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Gene sequencing diagnoses rare newborn diseases

Canada is examining the need for next-generation gene sequencing of newborns in neonatal intensive care units (NICUs). Their hope is to improve the diagnosis of rare diseases and deliver results quickly to anxious families.

Personalized medicine is a medical model that addresses patients as members of unique groups. Medical decisions, practices, interventions and/or products are being tailored to meet individual patients based on their predicted response or risk of disease. Such terms as: personalized medicine, precision medicine, stratified medicine and P4 medicine are used interchangeably to describe this idea.

"Next-generation gene sequencing has the potential to transform the practice of clinical genetics rapidly,"
writes Dr. David Dyment, clinical investigator at the Children's Hospital of Eastern Ontario (CHEO), Canada. "In particular, newborns admitted to the NICU with rare and complex diseases may benefit substantially from a timely molecular diagnosis."

Children with suspected rare genetic diseases usually undergo a battery of tests to determine their diagnosis. This is because of the difficulty in identifying the particular molecular event causing an ailment. Currently, specific genes or a panel of genes must be tested outside of Canada, meaning it could take months or even years before a diagnosis is completed.

There are few studies to date looking at the feasibility and diagnostic success rate of next-generation sequencing in the NICU.

Canadian researchers conducted a pilot study with 20 newborns to determine the effectiveness of a targeted next-generation sequencing panel that included all 4,813 genes currently known to be associated with rare diseases. These 20 newborns presented with a wide range of complex, medical issues, and half had neurologic symptoms such as seizures or hypotonia also known as "floppy baby syndrome". Next-generation sequencing provided a molecular diagnosis for 40%, or 8 of the 20 infants. In two of the infants, the molecular diagnoses had a direct impact on their medical management.

"This technique can be performed in a hospital-based laboratory without the need to send samples away, often out of the country," says Dr. David Dyment MD, geneticist at Children's Hospital of Eastern Ontario (CHEO). "This will allow for diagnoses to be made quickly, providing answers to anxious families and potentially life-saving interventions in some cases."

Researchers suggest adopting this type of technology in Canadian hospitals will greatly improve the diagnosis of rare disease and begin treatment of neonates accordingly.

Their results are published in the Canadian Medical Association Journal (CMAJ).

"Enabling the family to understand why their baby is ill can help to assuage the almost universal guilt felt by parents that they did something wrong to cause their baby's illness. It can also indicate whether other family members may be at risk of the same disease and provide an accurate recurrence risk for future pregnancies."

Dr. Sarah Bowdin, BM, MSc, Clinical and Metabolic Genetics, Hospital for Sick Children (SickKids), Toronto, Ontario, Canada

Building strong partnerships with specialists such as neonatologists, intensive care physicians and genetics laboratories is critical for ensuring the success of "next-generation genetic sequencing" as a critical diagnostic tool.

Background: Rare diseases often present in the first days and weeks of life and may require complex management in the setting of a neonatal intensive care unit (NICU). Exhaustive consultations and traditional genetic or metabolic investigations are costly and often fail to arrive at a final diagnosis when no recognizable syndrome is suspected. For this pilot project, we assessed the feasibility of next-generation sequencing as a tool to improve the diagnosis of rare diseases in newborns in the NICU.

Methods: We retrospectively identified and prospectively recruited newborns and infants admitted to the NICU of the Children's Hospital of Eastern Ontario and the Ottawa Hospital, General Campus, who had been referred to the medical genetics or metabolics inpatient consult service and had features suggesting an underlying genetic or metabolic condition. DNA from the newborns and parents was enriched for a panel of clinically relevant genes and sequenced on a MiSeq sequencing platform (Illumina Inc.). The data were interpreted with a standard informatics pipeline and reported to care providers, who assessed the importance of genotype-phenotype correlations.

Results: Of 20 newborns studied, 8 received a diagnosis on the basis of next-generation sequencing (diagnostic rate 40%). The diagnoses were renal tubular dysgenesis, SCN1A-related encephalopathy syndrome, myotubular myopathy, FTO deficiency syndrome, cranioectodermal dysplasia, congenital myasthenic syndrome, autosomal dominant intellectual disability syndrome type 7 and Denys-Drash syndrome.

Interpretation: This pilot study highlighted the potential of next-generation sequencing to deliver molecular diagnoses rapidly with a high success rate. With broader use, this approach has the potential to alter health care delivery in the NICU.

Related research
• European Journal of Human Genetics (2015) 23, 1142–1150; doi:10.1038/ejhg.2014.279; published online 28 January 2015

Partial list of international centers for the performance of next generation genetic screening:
• Australian Genome Research Facility - Australia
• Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) – Houston, TX, USA
• BC Genome Sciences Centre (BCGSC) – Vancouver, BC, Canada
• Beijing Genomics Institute (BGI) - China
• Broad Institute of MIT and Harvard – Boston, MA, USA
• Cold Spring Harbor Laboratory (CSHL) – Cold Spring Harbor, NY, USA
• DOE Joint Genome Institute (JGI) – Walnut Creek, CA, USA
• Garvan Institute - Australia
• Genome Analysis Center (TGAC) - Norwich, UK
• Genome Institute at Washington University (TGI) – St. Louis, MO, USA
• Genome Institute of Singapore - Singapore
• Genomic Medicine Institute - Seoul, Korea
• HudsonAlpha Genome Sequencing Center (HAGSC) – Huntsville, AL, USA
• Human Longevity Inc. (HLI) - San Diego/La Jolla, CA, USA
• Illumina (Fast Track) - San Diego, CA, USA
• J. Craig Venter Institute (JCVI) - Rockville, MD, USA
• Los Alamos National Laboratories (LANL) - Los Alamos, NM, USA
• Macrogen - Korea
• McGill University and Génome Québec Innovation Centre, Canada
• Mount Sinai, Icahn Institute of Medicine - New York, NY, USA
• National Center for Genome Resources (NCGR) – Santa Fe, NM, USA
• National Genomics Infrastructure, Science for Life Laboratory - Karolinska, Solna, Sweden
• New York Genome Center (NYGC) – New York, NY, USA
• NIH Intramural Sequencing Center (NISC) – Rockville, MD, USA
• Northwest Genomics Center, University of Washington - Seattle, WA, USA
• Novogene - Beijing, China
• NTU Center of Genomic Medicine - Taiwan
• Oak Ridge National Laboratory (ORNL) - Oak Ridge, TN, USA
• Okinawa Institute of Science and Technology - Okinawa, Japan
• Ontario Institute of Cancer Research (OICR) – Toronto, Ontario, Canada
• Princess Margaret Hospital (Genomic Center) (PMH) - Toronto, Ontario, Canada
• Queensland Centre for Medical Genomics (QCMG) - St Lucia QLD, Australia
• RIKEN Genome Sciences Center – Yokohama, Japan
• Stanford Center for Computational, Evolutionary and Human Genomics – Stanford, CA, USA
• Takara, Dragon Genomics Center - Shiga, Japan
• Translational Genomics Research Institute (TGen) – Phoenix, AZ, USA
• Vantage - Vanderbilt Technologies for Advanced Genomics - Nashville, TN, USA
• Wellcome Trust Sanger Institute – Hinxton, Cambridge, UK
• WuXi Genome Center - Shanghai, China
• Yale Center for Genome Analysis - Orange, CT, USA
• Yang Ming U Genome Research Center - Taiwan

CMAJ is a peer-reviewed general medical journal that publishes original clinical research, commentaries, analyses, and reviews of clinical topics, health news, clinical practice updates and thought-provoking editorials. CMAJ has had substantial impact on health care and the practice of medicine in Canada and around the world
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Schematic representation of the different applications of
“Next-generation” DNA sequencing technologies.
Image Credit: Subhash C. Verma, Microbiology and Immunology,
School of Medicine, University of Nevada; Viruses — Open Access Virology Journal



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