10X Genomics: Combining new and old techniques to unlock new insights

Illumina sequencing is by far the most common next-generation sequencing technique used today, as it extremely accurate and allows for massively parallel data generation, which is incredibly important when you’re working with a dataset the size of a human genome!

That said, there are inherent shortcomings that exist in the typical Illumina sequencing workflow. Illumina uses a very high number of short sequencing reads (usually about 150 bp for whole genome sequencing) that are then assembled together to cover the entirety of the genome. The fact that traditional Illumina can’t be used to identify long-range interactions can cause issues in some cases, such as samples with large structural variants or in phasing haplotypes.

However, a revolutionary new library preparation method designed by 10X Genomics can effectively solve these types of issues. The 10X Genomics GemCode technology is a unique reagent delivery system that allows for long-range information to be gathered from short-read sequencing. It does through usage of a high efficiency microfluidic device which releases gel beads containing unique barcodes and enzymes for library preparation. It then takes high molecular weight DNA, and partitions it into segments that are about 1M bp long; from here, these segments of DNA are combined with the gel beads. This means that each read that comes from that segment of DNA has its own unique barcode, which gives us knowledge about long-range interactions from traditional short reads.





Figure 1: Projections of 20,000 brain cells where each cell is represented as a dot. (A) Shading highlights major clusters identified in the dataset. (B) Cells were colored based on their best match to the average expression profile of reference transcriptomes [2].

Another application of 10X Genomics GemCode comes in the form of single-cell sequencing, which also uses the microfluidics device, but combines individual cells with the gel beads instead of DNA fragments. This allows for sequencing and barcoding of individual cells from a larger heterogeneous sample. This can work for DNA or RNA sequencing. 10X Genomics recently published an application of this technology using the Chromium Single Cell 3’ Solution on a mouse brain. 1.3 million cells from embryonic mice brains were sequenced and profiled using this technique; principal component analysis and clustering was then performed on the resulting data to separate out the distinct cell types, identifying 7 major classes of cell types, as seen in Figure 1 [1].


Traditional Illumina will still likely reign supreme for run of the mill applications, since at this point it is still more cost effective. However, 10X is certainly gaining in popularity for specialized applications where understanding structural variants or single cell sequencing is important to the goals of the project. We’ve certainly noticed an uptick in requests for 10X genomics recently and we look forward to even more advances being made with this amazing technology.

If you’re interested in 10X technology, please contact us at projects@genohub.com for more information!