COVER STORY: Lab to order

Most life science researchers could only dream about setting up a brand new lab and fitting it out with brand new state-of-the-art equipment. But for Assoc Prof Ian Findlay, who left the Australian Genome Research Facility at the University of Queensland (UQ) last year to become chief scientific officer at pathlab giant Gribbles' new molecular science division, the dream became a reality.

Gribbles, committed to move into the area of genomic testing, provided Findlay and his team with several million dollars to design, build and fit out a brand new, purpose-built genomic research laboratory. Findlay runs the research and development arm of the Gribbles Molecular Science (GMS) business, which is based in Brisbane. The researchers moved into their new home in March this year, picking up their UQ research where they left off, but now with all the equipment they need and a purpose-built lab in which to do it.

Setting up a new lab is a pretty hectic task, Findlay admits -- particularly when you're starting with just a concrete slab on the ground. "It's a brand spanking new lab," says Findlay. "When we moved in, there was just concrete on the floor. We drew out in chalk all our different labs and rooms and things on this concrete, then did the design and the equipment we wanted really from scratch and we put a design through and got the labs built."

Not only is Findlay's team developing a range of pre-implantation, pre-natal and forensic tests based on the analysis of DNA from a single cell, it is also expanding into predictive tests and veterinary applications. GMS work is based around three aims: working with the smallest possible sample, with maximum possible analyses, at the lowest possible cost.

Having pioneered the technique of DNA fingerprinting in single cells in 1994, then increasing the technique's specificity to reach forensic quality in 1997 -- detection of one cell's DNA in two or three billion -- Findlay's team has now increased this specificity to one in 10 billion.

"We can get DNA samples from dandruff, from scrapings under fingernails, from cells left on clothing, cells left on stamps and cigarette butts, because all we need is a single cell," he says. Because of those high levels of sensitivity, this technique can present problems. Findlay's team is up against contamination of samples from extraneous DNA floating around in the air, which can have serious consequences when a test is being used for pre-implantation diagnosis of an embryo, or forensics.

But designing a brand new laboratory with their own specific needs in mind was something the researchers relished. "We knew that contamination could be a major problem, so we designed things to eliminate contamination," Findlay says. "At the university, there would always be a contamination problem just from dandruff floating around in the air and contaminating samples.

"We also knew what equipment we wanted, so we bought it rather than inheriting it. Often, what happens when you move into a lab is that you inherit pipettes and you inherit centrifuges and things that aren't quite right. It has been great to actually buy the right equipment from scratch," Findlay says.

The new lab is fitted with ultraviolet lights, which denature most DNA floating around in the air, and a unidirectional (one-way) air flow system, where air comes into clean work areas, pushes through into general areas and then into ducted areas.

Most labs have normal air-conditioning that allows air to go anywhere. But because Findlay's team can get DNA fingerprints from things floating around in the air, such as dandruff and amplicon, a one-way airflow from clean to ducted areas makes sure clean work areas are not contaminated by feedback from ducted areas. In addition to this, the cell analysis and preparation areas are well isolated.

As well as having a brand new lab, Findlay's team is finding that being part of a major pathology company has its advantages. Access to human tissue samples has become much easier for Findlay's team -- now, it can makes use of the whole Gribbles network of pathology samples.

"On one project [at the university] we were getting five samples a week, and now we can get 500 samples a week," Findlay says. "We have the potential to access thousands of samples, both human and animal. In the university environment there is only so much you can do. What we want to do is take it to the next stage and actually get the samples and the techniques into practice. We can now move full steam ahead."

According to Findlay, Gribbles sees huge potential in the area of genomic testing.

"[The company is] very forward-looking, because many pathology tests use old, labour intensive, expensive technologies," says Findlay. "Even within Gribbles, which is already highly automated, many tests in common with other pathology companies use 20-year-old technologies because they are tried and tested.

"With the advent of the Human Genome Project, they are realising: 'Hang on a second, DNA is going to be big, and we have to get involved in DNA'.

"It's going to be enormous, and Gribbles has been very progressive in being really the first pathology company to really embrace molecular biology, and not only for humans, but for animals and plants as well as forensics."

Findlay's team has the task of improving current technology, as well as developing new tests that Gribbles can use in their pathology services. They are also moving the single-cell fingerprinting technique into the forensic field, helping police to solve unsolved crimes from years ago.

Using a very small sample, such as DNA from a single cell, is advantageous in pathology. Not only can more information be gleaned from these samples, it can be gleaned at a much lower cost. Rather than doing a single test at a time, as is the traditional procedure, to take one sample and do one test, many tests can now be carried out in parallel on the one small sample, making the process much more cost-effective.

"It does open up a whole new era of genetic testing, because combining unlimited capability with unlimited samples, there is almost nothing you can't test for and you've got the samples to develop new tests," says Findlay.

"At the moment, [pathology labs] take a very large sample for every single test. But if you can take a sample and cut it into a hundred different samples and then do 20 tests on each of those samples, it is therefore much more cost-effective and less invasive to use a single sample from the patient."

Gribbles Molecular Science is split into two groups: the Brisbane-based research arm, and the service arm, which is run by Keith Byron in Melbourne. The research arm develops the tests, and when they are ready for application, they are sent down to Melbourne where they are run. "The way it has been set up is very good," Findlay enthuses. "Keith has run a diagnostic service for years and I've done research for years. We can exploit expertise and maximise experience in different places."

Gribbles, listed on the ASX, is a multinational company, with labs in Singapore, India and Malaysia, a base on the Gold Coast, and large outfits in South Australia, Victoria and News South Wales.

Findlay is hoping to build up the Queensland arm of the business. Because of Queensland's closer proximity to Asia, Findlay says, it is easier to export tests from Brisbane directly to Asian markets -- so, rather than shipping samples from Asia to Australia for testing, they could be done in Asia.

"A lot of pathology testing is currently expensive, and we want to try to develop tests that are inexpensive so that everyone can have access," Findlay says. "There is an underclass in any population that just cannot afford tests, particularly the more complex tests. It's a real shame, firstly because they suffer, and secondly because the healthcare system has to pick up the tab much later on in life.

"What we want to try to do is get in early and also look at cost-effective predictive testing, look at testing much earlier on, and try to save healthcare dollars down the line -- have an investment now, in the beginning, rather than much later when people age, much like a stitch in time saves nine."

Findlay says the move to Gribbles has been synergistic, combining Gribbles' pathology testing expertise with the tests his team is developing to further progress their work.

"Nowadays you just can't sit back and relax, you've got to look to the future. We've got these clinical diagnostic and forensic tests, then we've got a whole bank of other tests we are looking at for the next year, two years, five years and into the future," envisions Findlay. "We have positioned ourselves so that we can be very flexible and look at new technologies and get into those areas as quickly as we can, in the best way that we can, using our R&D expertise and service expertise. GMS' expertise can also offer a wide range of cost-effective DNA sequencing, genotyping and SNP analysis services that are currently too expensive or inaccessible for many Australian researchers."

How to get the most out of a cell

Findlay's team has developed the basic technology of single-cell diagnosis and single-cell fingerprinting, and is applying it to three main clinical diagnostic projects: non-invasive pre-natal diagnosis, faster pre-natal screening, and pre-implantation diagnosis for IVF.

The two current widely-used pre-natal screening procedures used to detect chromosomal abnormalities and genetic birth defects, chorionic villus sampling (CVS) and amniocentesis, are invasive, and in about 1 per cent of cases they lead to miscarriage. Findlay says about 40 babies died as a result of these techniques in Victoria last year, and the babies were unaffected, or 'normal'.

Most women, particularly younger women, don't get tested because of the risks and the cost of the procedures. But women over the age of 35, and women with a family history of a genetic disorder, are in the 'high-risk' group that takes pre-natal diagnosis tests.

The pre-diagnostic test developed by Findlay's team is non-invasive and would enable all pregnant women to have a test, rather than only those at a very high risk. It would also help to determine whether a woman needed to have further, more invasive tests.

"In single-cell diagnostics, we are developing a test to do non-invasive pre-natal diagnosis from Pap smears," Findlay explains. "Rather than a woman going for invasive testing, such as amniocentesis or (CVS), which have a risk of miscarriage, she can have a Pap smear done, then we can isolate the foetal cells from the Pap smear and then do sexing, single-gene defects and tests for Down syndrome and other major chromosome abnormalities on the baby."

This technique first employs a Pap smear procedure to collect cells, and then uses forensic DNA fingerprinting techniques to decipher foetal cells from maternal cells. Once the foetal cells are confirmed, then genetic testing can be done, all from one cell.

Amniocentesis or CVS is still the gold standard -- Findlay's test can diagnose around 95 to 96 per cent of the major defects, whereas amniocentesis and CVS can look at a whole range of defects.

"It's an early screening process so that we can target much more effectively those women that really do need the amniocentesis or CVS test," he says. "We want to avoid unnecessary testing yet provide testing to those who really need it."

Findlay's team is also developing a very rapid pre-natal test. When an amniocentesis sample is taken, it is cultured for several weeks to generate enough foetal cells before the analysis can be done. Findlay's team is working on a technique where the test is done from the amniocentesis sample, generating results on the same day, rather than two weeks later.

The researchers are also developing a pre-implantation genetic diagnosis (PGD) program for IVF embryos, which involves taking cells from IVF embryos and diagnosing the same genetic defects.

"We know that about 30-50 per cent of IVF embryos are abnormal," says Findlay, but admits it's still unclear whether high levels of abnormalities are due to the IVF procedure or not -- the only embryos to which researchers have access are IVF embryos. Humans have a low pregnancy rate, which may be due to inherently high levels of genetic abnormalities. The only way of determining genetic defects in the embryo is by doing PGD before an embryo is implanted, a procedure in which one cell is removed from an embryo for testing.

"What we are doing is using a DNA fingerprinting system again," explains Findlay. "There have been quite a few mistakes, where the wrong embryos have been put into the wrong mother. What we are looking at doing is fingerprinting the embryos so that we can match the embryos to the patient and guarantee that the patients get the correct embryo, and at the same time do the genetic testing so that we can say we can be sure the embryo we are putting back has the best chance to form a normal healthy baby."

Findlay says most IVF clinics in Australia had success rate of about 50 per cent, which is still rather low, and about half a dozen perform PGD but using FISH rather than PCR.

"People tend to think of IVF as being a success story, but they don't hear of all the pain and the failures," says Findlay. "It's certainly a lot better than what it was, but at best it's still only one in three women that will get pregnant after the procedure."

Findlay's team is also applying the single cell fingerprinting technique to document security and forensics. The document security work involves embedding cells within documents, such as cheques, wills and bonds, to confirm their authenticity. Findlay, who recently presented the work at the International Symposium on the Forensic Sciences, in New Zealand, says the technique is generating plenty of interest -- its applications include anti-terrorist investigations, and investigations into illegal transfers of money.

Findlay's team is also applying the technique to obtaining and analysing DNA fingerprints from samples from crime scenes that previously were considered too small to analyse, or that could not be processed because they were contaminated or damaged.

The Findlay lab shopping list

MegaBace 1000 DNA sequencers (Amersham) Altra FACS cell sorter (Beckman Coulter) Gel Doc EQ (Bio-Rad) Laminar flow hoods (Email) Fume hood (Email) PCR machines (Applied Biosystems, Geneworks) Inverted microscope (Leica) Spectrophotometer (Quantum) Microcentrifuges (Sigma, Quantum) UV crosslinker (Biolab) Refrigerated centrifuge (Sigma, Quantum) Centrifuges (Sigma, Quantum) -80 freezer (Sanyo, Quantum) Autoclave (Tomy, Quantum) Icemaker (Scott)