“The infrastructure that we built enables laboratories to store information on genetic variants found in genes associated with disease, along with their detailed interpretation,” says Samuel J. Aronson, executive director of IT at Partners HealthCare Center for Personalized Genetic Medicine. The center’s IT platform, GeneInsight, provides the infrastructure to manage the interpretation of genetic information used in patient care, and report the data to healthcare providers.
Because of the dynamic nature of genetic knowledge, genetic variants of unknown significance at the time of testing may be discovered to be clinically relevant at a later point in time.
“It is important to ensure that new information reaches treating clinicians as soon as possible after variants are reclassified. GeneInsight is designed to help laboratories meet this challenge,” Aronson explains.
As part of the GeneInsight platform, treating clinicians receive alerts when previously identified and recorded genetic variants are updated in a manner that may be clinically meaningful. Historically, GeneInsight has focused on next-generation sequencing and single-nucleotide polymorphism data. “We are now deepening our support for structural and copy number variants,” Aronson says.
Compared with other forms of genetic variation, characterizing copy-number variants presents different challenges, some of which stem even from the manner in which these chromosomal changes are defined and described. “Information technology is critically important to support the expanded clinical use of these data,” he adds.
A major goal of GeneInsight is to facilitate testing processes that go beyond just capturing the state of knowledge at the moment a test is signed out. “There is no reason that clinicians should need to run a new physical test to get an updated interpretation for a previously conducted genetic assay,” Aronson says. “They should be automatically provided with an update whenever possible alerting them that our understanding of their patient’s genetic profile has evolved.”
Copy-number variations, which occur in at least 12% of the human genome, are estimated to account collectively for more genomic diversity than all single-nucleotide polymorphisms combined. The development of array CGH unveiled a new facet of chromosomal biology, and marked a shift in understanding its link to development, health, disease, and evolution. Addressing some of the existing difficulties, including the bioinformatics, computational, and statistical challenges, will be instrumental in enabling this already established and widely used approach to undergo further development and refinement.