October 2015

Vajta #icg10 Purpose is for healthy babies; but not for ‘better’ babies (sex selection, enhanced traits).

8:40pm October 23rd 2015 via Hootsuite

Vajta #icg10 Expect PGD to lower genetic abnormality than common IVF. Is it moral? Selection occurs via morphology already.

8:37pm October 23rd 2015 via Hootsuite

Gabor Vajta (Central Queensland Univ) PGD and screening from an embryologists’ point of view #icg10

8:34pm October 23rd 2015 via Hootsuite

RT @gabeinformatics: Correct in stating Illumina extracting de facto monopoly prices, but I'm not sharing the bet on eminent distruption ht…

7:20pm October 23rd 2015 via Hootsuite

OK, Theranos: Here's the Data the World Needs to See | WIRED https://t.co/pR2B1Zc27L

3:55pm October 23rd 2015 via Hootsuite

Boeke #icg10 Large project works- collaboration, governance, open participation and education opportunities.

5:38am October 23rd 2015 via Hootsuite

Boeke #icg10 Able to fuse syn1 to other chromosomes. Found that repeats and tRNAs were not critical for chromosome stability.

5:31am October 23rd 2015 via Hootsuite

Boeke #icg10 How many of the 5K genes be removed? Using loxP, can scramble and shuffle and perhaps find gain of function

5:27am October 23rd 2015 via Hootsuite

Boeke #icg10 Many groups including Tsinghua. Chr3 finished and reported; 5 more done. 750kb deleted, 215kb recoded.

5:22am October 23rd 2015 via Hootsuite

Hudson #icg10 Showed animation of their software deleting regions - introns, repetitive sequence, move all 275 tRNA genes to neo-chromosome

5:20am October 23rd 2015 via Hootsuite

Boeke #icg10 Preserve gene order, ncDNA untouched, delete repeats, relocate tRNA genes. Build synthetic DNA into larger and larger pieces

5:18am October 23rd 2015 via Hootsuite

Jef Boeke (NYU) Sc2.0 the Synthetic Yeast Genome Project #icg10 Goal: make it highly fit, and increase genome stability, flexibility

5:15am October 23rd 2015 via Hootsuite

Hudson #icg10 Pre-leukemia stem cells persist thru chemotherapy. Suspect can live in marrow for years in this pre-state.

5:11am October 23rd 2015 via Hootsuite

Hudson #icg10 Recurrent DNMT3a mutations are common in T-cells in AML. John Dick able to trace progenitor cells; 11/11 found 1st mut DNMT3a

5:10am October 23rd 2015 via Hootsuite

Hudson #icg10 For leukemia: Flt3, Npm1, Dnmt3a most freq mutated in AML; what is cell of origin? What’s the first mutation?

5:06am October 23rd 2015 via Hootsuite

Hudson #icg10 Shows CNV landscape in prostate cancer ‘PGA=% of Genome Altered’ https://t.co/YyzzDCkYad

5:04am October 23rd 2015 via Hootsuite

Lyon #icg10 15K genomes now available on ICGC website. Early cancer: before invasion. In prostate: PSA and pathology with scores

4:58am October 23rd 2015 via Hootsuite

Lyon #icg10 ICGC collects 500 t/n pairs from each of 50 cancer types. Genome, transcript one and methylome. 85 projects launched

4:56am October 23rd 2015 via Hootsuite

Hudson #icg10 Often 10k somatic mutations per cancer. Heterogeneity within and across tumor types.

4:55am October 23rd 2015 via Hootsuite

Thomas Hudson (Ontario Inst Cancer Res) #icg10 The DNA of early cancers.

4:53am October 23rd 2015 via Hootsuite

Lyon #icg10 Shared cases of Dx odyssey, where info was valuable. Exome Dx yield about 25%. Goes thru ACMG/AMP guidelines for pathogenicity

4:48am October 23rd 2015 via Hootsuite

Lyon #icg10 If no conclusion with panel, they go to WES or WGS. ‘Exome w/symptom-guided analysis’. Will do trios, for de novo muts

4:44am October 23rd 2015 via Hootsuite

Lyon #icg10 NGS gene panels useful for overlapping phenotypes. Illustrated with Marfan Syndrome. Their 17-gene panel doubled yield to 20%

4:41am October 23rd 2015 via Hootsuite

Elaine Lyon (Univ Utah) #icg10 The Value of Genomic Medicine https://t.co/UijbZUE74h

4:38am October 23rd 2015 via Hootsuite

Lai #icg10 Mentions @hail_cser to bring clinical WES to patient care.

2:43am October 23rd 2015 via Hootsuite

Lai #icg10 Clinical WES, how to develop it into a mainstream diagnostic? The need to seta higher bar for testing, not easily done.

2:42am October 23rd 2015 via Hootsuite

Lai #icg10 And phenotype heterogeneity, and cost. Boosting is now ‘the way to go’, also curation, manual validation all costs.

2:40am October 23rd 2015 via Hootsuite

Lai #icg10 Challenges include alignment, population db’s completeness, mutation db’s shortcomings. Shows ACMG gradient of pathogenicity

2:38am October 23rd 2015 via Hootsuite

Lai #icg10 FN’s: lists >20 genes missed in neuromuscular disorders. Most WES enrich 92%. They enhance 8K genes, still 23-28 genes missing

2:36am October 23rd 2015 via Hootsuite

Lai #icg10 Challenges: lack of standardization, diff methods and algorithms. Variant interpretation: greedy interpretation Vrijenhoek 2015

2:33am October 23rd 2015 via Hootsuite

Lai #icg10 Can ID pts who would be candidates for clinical trials (ex: exon skipping therapies) for neuromuscular disorders

2:32am October 23rd 2015 via Hootsuite

Chen #icg10 But genes involved are too large, so WES makes sense, along w/phenotypic variation. They get 40% Dx yield.

2:30am October 23rd 2015 via Hootsuite

Lai #icg10 Clinical WES ave. coverage 100-120x; 50-70x for WGS. Illustrates neuromuscular disorders considered rare

2:28am October 23rd 2015 via Hootsuite

Poh-San Lai (Nat’l Univ Singapore) Clinical sequencing - opportunities and challenges

2:25am October 23rd 2015 via Hootsuite

Chen #icg10 https://t.co/XXxITRGT3d open for other provinces to apply to get Dx and consulting, and how to submit samples.

2:24am October 23rd 2015 via Hootsuite

Chen #icg10 Points out tech maturity not the same; aCGH and FISH are mature, but NGS still maturing. Clinical trials for NGS PGD needed.

2:17am October 23rd 2015 via Hootsuite

Chen #icg10 Concludes PGD and NIPT ‘should be applied in managing genetic disorders’ in high risk cases.

2:16am October 23rd 2015 via Hootsuite

Chen #icg10 Example hearing loss, 1/1000 half is congenital. GJB2, case had compound het. Of 8 embryos, 5 carriers and 3 affected, healthy

2:14am October 23rd 2015 via Hootsuite

Chen #icg10 2/7 embryos were normal. Checked for aneuploidy, also SNP array to confirm. Healthy female birth.

2:11am October 23rd 2015 via Hootsuite

Chen #icg10 Example Sponal Muscular Atrophy, 1/6K Han Chinese. Carrier in Han is 1/40, del exon 7 of SMN1. MLPA ID’d parents, couple >40y

2:09am October 23rd 2015 via Hootsuite

Chen #icg10 Starting with genetic counseling, through PGD via aCGH, FISH, Sanger or NGS. Most effective way to prevent genetic defects.

2:06am October 23rd 2015 via Hootsuite

Chen #icg10 Reviews PGD/PGS assisted reproductive technique; lists a number of disorders and 4.5K disorders in OMIM w/o ID’d gene

2:04am October 23rd 2015 via Hootsuite

Zijiang Chen (Shangdong Univ) #icg10 Genetic diagnosis in reproductive medicine

2:01am October 23rd 2015 via Hootsuite

Download a Bear! https://t.co/50qQyMMv4o Browse like you’re in another country! @theTunnelBear https://t.co/dZE8Ts9hNW Happy user here.

12:29am October 23rd 2015 via Hootsuite

Poh-San Lai (Nat’l Univ Singapore) Clinical sequencing - opportunities and challenges #icg10

12:08am October 23rd 2015 via Hootsuite

Durbin #icg10 Found HTLV-1 in TGP data in indiv’s from Africa. GRC is now curating indiv genomes. @GA4GH mentioned, a new API approach.

12:06am October 23rd 2015 via Hootsuite

Durbin #icg10 Separate the good reads and compress - 450GB on a server, 200x compress. Can search all virus in GenBank in 2535 TGP in 2d

12:03am October 23rd 2015 via Hootsuite