Genetic Mutations Missed By Whole Genome Sequencing Can Be Found With New 'Deep Sequencing' Technique

genomic sequencing
By using a special "deep sequencing" technique, scientists have identified somatic mutations affecting only a percentage of cells in patients with brain disorders. Reuters

Disease-causing mutations do not necessarily affect every single cell in your body. This makes them easy to miss even during the most advanced genomic sequencing methods. Now, by using a special "deep sequencing" technique, scientists have identified somatic mutations affecting only a percentage of cells in patients with brain disorders. The new approach outlined in a newly published study opens the door to finding genetic causes for mysterious neurologic and psychiatric conditions.

What are somatic mutations?

Often causing cancer and other diseases, somatic mutations are those alterations in genetic structure acquired during your lifetime. Unfortunately, two kinds of somatic mutations often get missed when geneticists test patients for a disease. One is a mutation that is limited to specific tissues, for instance a mutation occurring only in brain cells. If doctors do a blood test, they will never find this particular genetic anomaly. Another commonly missed somatic mutation is the kind that occurs in all tissues, while only appearing in a fraction of the cells — a so-called mosaic pattern mutation.

The current study began by enlisting the help of 158 patients with brain malformations causing seizures, intellectual disability, and speech and language impairments. To search for the unknown genetic mutations in these patients, Dr. Christopher Walsh, chief of Genetics and Genomics at Boston Children's Hospital and Dr. Saumya Jamuar, a clinical geneticist at the KK Women's and Children's Hospital in Singapore, used a technique called "targeted high-coverage sequencing."

Rather than analyze the whole genome or exome — a smaller portion of the genome — the investigators focused on a panel of suspected genes, but drilled deeper than the traditional sequencing technique. For instance, whole genome or exome sequencing typically breaks the DNA into little fragments, each of which is read multiple times — typically 30 times — to find the disease-causing mutation. But 30 passes aren't enough to reliably catch mutations. So Walsh’s team scaled up the number of reads, sequencing each candidate gene not 30 times but 200 times or more. This enabled the team to find mutations in 27 of the 158 patients (17 percent). Of these, eight mutations (30 percent) occurred in only a proportion of the blood cells (so-called mosaic mutations).

"Traditionally, our genes are considered to be the same across all cells of our body, and disease-causing mutations are either inherited from one or both parents or occur in the parent's sperm or egg before conception," Jamuar explained. "Our study creates a paradigm shift, providing evidence that a significant proportion of mutations causing brain disorders occur after conception and would be missed by routine testing."

In fact, the findings suggest neuropsychiatric disorders can result from mutations detectable in as few as 10 percent of a patient's blood cells, according to Walsh. He believes the study may help explain other brain-based disorders such as autism, intellectual disability, and epilepsy that don't have an inherited cause but occur as a result of de novo mutations — those occurring spontaneously and sometimes after conception.

Source: Jamuar SS, Lam ATN, Kircher M, et al. Somatic Mutations in Cerebral Cortical Malformations. The New England Journal of Medicine. 2014.

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