In a remarkable new genetic discovery, researchers at the Peter Munk Cardiac Centre, University Health Network (UHN), Ted Rogers Centre for Heart Research, and The Hospital for Sick Children (SickKids) have found strong evidence that rare DNA variations can lead to Tetralogy of Fallot (ToF).

Published in Genetics in Medicine, the study is the first to use whole-genome sequencing for ToF—a cardiac abnormality with four heart defects that occur together. The causes and mechanisms that lead to ToF are as of yet largely unclear. For years, scientists have been studying the possible role of genetic changes.

Whole-genome sequencing is used to determine the identity and order of the three billion chemical building blocks or units—made from four different "bases"—that make up a DNA molecule. By analyzing the sequences, scientists are able to determine the type of genetic information that is in a DNA segment. Genes, which are made up of DNA, provide the code to produce proteins and help us understand how a protein functions in a system or pathway. In humans, genes vary in size from a few hundred DNA bases to more than 2 million bases.

Targeting the VEGF pathway

A collective effort supported by The Dalglish Family 22q Clinic at the Peter Munk Cardiac Centre, the Ted Rogers Centre, and SickKids, the team found that the “vascular endothelial growth factor” (VEGF) signaling pathway was strongly implicated in adult patients with ToF.

Specifically, the researchers discovered harmful changes in the genetic code for proteins important in blood vessel and heart development. These proteins were all part of the VEGF cellular pathway. By understanding the changes to cell signaling in this important pathway, diseases like ToF may be treated more effectively.

“VEGF is a well-known pathway in such areas as cancer or vascular biology, but here we have identified that it is likely to play an important role in the formation of our heart,” says Dr. Raymond Kim, scientific lead at the Ted Rogers Centre’s Cardiac Genome Clinic, and one of the authors of the study.

Researchers have found that these rare DNA changes in genes associated with the VEGF pathway—unobserved in the general population—accounted for over 10% of the 175 adult patients with ToF whose genomes were sequenced at The Centre for Applied Genomics at SickKids.

Today, around 20% of patients with ToF are diagnosed with genetic conditions, such as 22q11.2 deletion syndrome. Researchers are still looking for answers as to what may have caused this heart abnormality for the remaining 80% of patients.

“We have been searching for genetic causes for ToF for several years and this represents a major step towards understanding this condition,” says Dr. Miriam Reuter, Research Associate, Genetics and Genome Biology, The Hospital for Sick Children and member of the Ted Rogers Centre, and first author of the study.

In ToF, the four cardiac defects begin in utero and require specialized lifesaving surgery typically performed within the first month of life. ToF represents around one in ten of all cases of congenital heart disease.

Surgery can repair the defects and most patients with ToF now live well into adulthood. However, patients require life-long follow-up and may need repeated surgeries or further treatment to address a failing right ventricle while facing a higher risk for complications. including endocarditis, arrhythmia, and heart failure.

“Whole-genome sequencing will allow us not only to better understand causes for ToF, but the results could have implications on how we treat patients and support them throughout their life,” says Dr. Anne Bassett, senior scientist at the Toronto General Hospital Research Institute, director of The Dalglish Family 22q Clinic at the Peter Munk Cardiac Centre, and senior author of the study.

A firehose of data

Because of its broad lens, analyzing whole-genome sequencing data is like searching for the proverbial needle in the haystack. In this study, that search was performed by Dr. Reuter, who combed through sequencing data on a very large number of genetic variants.

“Among several million variants per person, you must prioritize which ones to look at,” she says. “You need a hypothesis first about which are most likely to cause disease.”

One way to build a hypothesis is to concentrate on a cellular pathway. This research focused on VEGF because a recent study suggested one of its receptors to be involved in ToF. Dr. Reuter used this information to look deeper into other genes associated with VEGF signaling, and analyzed patient data for rare variants in these genes.

The vast majority of genetic variations are not associated with a disease. “So you must filter out all these variants to find the needles in the haystack,” says Dr. Kim.

Armed with the data, details about the biology of ToF, expertise in WGS studies, and about ToF in the patients from UHN and SickKids, the researchers dug through 175 “haystacks” looking for a pattern amongst them. The pattern that threaded the “needles” in many of these cases turned out to be the VEGF pathway.

This represents a significant step toward individualized patient care in ToF. Understanding the mechanisms of a disease is essential to create truly individualized diagnostic and treatment strategies for patients.

“The results of this study represent many years of research participation by patients followed at the Adult Congenital Cardiac Clinic at Toronto General Hospital. Our next exciting steps will be to perform further whole-genome sequencing studies of patients with ToF, investigate the role of the VEGF pathway in cardiac development using cellular models, and translate the benefits of this research to patients and their families,” says Dr. Bassett.

—Newswise