Astral Codex Ten

Illumina

3 min read

Illumina

Article

Illumina is a recurring brand in the Astral Codex Ten archive, appearing 2 times across 2 issues between July 01, 2022 and July 03, 2025. The archive places it in contexts such as “Illumina’s suspected-of-being-sinister monopoly on sequencing”; “Illumina short-read sequencing/SNP panels have been the major source of data”; “TOPMED dataset, which is from Illumina short reads”. It most often appears alongside Wikipedia, 23andme, @a_centrism.

Metadata

  • Category: Brands
  • Mention count: 2
  • Issue count: 2
  • First seen: July 01, 2022
  • Last seen: July 03, 2025

Appears In

Source Context

Recovered passages from the original issue text. When the raw archive preserved outbound links inside the source passage, they are listed directly under the quote.

Links For June
July 01, 2022 · Original source
34: New-ish startup Ultima Genomics claims to have lowered full genome sequencing costs by an order of magnitude, to $100/genome (and incidentally to have broken Illumina’s suspected-of-being-sinister monopoly on sequencing). Here’s some fair criticism, but overall I find this exciting.
Inline links: to $100/genome, Here’s some fair criticism
Highlights From The Comments On Missing Heritability
July 03, 2025 · Original source
Sequencing technology doesn't get discussed nearly enough in this area. Illumina short-read sequencing/SNP panels have been the major source of data for all of these studies, and they are absolutely delightful at finding SNPs but are crap at anything else. I think it will be appreciated that generally things that impact function aren't SNPs, they are broad changes, and so much human genomics seems to be hoping that the thing that is contributing to a change is able to spotted by being close to a SNP, instead of actually looking at the thing that is causing the change.
Genomes aren't lists of SNPs, they are mostly repeats and 2x150bp isn't going to get anywhere near close to capturing that variation, no matter how 'deep' you sequence. Long-read sequencing (PacBio & ONT, not Illumina's synthetic tech) is clearly better, and continues to demonstrate that there is massive variation that is easy to see when you have a bunch of 20kbp fragment, while almost impossible when you're just aligning little chunks of text to a 3gbp genome.
I work in non-model genomics and long-read sequencing is such a clear winner I keep getting surprised when Illumina gets contracts for these massive human studies. The Human Pangenome Consortium is going to be providing a dataset that is way more useful than anything that's come before. Anecdotally, I hear that for some non-European genomic data they know that ~10% of the data from an individual DOESN'T EVEN MAP to the human reference (but is human genomic data). This is all invisible to analysis, or even worse, just confounds things, as the 'true' causal SNP is somewhere in the data that doesn't get analysed, and so we're stuck looking at noise and trying to make sense of it.