By Kirell Lakhman

Good question. I’ll let you know as soon as I find out.

But for the moment let’s say it’s missing in action, a victim of the upheaval that occurred at the company late last month that deep-sixed its CEO and a handful of other C- and EVP-level officials for mishandling test data surrounding its important SEQureDx Down syndrome test.

The pain quickly spilled over to the company’s shareholders, who were forced to watch their shares lose 87 percent their value since the beginning of the year, most of it in the days following the results of the “mishandling” investigation.

To be sure, most industry insiders with whom I’ve spoken say the DNA-based assay, which is designed to test for trisomy 21, could be a winner if given the chance to shine in a properly run trial.

How is any of this related to the $2.3 million, which Sequenom appears to have promised to use to further develop its prenatal play? The shop last fall did promise to make certain investments in its prenatal test menu when it acquired the Grand Rapids, Mich.-based lab that became the Sequenom Center for Molecular Medicine.

For more color, read the seventh paragraph of this Michigan business press story describing how Sequenom won a prize in an annual award ceremony for buying the lab, then called the Center for Molecular Medicine. Sequenom bought the lab last November for $4 million. The business awards story is also the first to mention the $2.3 million prenatal investment and 500-person hiring plan.

An investment of $2.3 million would be important because Sequenom’s prenatal play represents a linchpin in the company strategy of regaining market share, not to mention investor respect. (It’s also important because at the end of June 30 the company had $69.3 million in cash, equivalents, and short- and long-term marketable securities).

And how it handles (read: invests in and mollycoddles) the technology behind its prenatal tests will make or break — presumably for good, this time — Sequenom’s ability to remain in business as is. I’m not exaggerating: Business media reporters began chatting up bookmakers while former-CEO Harry Stylli’s body was still warm to gauge who would be first in line to acquire the badly listing company.

To be sure, this could signal that Sequenom may have some supporters, if only of the life-line variety. Playing Devil’s Advocate, I suggested to several industry watchers that the SEQureDx test may be dead in the water, so who would ever buy the company? One knowledgeable source told me “[i]t may be premature to classify the Sequenom prenatal test” in that way. “The company is still insisting the technology works,” and there have been “noises that the RNA test can be inconsistent,” he said.

“The previously announced trial data [for the T21 assay] is toast, but enough people have used the technology that it’s hard to believe there’s nothing there,” he added.

Fair enough. So where do things stand right now? As I said before, the trisomy 21 test is currently MIA. That is equally true for Sequenom’s other prenatal test, the one that can simultaneously test for trisomies 21, 18 (also known as Edwards syndrome), and 13 (known as Patau syndrome). The company said in January it is pursuing development of that assay.

Of course, the company made that pronouncement in the same breath that it said it remains on track to launch trisomy 21 in June. Two weeks ago, when I spoke with Ian Clements, Sequenom’s spokesman, he told me Sequenom still plans to develop the assay, though deadpanned that “timelines have obviously changed.”

Today, Clements said those and other plans ”have been set back, and therefore any plans [in which] we may have talked about investment numbers or timelines or employment will have been delayed” because of the SEQureDx issue,” he said. “We may still be able to do this; the question now become ‘when.’

“I don’t want to say that these plans” — the investment and the new hiring, whether $2.3 million and 500, or some other version — “are off the table, but certainly some plans are delayed and they would be slightly different because the roll out of the [SEQureDx T21] test has changed.”

“Whatever we said … about expansion plans may well still be true, but we don’t know when that necessarily will happen because it was all based around the June 2009 launch of the T21 test, which is now will happen at a later date,” he added.

Sequenom still won’t say when it would releases that test.

Despite Clements’ dodging and weaving in the dark, one thing remains clear for Sequenom: The Grand Rapids CLIA lab “is still an important part of our strategy,” he said. In fact, the facility has been running a CF test since September, and still plans to debut two more assays there: a Rhesus (D) test and a fetal sex-determination test, he said, without elaborating.

In addition, “as we go through the development process of the T21 test, when that gets ready for launch that would also be run out of [the Grand Rapids] CLIA lab,” he said. “Having all of these tests ramp up and roll out will require some personnel investment. So all the plans remain the same; what’s different is — and what we haven’t spoken about to the public, I think — is a) what is the timing of those things, and b) what is then ramp-up rate?” Clements said.

“We’ll talk about stuff when everything is re-locked and loaded,” he added. “Clearly there will be some ramp-up.”

One final point: I could find no mention of the $2.3 million prenatal investment or the 500-person hiring plan in any of Sequenom’s written public statements. The only thing the company said on the topic, in its Sept. 28, 2009, press release announcing its planned Center for Molecular Medicine acquisition, was that it had “received a tax incentive package valued at up to $20 million over 12 years” and that “[t]he project [acquisition] includes a potential, near-term capital investment of approximately $10 million and the potential creation of several hundred jobs over five years.”

One has to wonder whether the larger dollar and head-count projections were floated at the business awards soiree by giddy Grand Rapids city officials. As bad as Sequenom’s outlook is at the moment, Michigan’s is far more grim.

I have a call out to them and will update the story if I learn anything.