About the Study

Mission

Our mission is to determine how and when we can use DNA sequencing to diagnose, inform and guide clinical management and treatment for individuals with unexplained health problems.

We seek to deliver information and care that are appropriate, cost-effective, and sensitive to evolving social perceptions about access to and protection of genetic information.

We strive to do the best science in the most responsible way. Our ultimate goal is to improve the outcomes of the patients in our study.

The Duke Task Force for Neonatal Genomics (TFNG) is a research partnership involving clinicians, researchers, and families to determine the Oak2006underlying genetic contributors of congenital defects.

  • Inclusion criteria
  • Informed consent for enrollment
  • Sample and information collection
  • Genome-wide sequencing
  • Functional interpretation of candidate DNA changes
  • Clinical confirmation of clinically actionable results
  • Regular internal review of progress by the TFNG

About the Research Process

Inclusion criteria

Our research team is currently recruiting neonates and young children who meet all of the criteria listed below.

  • Have a medical condition detected prenatally or early in life that is likely to be genetic
  • No DNA-based diagnosis at the time of enrollment.
  • Both parents must be over the age of 18 years and willing to participate.
  • Children with a known environmental or maternal condition (e.g., maternal diabetes) will be excluded.

Informed consent for enrollment

If a family meets all Task Force inclusion criteria and is interested in participating in our study, a Board Certified genetic counselor will serve as the point of contact to the family during the consent process.

Sample and information collection

Following informed consent, we will arrange for collection of either a blood or saliva sample for extraction of DNA. We may also obtain residual DNA samples banked in a clinical laboratory. We will obtain a detailed medical history from the family and thorough review of medical records.

Genome-wide sequencing

Using the latest sequencing technologies, we will sequence the exome of the affected child and each of the parents. The exome accounts for the ~2% of the genome that makes up genes, which encode the ~25,000 proteins that make up all cells and tissues of the body. In some instances, we may extend our studies to whole-genome sequencing (that is, the exome plus the 98% the genome that does not code for proteins and is not as well understood). We will then analyze the data to identify candidate causal variants. We will use traditional “Sanger” sequencing methodology (the most accurate approach) to confirm variants of interest.

Functional interpretation of candidate DNA changes

In many instances we identify candidate causal variants that have not been reported previously in the scientific literature, or reside in a gene that has not previously been implicated in human genetic disease. In these cases we test whether the variant has an effect on protein function. Depending on the organ systems affected in the child, we carry out these tests either in a model organism (a zebrafish) or else in a cell line (a layer of cells that grows in a dish).

Clinical confirmation of clinically actionable results

We report findings that are of immediate clinical relevance to the family’s referring physician in the form of a written report. Typically we confirm these results in a certified diagnostic laboratory before the physician reports them back to the family.

Regular internal review of progress by the Task Force

During regular or ad hoc meetings with referring physicians, the Task Force reviews:

  • Candidate families for enrollment
  • Candidate DNA variants for functional testing
  • Formal reports to referring physicians

We also re-review sequencing data every 18 months.

About the Task Force Team

Duke’s Task Force for Neonatal Genomics is an interdisciplinary group whose members have expertise in:

  • Neonatal medicine
  • Maternal fetal medicine
  • Medical genetics
  • Molecular biology
  • Genetics of human disease
  • Statistical genetics
  • Genetic counseling
  • Clinical genetic testing
  • Genetics policy
  • Human participants research

Though its members come from multiple centers, institutes, and departments at Duke, the organizational hub of the Task Force is the Center for Human Disease Modeling (CHDM). The Duke Task Force collaborates with Baylor College of Medicine for genomic sequencing and GeneDx, Inc. for clinical confirmation of potential causative variants.

Nicholas Katsanis, PhD

Amy Murtha, MD

Charles Michael Cotten, MD, MHS

Erica E. Davis, PhD

Sara Huston Katsanis, MS

Misha Angrist, PhD

Heidi Cope, MS, CGC

Azita Sadeghpour, PhD

Allison Ashley-Koch, PhD

Ronald Goldberg, MD

Yezmin Perilla, MS, CGC

Michael Hauser, PhD