what happens when you leave the extra quilt out

Wednesday, May 13, 2015


We are so late with these test results. February was killed by moving half the lab into new quarters.

March one of the techs was out sick the whole month, and we (finally) received our new sequencer. But, you can’t do anything with a new machine without fully testing and validating it, and we’ve got the whole Methods Validation dossier to construct there. No catching up the backlog in March.

April the one tech was still out sick and then there were the spring vacations to deal with. All my techs are moms, and when school is out, so are they. Legally, I cannot prevent people from taking their days, I can only say which days. So, minimal work done in April.

May the tech is _still_ out on leave, and the rest are threatening to follow suit if the workload doesn’t lighten up. (wha? you just took all that vacation!). Plus May is the month of holidays. Four of them, and since one is on a Thursday the lab is closed Friday as well, boss’s orders. No point working just one day, is there? Oh, and the end of May is the end of the annual vacation cycle, so any days or hours off left hanging around have to be taken.

And now today, we called to inquire where our order of polymer to run our machines has gotten to, we’re informed that the manufacturer is out of stock and will not have any more before the end of the month. So even if we wanted to work, we couldn't. Just forget it.

Is it any surprise that productivity is crashing?

At the end of the year when we find we have delivered just 70% of the tests we were supposed to, and that most of the ones we did do were horribly late, will the bosses remember this disastrous spring? Will I be excused? Or will I have failed in my objectives and gain black marks on my performance review for poor management?

Monday, May 11, 2015

Aw, no!

It's getting quite summery out, and the cats have been taking advantage.
Natalie went Out in the evening of April 29th, and has not been seen since. Not a sign of her. She's often gone for a day or two, and once she did disappear for a week. But it's almost two weeks now, and none of the neighbors have seen her either.
And then, while that was going on, Bandersnatch got sick and died.
The Bandercat!
Started looking woozy just around the time Natalie went out. Stayed out & hidden away the first & second of May, then when I saw her on Sunday a week ago, I scooped her up and kept her under my thumb waiting for the vet's to open up Monday morning. Kidney failure, no obvious cause. She didn't get any better at the vet's for 3 days, and Wednesday I had her put down. The poor little sweetheart.
Sienne is just now giving up looking for them both. She is still quite anxious (though, Sienne is always anxious).
Sienne rarely goes out; only when I'm out doing yard work, really. So if there was something the others got into, she wouldn't have found it. You have to wonder at the coincidence of Natalie disappearing just when Bandersnatch got sick. Did they catch some poisoned mice, perhaps? Or maybe the two events are unrelated.
In the meantime, the cherries are starting to blush. It's only the 11th of May - they're weeks early.
Crazy world.

Tuesday, April 28, 2015

Future: here we are.

NY Times headline : Chinese Scientists Edit Genes of Human Embryos, Raising Concerns. Since work with the Crispr system has shown that gene splicing can be quick and easy in many systems, the scientific community has been urging restraint on human embryo manipulation until such time as we’ve had to think about all the ethical complications of being able to do so.
Lots of people are going to be getting into this, very fast. They don’t care that changing an embryo’s genetic makeup might be the wrong thing to do. They care that they can be paid big time for doing so. Well, eventually. Once it actually works. Though maybe even if it works a little bit once in a while.
What the Chinese article showed was that trying to splice a gene into an embryo (ones already declared to be non viable), specifically a normal copy of beta-globin gene, to correct a very serious genetic condition known as beta-thalessemia, was a disaster. That was their basic question – could you do it. They weren’t trying to fix a real case and have a child born from their experiments. (well, yet...)

In a collection of cells, some underwent the editing as planned. In others, a similar gene was incorrectly targeted. In others still, a variety of mutations happened. Overall, it was a mess, far, far from generating a viable embryo.

So there’s a ways to go before this new gene splicing kit allows anyone to make babies to order.

What I think is that calls to go slow and think it through before diving in, calls to wait for national and international guidelines, may have little effect on ambitious labs trying to be first across the finish line. Scientists are asking for a ban on such research, but bans on cloning or embryonic stem cells didn’t stop such research from happening, only drove it toward different funding and/or different countries.

Monday, April 27, 2015

A bit of paper

Actually, a file sent by email.

But yes, folks, we are officially
by the COFRAC.
We were pretty sure we would be, but it makes a certain difference to have that certificate in hand.

Break out the champagne!

Friday, April 24, 2015

Superpower: variant detection

Warning! Highly technical post today!
This week is pretty calm at the lab, with nearly half our staff on vacation. That means 4 of the 5 diagnostic techs. Since we're pretty far behind in signing out cases, I've been picking up some of the slack in reading sequences. All our sequences are read twice, to maximize the chances of actually seeing any variants that are there, and getting them onto the summary table with the right name and all.
You'd think with all the sequence alignment software that's been out there for so very, very long, that you'd barely need one person to read all the sequence, let alone two. Differences should just pop out. Gotta be blind not to notice one bold red base in a whole field of grey.
Weeeeellll, it's not always so easy as that.
This particular case we signed out last year as having no mutation. But it bugged me, because the patient's tumor had all the signs of mutation in this one gene. Not everyone with all the signs has an inherited mutation, but most of them do. All the analytical steps checked out, though. No mistakes in testing the right sample or anything.
These days with every new analytic series, we include a rerun of something we've run before. So in the current series I reran this sample.

Because 80% of my techs are out on vacation, there wasn't anyone to do the second read of the sequences this week, so I've been doing some of that, both to stay in shape and to move things along. But what's this? Oh, look, a little secondary signal when there should only be one.
The software missed it, because it's just a little bump, far below the 35 % threshold to be flagged. The technician missed it. Really, the second signal accounts for less than 20 % of the signal at that position. Maybe just 10 %. Sometimes we have little peaks at around 10 % in all the samples, though only on one of the two strands of the DNA. Just artifacts when they're systematically present like that. Certain exons are notorious for this sort of thing - you can't get rid of it, and it means nothing.
This one is different. The second peak is only in this one sample out of the 47 in the series. It's present on both strands. The rest of the sequence is nice & clean. And the kicker is that the normal signal is diminished (which doesn't happen with artifacts). The two signals added together equal the intensity of the normal signal in all the other samples.
Hmmm. Normally, inherited mutations are 50-50, because you have one mutated and one normal copy. The patient's family history clearly indicates an inherited mutation, not one that is new in her and doesn't affect all of her cells. No reason for me to look for something 85-15.
So I have my computing guy dig up the archive of this bit of sequence for the first time we ran the sample. This time you really have to look for it, but it's there. No way anyone would have caught that.

There can be technical reasons why a mutation might not show up 50-50. In special genetics cases it might just not be 50-50, like when you have a chimera (a patient whose cells do not all come from a single fertilized egg, but who is a mix of two, only one of which carried the mutation in question) or a mosaic (where the mutation was not present in the egg or sperm, but happened in the early rounds of cell division so that only a subset of the cells in the body have it). Then there's the technical case where there is a second sequence variant farther on which just happens to sit within the sequence of the primers we used to amplify the bit in question - and the amplification of the mutant copy is much less efficient than for the normal copy.
We'll be looking into all that. A chimera will have this lopsided ratio at any sequence variant in the gene, and there are plenty of neutral variants to look at. A mosaic we should be able to rule out, based on family history. And the technical case we can resolve by designing new primers farther away and capturing that second variant. Oh, and the bugaboo of DNA labs, the sample itself is contaminated with a second person's DNA. We'll be looking at an independent sample from the same person, just to be sure.