-Seq data? A:Done to look for regulatory mut's (FOXP1 splicing defect, exon-skipping); validates some var's in this way #AGBT15
MG: Large dataset - to serve as a resource to help others choose optimal strategy. Hope to make it avail 'soon' #AGBT15
11:50am February 27th 2015 via Hootsuite
RT @obahcall: Enjoyed interesting, helpful #SciComm discussions at #AGBT15 @illumina @NatureRevGenet Tweetup, Thanks to all who joined &
11:50am February 27th 2015 via Twitter Web Client
MG:As WGS depth downsampled - check this out (animation of downsampling) Cool!
11:49am February 27th 2015 via Hootsuite
MG: Primary tumor VAF, plot against relapsed tumor VAF; each driver corresponds to variant cluster #AGBT15
11:47am February 27th 2015 via Hootsuite
RT @CIgenomics: MG: at 50x you lose lots and lots of variants; 50x disappointing (JH: increase coverage @GenomicsEngland XTen is only 30x!)…
11:46am February 27th 2015 via Twitter Web Client
MG: Plot of PPV against sensitivity - with 8 different callers. Many callers were similar PPV, sens had a range #AGBT15
11:46am February 27th 2015 via Hootsuite
MG: Complex list of ~8 datasets; ended up with 'platinum var's' list. Downsampled to test sensitivity of 'std' coverage levels #AGBT15
11:45am February 27th 2015 via Hootsuite
RT @bioinformer: Great example of CBEP efforts by @broadinstitute for genomics in Africa. @illumina @USAID #AGBT15 http://t.co/ywyxKLUAjB
11:43am February 27th 2015 via Hootsuite
MG: 350X WGS, 350x WES, 1200x of 260 AML genes, 10,000x 144 high priority SNV sites. 240K ddPCR (15 sites) 30 'lanes' RNA-Seq #AGBT15
11:42am February 27th 2015 via Hootsuite
MG:Indiv. w/AML31 char in Ding et al 2012 http://t.co/r7SdJ3kMbY After WGS 400x targeted validation. Showed fish-eye plot figure #AGBT15
11:40am February 27th 2015 via Hootsuite
MG:Heterogeneity and aneuploidy: non-optimal strategies WGS/30-60x and WES/100x- insufficient coverage. Same w/RNA-Seq read numbers #AGBT15
11:38am February 27th 2015 via Hootsuite
Malachi Griffith, Washington Univ. Optimizing Tumor Genome Sequencing and Analysis #AGBT15
11:36am February 27th 2015 via Hootsuite
CM:Q:(Plon) How were you contacted? A:'We were poised and ready'. Obv. other places affected #AGBT15
CM:Q:Samples from Africa or seq in-country? A:'A lot of hurdles', still gets samples shipped #AGBT15
11:35am February 27th 2015 via Hootsuite
.@clcbio I WANT. Will
11:34am February 27th 2015 via Hootsuite in reply to
CM:Was able to track spread through Sierra Leone, published in Science '14 http://t.co/oByvytKOg4 Mut's cluster into clades #AGBT15
11:29am February 27th 2015 via Hootsuite
CM: Also carryover of poly(A) carrier a problem; depletes w/method. Showed coverage plot pre- and post-depletion. #AGBT15
11:28am February 27th 2015 via Hootsuite
CM: Cold chain a challenge. Have est relationships with local hospitals. RNA quality/qty. RIN of 1.2 (!) Need qRTPCR for quant #AGBT15
11:25am February 27th 2015 via Hootsuite
CM: Goals - Dx, therapy, origins, transmission, host-interaction. Had lessons from working with Lassa virus - logistics is hard #AGBT15
11:24am February 27th 2015 via Hootsuite
CM: Starts with Genome Biol '14 ref: http://t.co/NJo4sq96ji Suspected: 22.8K; >9K deaths. Unprecedented outbreak #AGBT15
11:23am February 27th 2015 via Hootsuite
Christian Matranga, Broad Inst Rapid Full-Length Sequencing of Lassa and Ebola Viruses: A Model for Genomic Pathogen Surveillance #AGBT15
11:21am February 27th 2015 via Hootsuite
SK:Q:Navigating LDT? A:A research test, Sanger confirmed. Only needed to report back 1x in 35 cases before confirmation (FDA OK'd) #AGBT15
11:20am February 27th 2015 via Hootsuite
SK:Q(Plon):Unusual presentation of HLH - something add'l? A:Addressed the acute, could be add'l conditions #AGBT15
11:19am February 27th 2015 via Hootsuite
SK:NSIGHT = NGHRI's Newbork Sequencing In Genomic Medicine and Public Health for prospective work http://t.co/U549af5phJ #AGBT15
11:18am February 27th 2015 via Hootsuite
RT @bioinformer: SK: drilling down and tying phenome to genome in under 50h for #wgs #neonatal #genomics #AGBT15 http://t.co/IXHfBWC2Nf
11:15am February 27th 2015 via Hootsuite
SK:Nov 11 to Oct 14 shows unpubl data, will stop tweeting now.
11:14am February 27th 2015 via Hootsuite
SK: Sanger confirmation. Clin picture - change in medication, high dose Ig/steriods. Now healthy w/normal liver fn #AGBT15
SK: From 341 possible diseases, matches to 2 symptoms. PRF1 cmpd heterozygous. Dx: hemophagocytoic lymphohistiocytosis type 2 #AGBT15
11:13am February 27th 2015 via Hootsuite
SK: 913 ID ACMG var's cat 1-3. EMR has unstructured text; symptoms entered; automated OMIM/EntreGene differential dx gives 341 #AGBT15
11:12am February 27th 2015 via Hootsuite
SK: Uncommon, likely pathogenic vars in known disease w/high penetrance. E.g. sickle-cell SNV w/300K affected/y #AGBT15
11:10am February 27th 2015 via Hootsuite
SK: 28h var called and annotated. 1.6TByte DNA sequence (120Gbase), 2.8B genotypes. 4.8M var's. 1.085M <1% AF left #AGBT15
11:09am February 27th 2015 via Hootsuite
SK: (He's admits he's at risk for losing his @illumina t-shirt by saying the 18h figure.) #AGBT15
11:07am February 27th 2015 via Hootsuite
SK: Acute situation; organs not completely formed; difficult group. After ID an emergency: 26-34h turnaround time 2x100 in 18h poss #AGBT15
11:06am February 27th 2015 via Hootsuite
SK:23 deaths / 563 adm. in their institution. Infant monogenic diseases: 4.4K known, 20 discovered/month. Affect 4-8% of children #AGBT15
11:04am February 27th 2015 via Hootsuite
SK: Starts with NICU: 71d old w/acute liver failure. 14.4% of newborns in LII-LIV admissions in US; 49% preterm; 13.2d; $76K cost #AGBT15
11:03am February 27th 2015 via Hootsuite
Stephen Kingsmore, Children’s Mercy Kansas City. Newborn Sequencing: Rapid Genome Sequencing for Genetic Disease Dx in NICU” #AGBT15
11:01am February 27th 2015 via Hootsuite
LG:Q:Single-cell CN from RNA data? A:Largely not somatically seen. #AGBT15
10:35am February 27th 2015 via Hootsuite
LG:Q:WES vs WGS:we looking wide enough? A:Material is a limitation; targeted fits into clinical workflow, timeframe #AGBT15
10:34am February 27th 2015 via Hootsuite
LG: Clear there remain 'significant discovery opportunities' in clin cancer genomics. Response, resistance to therapy #AGBT15
10:31am February 27th 2015 via Hootsuite
LG: final point - key component is computational analysis geared toward questions asked in the clinic. #AGBT15
LG: Distinguishing from CNV's in tumor against TIL's. Further, subdividing T-cell subtypes, look at T-cell 'exhaustion' via profile #AGBT15
10:30am February 27th 2015 via Hootsuite
