300 Exomes Analyzed, Genes Assigned to Undiagnosed Disorders

Exome Sequencing Reveals Atypical Cases of Single-Gene Disorders

Ricki Lewis, PhD

November 09, 2012

SAN FRANCISCO, California — An update on the use of whole-exome sequencing to diagnose patients who have exhausted conventional approaches kicked off the American Society of Human Genetics 62nd Annual Meeting. It was presented by researchers from the Baylor College of Medicine in Houston, Texas. Baylor merged its human genome sequencing center with its medical genetics labs to form the Whole Genome Laboratory.

Targeting the Exome

Of the patients who undergo a work-up at Baylor, consisting of imaging, metabolic tests, cytogenetic analysis, and genetic tests, roughly 40% are not diagnosed. Answers often lie within the exome — the part of the genome that encodes protein.

The exome consists of exon (coding) sequences within the 22,000 or so genes in the human genome. It is a goldmine of medical information. "The exome is about 1% of the human genome, but it constitutes about 85% of disease-causing mutations," said Yaping Yang, PhD, codirector of the Whole Genome Laboratory.

Exome sequences can reveal variants in genes omitted from a differential diagnosis because presentation is atypical or because the symptoms are common. "In general, exomes are more cost-effective if a number of genes contribute to a general phenotype, such as developmental delay," said Arthur Beaudet, MD, chair of the Department of Molecular and Human Genetics at Baylor.

Clinical Exome Sequencing Began in 2009

The case of Nicholas Volker launched clinical exome sequencing. He had intractable intestinal illness that turned out to be an atypical presentation of X-linked inhibitor of apoptosis (XIAP) deficiency. Scientists from the Medical College of Wisconsin and the Children's Hospital of Wisconsin in Milwaukee conducted this ground-breaking work, and the boy had a successful cord blood transplant once DNA sequencing revealed the underlying immune disorder.

More recently, Anna Need, PhD, and colleagues from the Center for Human Genome Variation at the Duke University School of Medicine in Durham, North Carolina, used exome sequencing to diagnose 7 of 12 children who had unexplained intellectual disabilities, developmental delay, congenital anomalies, and/or facial dysmorphisms.

The Baylor program provides a snapshot of whole-exome sequencing on a larger scale. In many cases, the exome-facilitated diagnoses suggest preventative measures and treatment modifications.

Since Baylor launched its whole-exome sequencing program in October 2011, more than 600 samples have come in, mostly from academic medical centers. About 85% of the samples are from children, and most represent unexplained neurologic disorders. Geneticists referred 61% of the cases and pediatric subspecialists referred 24%, said Christine Eng, MD, director of the DNA Diagnostic Laboratory at Baylor.

The researchers have analyzed 300 cases so far and have found causative deleterious mutations in 25% of them. Unlike the 12-patient study that considered the same phenotype, the Baylor sample included diagnoses of several rare syndromes (CHARGE [coloboma, heart disease, atresia choanae, retarded growth and retarded development, and/or central nervous system anomalies, genital hypoplasia, and ear anomalies and/or deafness], Kallman, Kabuki, Rubinstein-Taybi, Mowat-Wilson, Ehlers-Danlos type IV, and TARP). They found 400 to 700 variants per sample.

"Focused" and "Expanded" Reports Provided

The Baylor program provides 2 levels of reports. The initial "focused" report shows mutations in genes whose functions are consistent with the symptoms, and the "expanded report" includes deleterious mutations in genes that seem unrelated to the phenotype. Physicians and patients varied widely in the amount of information they wanted.

Two Cases

Dr. Eng described several cases in which the exome sequencing results affected medical management.

A 2-year-old boy presented with severe feeding problems and failure to thrive. Extensive testing ruled out Angelman syndrome, Rett syndrome, infection, and mitochondrial disease.

Exome sequencing, which the family's insurance covered, revealed an autosomal dominant mutation in the SYNGAP1 gene, which arose de novo in the child. "The gene is critical for cognition and synapse formation. The mutation causes global delay, intellectual disability, and seizures," Dr. Eng explained.

Further testing showed abnormalities on electroencephalography (EEG), and monitoring for seizures began. The boy's exome sequence also revealed a fibrillin mutation, but he did not have the classic symptoms of Marfan syndrome. "It was an incidentaloma but a reported mutation so we decided to disclose it," Dr. Eng said. On echocardiogram, an enlarged aortic root was discovered; treatment with losartan will begin if expansion continues, she added.

In a second case, a 9-year-old boy had episodes of extreme weakness, apnea requiring intubation, ptosis, increased respiratory secretions, dysphagia during febrile illness, and cardiac myopathy. A younger sister had died at 20 months while feverish.

Exome sequencing revealed 2 mutations in the RAPSN gene, causing congenital myasthenic syndrome, which is associated with acetylcholine-receptor deficiency. Febrile illness provokes the attacks, so the patient began taking prophylactic acetylcholine esterase inhibitors. Another mutation, in the ABCC9 gene, caused cardiomyopathy in this patient. Seeing patients with more than 1 genetic disease will become more common with exome sequencing, Dr. Eng predicted.

To date, exome sequencing seems to be a win–win scenario for patients, physicians, and researchers. "We must move from a single-gene model to a comprehensive approach that will have clinical utility for adult and pediatric populations and present the opportunity for disease discovery," Dr. Eng explained.

American Society of Human Genetics (ASHG) 62nd Annual Meeting. Presented November 7, 2012.