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Linked-Reads provide long-range information enabling structural variant detection and phasing of genome and exome sequencing data.  In our third 10x-pert Workshop session, our R&D 10x-perts provided an overview of the Loupe™ Genome Browser for structural variant detection and took closer look at visualizing simple structural variants and deriving complex events.
Researchers at Stanford University have developed novel bioinformatics tools that leverage 10x Genomics’ Linked-Read sequencing to phase and resolve the complete structure of cancer genomic rearrangements. 
Two recent publications applied the power of Linked-Reads and the Chromium™ Genome Solution to genetically characterize gastric and triple-negative breast cancer. In both cases, the researchers discovered complex genomic rearrangements that they associated with the amplification of oncogenic driver genes.
Using 10x Linked-Read technology combined with standard, short-read sequencing, Dr. Noah Spies and his team at Stanford University were able to develop a statistical method for complex structural variant detection—Genome-wide Reconstruction of Complex Structural Variants (GROC-SVs).
There’s a growing number of data analysis tools being developed for single cell and Linked-Read applications, including gene expression, genome assembly, structural variant detection and more.  Check out the list we’ve compiled so far.
In a recent publication from the Broad Institute of MIT and Harvard, researchers identified >11,000 distinct structural variations among participants with autism spectrum disorder. These results provide new insights into the extent and diversity of structural variation present in the morbid human genome.
The InPSYght schizophrenia and bipolar disorder sequencing project seeks to produce Whole Genome Sequencing (WGS) data to identify variants associated with disease, build a reference panel of structural events and haplotypes to impute into large genotype data sets, and create and share data and methods with the community.
The Chromium™ Genome and Exome Solutions use Linked-Reads to provide long range information from short read sequencers, giving you the power to detect complex SVs.