New Technique Detects Breaks in Mitochondrial DNA

The Splice-Break pipeline is a recently described technique that can detect and quantify mitochondrial DNA (mtDNA) deletions at a high level of resolution.

Deletions in the mitochondrial genome have been implicated in numerous human disorders that often display muscular and/or neurological symptoms due to the high-energy demands of these tissues. Among these "mitochondrial myopathies" are Kearns–Sayre syndrome (KSS), Pearson Syndrome (PS), chronic progressive external ophthalmoplegia (CPEO), Leigh syndrome, and diabetes mellitus.

Investigators at the University of California, Irvine (USA) described a catalogue of 4,489 putative mtDNA deletions, including their frequency and relative read rate. To do this, they employed a combinatorial approach of mitochondria-targeted PCR, next-generation sequencing, bioinformatics, post-hoc filtering, annotation, and validation steps. Their bioinformatics pipeline incorporated MapSplice, an RNA-seq splice junction detection algorithm, to detect and quantify mtDNA deletion breakpoints rather than mRNA splices.

The investigators used their technique to analyze 93 samples from postmortem brain and blood. They found that the 4977-base pairs "common deletion" was neither the most frequent deletion nor the most abundant and that brain contained significantly more deletions than blood.

“Taken together, the pipeline will enable us to look in many brain regions for an accumulation of damage to mitochondria DNA for individuals with various psychiatric symptoms such as depression and psychosis. The ultimate use will be to test other more accessible samples such as blood, saliva, or cerebrospinal fluid from patients to estimate the damage to mitochondria, and quickly identify those individuals who may benefit from drugs and other treatments that give a mitochondria boost and improve psychiatric symptoms,” said senior author Dr. Marquis P. Vawter, a researcher in the department of psychiatry and human behavior at the University of California, Irvine. “This technique allows us to use a single test to measure the accumulation of many types of these deletions and to determine an overall burden of these deletions upon mitochondria functions.”

The study was published in the March 14, 2019, online edition of the journal Nucleic Acids Research.

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University of California, Irvine