PracticeUpdate Conference Series - SSIEM 2018

Though NGS Can Detect Genomic Deletions in Metabolic

Disorders, Precise Characterization Is Lacking

Next-generation sequencing (NGS) can detect genomic alterations but further methods are needed to characterize the alterations precisely.

I n a series of 15 genes sequenced by two NGS panels, 17 large deletions were identified. Nevertheless, 30% involved Alu sequences and two were not identified by either panel, reports an evaluation of two NGS panels.

The group of Belen Perez Gonzalez, PhD, of Centro de Diagnóstico de Enfermedades Moleculares, Universidad Autónoma de Madrid in Spain, evaluated the two NGS panels. Panel 1 was an in-house, targeted, customized exome sequencing panel to capture the exome of 120 genes involved inmetabolic disorders. The panel included the entire sequence of the PAH, ALDOB,

Belen Perez Gonzalez, PhD

Inborn errors of metabolism comprise heterogeneous, rare genetic diseases with a variety of overlapping or unspecific clinical phenotypes. Multiple proteins with enzymatic, transporter, regulatory, and other functions participate in the intricate complexity of metabolic pathways. A breakdown in normal function of some of these proteins may impair the metabolic state of an organism. These disruptions can generally be assessed biochemically by detecting metabolites in various biological fluids. Specificity and sensitivity of some of cases, the disease-causative gene could be involved in another pathway while yielding a similar phenotype. " " …metabolic diseases are highly heterogeneous. Overlapping phenotypes may confuse the clinical orientation. In these

OTC, SLC22A5, and PCCA genes. Panel 2 was an extended panel including all known disease- associated genes described in the Online Mendelian Inheritance in Man database (Mendeliome panel) as of 2013. Quantification of coverage and comparison between controls and cases revealed that the two panels were able to detect large deletions in 20 patients. The analysis detected 17 different large deletions in 15 genes ( SLC7A2, GK, ALG1, MLYCD, PHKA2, BCKDHA, IVD, ASS1, PAH, GLDC, ACADM, DBT, PDHX, and BCAT2 ). Of these, 10 are novel genomic deletions. Further characterization by long-range polymerase chain reaction was conducted. Results showed that 30% of deletions detected involved Alu sequences. Furthermore, two cases also exhibited an Alu insertion in SLC7A2 or PHKA2, which was not identified by either panel due to incorrect alignment of the inserted Alu with the reference genome. Dr. Perez Gonzalez explained that recent developments in high- throughput sequence capture have led to the feasibility of NGS for routine genetic diagnosis. Improvement of depth in coverage allows for detection of large genomic deletions in addition to single-nucleotide variants.

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PRACTICEUPDATE CONFERENCE SERIES • SSIEM 2018