Identifying bizarre samples using DNA sequencing data

In the early morning, London’s Natural History Museum (NHM) is eerily quiet. The only sounds to be heard are echoes of the staff discreetly bustling through the halls lined with all sizes of specimens and species. Claire Griffin, the NHM’s Core Labs senior sequencing technician, has her laboratory hidden away in the labyrinthine catacombs spread out underneath the museum. Tucked behind the exhibition walls, she seeks the answers to questions that someone, somewhere in the world, is waiting to hear. Griffin has worked at NHM for over 20 years. She started her professional career in Oncology but decided to apply for a job as sequencing technician at NHM in 1999 and has not looked back since. “I have always been fascinated by the natural world, and can’t stop myself from collecting interesting and possibly useful sample material. I always have gloves and collection tubes on my person somewhere, much to my family's embarrassment sometimes.”

It goes without saying that Griffin is still excited about sample that end up at her desk from all over the globe. The samples she receives are often in terrible condition. They’ve been exposed to high temperatures or industrial processes – or they are old, degraded, and have come into contact with a wide variety of people and places. Samples received can be wet or dry. She receives samples that are badly preserved or freshly collected. Some are floating in preservatives. The specimens are often contaminated with DNA from bacteria, fungi, or even rodents. Despite their state, Griffin has to prepare those samples in a way that allows her to sequence and identify the DNA of the samples, avoiding any false traces of the people or microorganisms they may have interacted with.

Natural curiosities

Each sample Griffin receives is as unique as its journey: an unknown moth found in a wine bottle in Europe; a strange frog discovered in a Caesar salad in North America, and someone just sent her an antique Japanese mask adorned with animal hair. The week before, an auction house asked her to verify that the inlay of a table was not ivory, and she often receives pelts ceased by customs at the UK airport.

“The work at the museum is really varied, and in the molecular labs we receive a lot of different types of tissues and materials. It’s our job to provide DNA sequencing data, or molecular data, for those samples,” she explains. “I have helped analyse all kinds of items from the museum’s collection – termites, spiders, reptiles, seaweed, jelly fish, bird excrement, 200-year-old bird foot pads, as well as the menagerie of other items, some decades old, that come in from private collections and auction houses,” Griffin muses. The stranger the sample, the more likely it is to end up on her desk. Her mission is to work out the best method to reveal the sample’s secret, to identify the species, no matter what condition it may arrive in at her lab.

Testing millions of samples

Griffin is responsible for maintaining the lab’s Sanger sequencing system, as well as implementing quality control in the museum’s sequencing lab. “Wherever the samples come from, I use my experience to think about the kind of sample it is, its strengths and weaknesses, and what sequencing method makes the most sense for it,” she explains. The extraction kits that she and the other researchers use depend on the sample type. She explains how the kits have to be able to provide a good yield of DNA regardless of the amount of tissue she’s working with, and for that, she often prefers using QIAGEN kits. “We use QIAGEN’s nucleic acid extraction kits quite frequently,” she says. “The DNeasy blood and tissue kit is the one I opt for most often for a wide range of sample types, because it gives us high-quality DNA, even with tricky samples.”

She uses the kits for specimens as diverse as sponges, pieces of insect legs, beetles and beyond. “I've always found the QIAGEN kits are extremely reliable and they work on a wide range of tissue types.” Oftentimes new tissues come into the lab that she’s never seen before, but Griffin welcomes the challenge. “I often get new tissues I've never handled before, but through the experience and knowing what the kits can do, I apply that knowledge and use it for novel and different types of tissue.” From the smallest remnants, I can determine not only the species but sometimes also the sex,” she says.

Discovery of new species

DNA sequencing data recently revealed the genetic signature of a wasp in an unknown ant species Griffin received from Singapore. Initially suspected to be one of the contaminants she frequently encounters, the wasp actually turned out to be a never before seen species of parasite that lays its eggs in the ants. Thanks to her work, a new species of parasitic wasp may have been discovered.

With mystery samples submitted to the lab from all over the world, Griffin’s work can sometimes uncover unexpected results. “I’ve been working here for more than two decades and every day is different,” she says. “I must have seen thousands of samples in that time, all weird and wonderful in their own way.” A new sample is currently sitting on her desk. A customer found a gecko in a bag of steamed vegetables from a UK supermarket. No one knows what species this is, yet. But Griffin intends to find out.