Identifying the genetics behind obesity using dPCR

Social stigmas often dictate that obesity is determined by lifestyle choice, but the genetics behind obesity is much more complex than that. Obesity is a condition known to have adverse effects on health and is one of the world’s most complex chronic diseases. Linked to a variety of illnesses, the majority of the global population lives in countries where overweight and obesity kills more people than diseases connected to underweight. Worldwide, it has nearly tripled since 1975, and in 2016 alone, more than 1.9 billion adults (18 years and older) were recorded as being overweight. Of these, over 650 million were obese.

Despite being on the global rise for many years, research providing insight into this multifaceted disease has merely scratched the surface. Dr. Johanna Andersson-Assarsson, a researcher and coordinator for the Swedish Obese Subjects (SOS) study, is looking for answers to why some people are prone to obesity, while others are not. She spends her days at the University of Gothenburg researching the root cause of obesity from a genetic perspective.

The only study of its kind

The SOS study, which began in 1987, examines the long-term effects of the disease, measuring everything from comorbidities, such as diabetes, cardiovascular disease and cancer, to social life and self-esteem. “It’s the only study of its kind in the world,” says Andersson-Assarsson. The gene AMY1A is the focus of Andersson-Assarsson’s research. It encodes the amylase in the saliva, an enzyme needed to break down starch.

“Having increased copies of this gene is probably an adaptation to when humans transitioned from hunter-gathering to agriculture,” she says. “Fewer copies means lower amylase production. People with few copies of the AMY1A gene avoid starchy food such as potatoes. It simply doesn't taste good; the texture feels wrong,” she explains. “Instead, they tend to replace starch with fatty foods, which are more energy dense, and lead to weight gain. Twin and family studies have shown high heritability, 40–70% for obesity, but the variants discovered only explain a small part of that. My hypothesis is that copy number variation may explain parts of this postulated heritability.”

Old study, new technology

Far from the buzzing corridors of the hospital, the air in the archive is crisp, ideal for storing paper. This is where all the questionnaires are kept, from the 4,047 participants and 505 clinics, in row upon row of binders. The vast scale serves as a reminder that the project now spans five decades. It has evolved, along with new PCR-based technology. She picks up a nanoplate, indicating that this is where it all begins, amplifying a faint genetic signal. Reagents, enzymes and building blocks are added to DNA extracted from blood samples. After putting the plate in the digital PCR instrument, a separate reaction takes place in each nanowell, up to 26,000 simultaneously. When finished, Andersson-Assarsson can determine copy numbers of a single gene. The entire process takes no more than two hours.

There had long been indications that copy number variations had a key effect on disease, including obesity; however, traditional PCR couldn’t capture the required resolution. But with digital PCR, such as the QIAcuity digital PCR system, Andersson-Assarsson can accurately determine the copy number, even in individuals with any copies. “The number of copies of AMY1A ranges from 2 to 20. With the previous PCR techniques, the upper limit to determine the exact number of copies was around 10. Precision is crucial when small variations make a big difference. The average person has six copies of AMY1A – people who have four or fewer have an increased risk of developing obesity.

The future of obesity genetics

“I'm using digital PCR because of the resolution. The traditional PCR-based technique and quantitative PCR-based technique works really well for copy number variation when you have fairly few copies, maybe up to eight or ten. But when you have a gene that's really highly variable with a large number of copies, the resolution is not good enough. You can tell that there are many, but not if there’s 10 or 12 or 14. But with digital PCR, just because you subdivide your reaction into so many partitions, it's twenty-six thousand reactions per sample, the resolution is really good”, she explains. 

Andersson-Assarsson states that digital PCR has been somewhat of a revolution in the field of copy number analysis. “There are different solutions for digital PCR that give good results; what I like about the QIAcuity system is the simple and fast workflow and that you use less plastic tips and plates in the process which is good for the environment.”

Andersson-Assarsson believes that, in the future, as the complex genetics of obesity gets untangled, new therapies will emerge. “Bariatric surgery is a great treatment for many individuals with obesity but not for everyone,” she says. “Other treatment options are needed, and an increased knowledge of the genetic factors driving obesity will help us identify new treatment targets in the future.”