Exploring a Patent Application for Single-Cell Whole-Genome Library Technology

A few weeks ago I posted about single cell transcriptomics technology and patents. In this post, building off of that, I want to look at a published patent application for single cell genomics, titled Single Cell Whole Genome Libraries and Combinatorial Indexing Methods of Making Thereof. It’s publication number 2023/0323426, and it published back on October 12th, 2023. The inventors are Adey et al., and it was filed by Oregon Health Science University and Illumina Inc., and assigned to both OHSU and Illumina.

Remember that I’m not a lawyer, and nothing in this post is legal advice. While I am a registered patent agent, nothing in this post constitutes advice for a client.

This is a pretty cool piece of technology. The basic idea is to build a sequencing library with entire genomes from single cells. Part of the technology is to chemically treat nuclei to remove nucleosomes without harming the integrity of those nuclei. This involves pooling nucleic acids from cells, labeling them, separating them, and relabeling, which is similar to the idea behind the transcriptomics technology I linked to above. Indexed genomic data from single cells could be useful for applications such as looking at genomic differences among cells within a tumor. In Gawad et al. 2014, for example, the authors went through a lot of trouble to show the development of leukemia by looking at single cell genomics. Certainly there is interest in this approach, and the patent application claims to disclose new ways of accomplishing this.

This is still a pending patent application, and in the file wrapper it recently received a non-final rejection. For those who don’t know, the patent office may make either final or non-final rejections. Confusingly, a final rejection is not especially final in the normal sense of the word, but that’s a topic for a different blog post. (Many IP attorneys have such a blog post, here’s a link to one.)

The basis of the rejection mostly has to do with claim language, and the lack of an antecedent basis for some of the terms used in the patent application. The examiner noted several instances – I counted fourteen – where terms were introduced in the claims without a clear meaning. This can be a problem under 112(b). I expect that these are problems that can be overcome, and I’ll keep an eye on this application to see what happens to it.