Mystery solved: The evolution of 
diagnostic abilities in genetic testing

Genetic testing has undergone significant changes during the past several years. Advances in cytogenetic and molecular technology have expanded our ability to identify underlying genetic abnormalities in patients for whom these findings previously went undiagnosed. The following clinical case illustrates the benefits of these new advances and how they can be used to improve our diagnostic capabilities.


CASE


In early 2003, we first evaluated a newborn boy who was transferred to our facility for assessment of dysmorphic features. He was a 3.1-kg product of a normal pregnancy born to his 31-year-old primigravid mother. Labor and delivery of the baby had been complicated by a short umbilical cord and vacuum-assisted extraction. Apgar scores were 8 and 9 at 1 and 5 minutes, respectively. The patient was admitted to the neonatal intensive care unit (NICU) for respiratory distress and dysmorphic features. Routine chromosomal analysis was normal, but MRI of the brain revealed an underdeveloped corpus callosum and temporal lobe. Metabolic screening was normal. Additional problems identified at transfer included stridor from laryngomalacia, gastroesophageal reflux, and cryptorchidism.


The infant's initial genetics physical examination in the NICU was notable for a large anterior fontanelle, craniofacial disproportion, prematurely aged facies, short palpebral fissures, low-set overfolded ear helices, stridor, wide internipple distance, pectus excavatum, undescended testes, and a small scrotum. Neurologic examination was symmetric and nonfocal with axial hypotonia noted. Two genetic databases were searched during the evaluation, and the results suggested a premature aging syndrome as a unifying diagnosis. No tests were available for this disorder, and the clinician recommended that the infant receive medical genetics surveillance as follow-up.


During surveillance visits to the genetics clinic at ages 3 and 6 months, the patient was thriving with feedings from the gastrostomy tube that had been placed prior to his initial discharge. This clinical finding eliminated concerns for a premature aging syndrome. A skeletal survey at age 6 months revealed persistent delay in skeletal maturation. Subsequent genetic database searches were unrevealing. At 1 year of age, high-resolution chromosomal analysis—a genetic test to identify subtle chromosome abnormalities—and subtelomeric fluorescence in situ hybridization (FISH) probe study results were both normal.


At 18 months, the infant's developmental progress was essentially normal. His physical features remained striking, with a wide nasal root, short palpebral fissures, and low-set overfolded ears. At 2 years, short stature was evident. An endocrinology evaluation was unrevealing. He returned to the genetics clinic at age 4 years, and clinical features suggested Noonan syndrome, an inherited condition characterized by pulmonary stenosis, a wide or webbed neck, and sternal deformities. At 6 years, when he next returned to the clinic, Noonan syndrome seemed less likely. However, chromosomal microarray analysis (CMA) had been established at our facility since the time of the patient's last visit, and this technology finally revealed a deletion of a small region on the long arm of chromosome 2 (Figure 1). 


After a 6-year odyssey to identify the cause of their son's clinical abnormalities, CMA was finally able to yield an explanation for his parents. The process took many steps, each step offering some hope of finding an answer—from routine chromosome analysis to high-resolution chromosome analysis to FISH subtelomere studies and, finally, to comparative genome hybridization. 


Chromosomal microarray analysis is a method of comparing a patient's genome to a normal control genome while simultaneously hybridizing the samples to short-target DNA sequences bound in a matrix of small dots on a glass slide, or microarray chip. As the target sequences have become shorter, the resolution of this study has increased dramatically, increasing the diagnostic yield 10-fold compared to other methods.¹ CMA also allows the molecular cytogeneticist to identify imbalances in the genome, regions that are lost or duplicated. Some of these imbalances are found in normal individuals and considered benign genetic variants. Other imbalances that are never found in normal controls, those that involve deletion or duplication of significant genes, are considered pathogenic variants. In this case, the identified deletion abnormality involved an important gene, Reprimo, which plays a role in cell and gene regulation. Therefore, our patient's DNA loss was likely a pathogenic variant.


Chromosome microarray analysis provides a great advance in genetic testing and has improved the detection rate of genetic abnormalities. However, a large number of cases remain unresolved. With the ongoing development of affordable genome sequencing, more genetic mysteries may be able to be solved in the future. JAAPA


Gary Gottesman is an associate professor in the Department of Physician Assistant Education at the Doisy College of Health Sciences and adjunct associate professor in the Department of Pediatrics at Saint Louis University School of Medicine, St Louis, Missouri. Jacqueline Batanian is director of the Molecular Cytogenetics Laboratory at Cardinal Glennon Children's Medical Center and a professor of pediatrics at Saint Louis University School of Medicine. The authors have indicated no relationships to disclose relating to the content of this article. 

REFERENCE


1. Ahn JW, Mann K, Walsh S, et al. Validation and imple­men­tation of array comparative genomic hybridisation as a first line test in place of postnatal karyotyping for genome imbalance. Mol Cytogenet. 2010;3:9.