Apr 4, 2017

10x Genomics at #AACR17 - April 4, 2017

Shauna Clark

It’s day four at #AACR17 and the inspiring science continues.  Refuel with some coffee and check out these posters that utilized 10x technology for single cell analysis and whole genome sequencing (WGS) with Linked-Reads.

During the morning session, PO.IM01.04 - Inflammation in the Tumor Microenvironment, stop by Poster 3693 "Single cell RNA-Seq of primary lymphomas reveals the diverse transcriptional states of the cancer immunologic milieu" presented by Noemi Andor, Stanford University, from 8am – 12pm in Section 28, Board 6.  For this study the authors used 10x Genomics for single cell RNA-Seq of tens of thousands of the cells from 5 primary Follicular lymphoma (FL) tumors.  Comparing gene expression researchers identified diverse transcriptional states among tumors and specific genes that were aberrantly expressed compared to normal B-cells within the same tumor microenvironment.  Read the full abstract here.

Be sure to also check out Poster 3976, "Resolving cellular complexity in renal cell carcinoma with droplet-based single cell transcriptomics", presented by Siva Vijayakumar, The Jackson Laboratory, from 8am – 12pm in Section 42, Board 19 during a concurrent morning poster session, PO.TB06.05 - Tumor Microenvironment 5.

In an attempt to better elucidate the roles of cell types in renal cell cancer progression, researchers used 10x Genomics Chromium™ Single Cell 3’ Solution to perform single cell sequencing on primary renal tumors and cells in the tumor microenvironment.  Single cell analysis of these samples revealed pathways enriched in specific cell types that have been previously masked by bulk RNA-seq studies, providing insights into potential new drug targets. Read the full abstract here.

In the afternoon poster session, PO.TB08.04 - Pediatric Cancer 3: Genetics and Genomics we are switching gears from single cell analysis to WGS with 10x Linked-Reads with Poster 4877 "Transcriptome sequencing of pediatric hepatocellular carcinoma reveals genomic events involving APC and TERT" presented by Katherine Haines, Baylor College of Medicine, from 1pm – 5pm in Section 42, Board 11.  In this study researchers were interested in identifying possibly pathogenic gene fusions in Hepatocellular carcinoma (HCC), a rare pediatric liver tumor. After using RNA-Seq data to predict gene fusions, the researchers used WGS with 10x Linked-Reads to confirm an inversion disrupting APC resulting in two in-frame fusion transcripts between APC and AP3B1.  They were also able to use 10x Linked-Reads to map the breakpoints in the tumor and germline DNA, which had proved historically difficult for APC inversions.  Read the full abstract here.

After checking out the posters, don’t forget to stop by Booth #1644 to see how you can incorporate single cell analysis and Linked-Reads into your cancer research.  Be sure to also learn more about our latest single cell analysis tool, the Chromium™ Single Cell V(D)J Solution for the assembly of full V(D)J sequences —5’ untranslated region (UTR) to constant regions— from short-read sequencing.

Stay tuned for tomorrow’s blog post to learn about some great posters to check out at #AACR17!

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