Expert: Keep up with latest discoveries through automated updates in reporting genetic test results

October 1, 2018, Children's Hospital of Philadelphia
Mahdi Sarmady, PhD, is Director of Bioinformatics in the Division of Genomic Diagnostics at Children's Hospital of Philadelphia. Credit: Children's Hospital of Philadelphia

Maybe the genetic test report your doctor ordered says your DNA contains many "variants of unknown significance." Currently, up to 70 percent of such reports are negative or inconclusive. But suppose at a later date a researcher discovers one of those changes causes a disease? You may be able to take preventive steps or receive early treatment—but how will you learn this new piece of information? You can't even be sure your doctor will find out about it.

A scientist in the Division of Genomic Diagnostics (DGD) at Children's Hospital of Philadelphia (CHOP) proposes a new model to generate ongoing automated updates to account for new evidence—and enable genetic counselors and physicians to better communicate clinically relevant information to patients and families, not just when the test results are initially reported, but for years to come as new knowledge accumulates.

"Since the Human Genome Project was completed, the flood of new genetic information and the accelerated pace of discovery represent a paradigm shift in the practice of ," said Mahdi Sarmady, Ph.D., a genome informatics scientist and Director of Bioinformatics in the DGD. He points out, for instance, that clinical sequencing is increasingly being incorporated in pediatric clinics as a routine diagnostic tool.

To enable faster, more systematic use of sequencing results, Sarmady and Ahmad Abou Tayoun, Ph.D., a former CHOP geneticist now at Al Jalila Children's Specialty Hospital in Dubai, U.A.E., propose a for genomic interpretation and continuous reanalysis in a Viewpoint article published online today in JAMA Pediatrics.

Under the traditional approach in clinical genetics, a physician or genetic counselor would order a laboratory test on a specific gene to determine whether a patient carried a known mutation linked to a genetic disease. Now labs offer gene panels to test all known genes associated with a specific disorder, or exome sequencing, to search all protein-coding genes in a person's DNA.

But managing and interpreting the fire hose of data provided by new high-throughput sequencing methods has led to a bottleneck in keeping up with and delivering useful information to patients and clinicians.

The proposed model outlines a two-way exchange of information between laboratories and the clinic. Automated algorithms would collect new evidence from scientific literature and various knowledge bases of gene variants linked to specific disorders, and would notify a clinician that a patient's previously discovered variant could be pathogenic. A physician or genetic counselor, for their part, could use an app in the platform to order reanalysis and to enter the most up-to-date phenotypic information on a patient's health status—adding details about the course of a genetic disease, to inform other researchers and clinicians.

"Instead of a one-time test result, there would be continuous, systematic interaction between the clinic and the genetic testing lab, and reanalysis of changing data," said Sarmady. "This could enable clinicians to provide better diagnoses and change treatment plans for their patients as new information becomes available, and help advance the promise of precision medicine."

Explore further: Rapid genomic sequencing to diagnose critically ill children with rare diseases

More information: Mahdi Sarmady and Ahmad Abou Tayoun, "Need for Automated Interactive Genomic Interpretation and Ongoing Reanalysis," JAMA Pediatrics, online Oct. 1, 2018. doi.org/10.1001/jamapediatrics.2018.2675

Related Stories

Rapid genomic sequencing to diagnose critically ill children with rare diseases

September 17, 2018
A multidisciplinary team at KK Women's and Children's Hospital (KKH) has developed a test to enable faster diagnosis of rare diseases to help critically ill children. Rapid genomic sequencing or RapidSeq of critically ill ...

Clinical gene discovery program solves 30 medical mysteries

September 17, 2018
A table in a recently published paper tells the story of 30 families who have, sometimes after years of searching, finally received an answer about the condition that has plagued one or more family members. The Brigham Genomic ...

Blood cancer patients benefit from breakthrough genetic testing service

August 27, 2018
Cutting-edge DNA sequencing technology has been used by QUT researchers at the new Australian Translational Genomics Centre (ATGC) to identify genetic mutations in 100 patients with blood cancers, with this testing providing ...

A new era for genetic interpretation

May 27, 2015
Millions of genetic variants have been discovered over the last 25 years, but interpreting the clinical impact of the differences in a person's genome remains a major bottleneck in genomic medicine. In a paper published in ...

ClinGen Panel evaluates validity of genes reported to be associated with Brugada Syndrome

June 29, 2018
Clinical laboratories often rely on medical articles and public information on gene disease associations in determining the genes to include on genetic testing panels for specific conditions or the specific results to return ...

How will genomics enter day-to-day medicine?

June 30, 2016
A quiet transformation has been brewing in medicine, as large-scale DNA results become increasingly available to patients and healthcare providers. Amid a cascade of data, physicians, counselors and families are sorting out ...

Recommended for you

Breastfeeding protects infants from antibiotic-resistant bacteria

October 18, 2018
A recent study completed at the University of Helsinki investigated the amount and quality of antibiotic-resistant bacteria in breast milk and gut of mother-infant pairs. The findings have been published in the journal Nature ...

Making gene therapy delivery safer and more efficient

October 18, 2018
Viral vectors used to deliver gene therapies undergo spontaneous changes during manufacturing which affects their structure and function, found researchers from the Perelman School of Medicine at the University of Pennsylvania ...

Student develops microfluidics device to help scientists identify early genetic markers of cancer

October 16, 2018
As anyone who has played "Where's Waldo" knows, searching for a single item in a landscape filled with a mélange of characters and objects can be a challenge. Chrissy O'Keefe, a Ph.D. student in the Department of Biomedical ...

Researchers use brain cells in a dish to study genetic origins of schizophrenia

October 16, 2018
A study in Biological Psychiatry has established a new analytical method for investigating the complex genetic origins of mental illnesses using brain cells that are grown in a dish from human embryonic stem cells. Researchers ...

Why heart contractions are weaker in those with hypertrophic cardiomyopathy

October 16, 2018
When a young athlete suddenly dies of a heart attack, chances are high that they suffer from familial hypertrophic cardiomyopathy (HCM). Itis the most common genetic heart disease in the US and affects an estimated 1 in 500 ...

Importance of cell cycle and cellular senescence in the placenta discovered

October 15, 2018
Working with researchers from Stanford University and St. Anna Children's Cancer Research, researchers from Jürgen Pollheimer's laboratory at the Medical University of Vienna's Department of Obstetrics and Gynecology have ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.