Blog @ Illumina
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Opening Sessions AGBT- Socks for Christmas: Actually Quite Useful

Abizar Lakdawalla, Ph.D.
| Feb 14, 2014

After an introduction and welcome address by Eric Green, Aviv Regev from the Broad Institute took the podium and gave an interesting talk on unraveling intra- and inter-cellular gene interactions in dendritic cells by single cell RNA-Seq of stimulated cells. Stimulating bulk cells followed by single-cell sequencing produced a different pattern than isolating single cells and then stimulating them, as a few eager beaver cells respond more quickly to LPS and then secrete signals to the surrounding cells. She used Illumina sequencing on ~2 x 10^3 cells but plans to scale up to 10^5 -10^ 6 cells. Part of her talk was embargoed.

Wendy Winckler gave us an update on her recently-formed group at Novartis and their work towards an NGS pan-cancer assay for lung cancer. She requested that we honor her embargo on this information, so no further info here.

In the last talk for the day, Valerie Schneider gave us an interesting tour of the new GRCh38 human reference assembly released on 12/24/13, including patches and novel sequences, 1000+ reported issues resolved with improvements in transcript annotations, and new centromeric model sequences (from the work of Karen Miga). New information was added, including human-specific gene duplications for SRGAP2a and the HYDIN genes. New assembly models use the linear chromosome coordinate system but allow alternate loci, pieces that align in parallel to a region of the standard chromosome, for displays of alternative haplotypes and paralogs. GRCh38 contains over 250 alternate sequence representations at more than 200 genomic regions. As the analogy goes, it was actually much better than getting socks for Christmas!

After this last plenary talk from an excellent lineup, we migrated to the Sunset Terrace for the welcome dinner reception where we connected with folks not seen for the past year. The warm camaraderie was interrupted by a downpour averaging about 5 ml/per drop. We quickly leaped towards the single large door that led us back into the foyer. After a reasonable delay giving an opportunity for our clothes to absorb the large drops of rain, we all managed to continue our conversations late into the night.