By Kirell Lakhman
Sequenom last week said it has decided to develop its trisomy 21 Down syndrome test solely on a next-generation sequencing platform, and that it plans to launch it as an LDT by the end of next year.
But first it needs to choose a sequencing platform — an idea it has been tinkering with since at least 2008. As of last week, there are three in the running: Illumina's Genome Analyzer II and HiSeq 2000 platforms, and ABI's SOLiD instrument.
With capital no longer a chief concern — Sequenom recently banked $51.6 million from a private stock placement — the shop must now decide which of these platforms will run the T21 test, which will be the first one for the company that uses next-gen sequencing technology.
Last week, during the company's first-quarter earnings call, Ron Lindsay, interim senior vice president of R&D, said Sequenom has been using Illumina's GA II to develop the T21 ever since the firm abandoned its MassArray platform.
But the company has also recently begun considering switching to the newer, higher-throughput HiSeq 2000, and has started validating the SOLiD.n
"On technical, cost, and performance grounds, we will make a decision as to which way we go," Lindsay said during the call.
Discussing cost, he said he expects reagent outlays, which today run around $200 per sample, to drop by half over the next 12 to 18 months — which is before Sequenom plans to debut T21.
With reagent at $100 per sample, "we are pretty comfortable that sequencing is no longer an expensive platform to do a test like this," he added. However, he did not factor in the cost of the instrument itself, which would increase the price of the test accordingly.
On technological and performance grounds, Sequenom reckons it will take around one week to run T21, including sample prep, sequencing, data analysis, and reporting, regardless of the platform.
Annual throughout — and therefore potential revenue — is another story: Lindsay said one GA II instrument could process as many as 3,000 samples per year, the HiSeq could run 10,000, and the SOLiD "potentially more than that."
To be sure, Sequenom has been studying the feasibility of developing a sequencing-based method for noninvasive prenatal testing for Down syndrome since 2008, and in a paper that year it said it can be done.
The paper, which appeared in the Dec. 23 that year in PNAS, said that Illumina's first-generation Genome Analyzer "accurately quantified maternal plasma DNA sequences for fetal Trisomy 21, or Down syndrome, in samples taken from women in the first and second trimesters of pregnancy."
Dennis Lo, a co-author of the study, said in a statement at the time that the method is likely “several years away as a commercially viable test,” but may offer “a complementary approach” to the ill-fated T21 test Sequenom had been developing.