1. Custom Pediatric Oncology Next-Generation Sequencing Panel Identifies Somatic Mosaicism in Archival Tissue and Enhances Targeted Clinical Care.
- Author
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Quindipan, Catherine, Cotter, Jennifer A., Ji, Jianling, Mitchell, Wendy G., Moke, Diana J., Navid, Fariba, Thomas, Stefanie M., VanHirtum-Das, Michele, Wang, Larry, Saitta, Sulagna C., Biegel, Jaclyn A., and Hiemenz, Matthew C.
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PEDIATRIC oncology , *NUCLEOTIDE sequencing , *MOSAICISM , *BLOOD sampling , *PEDIATRIC hematology , *MEDICAL care use , *NERVOUS system abnormalities , *PILOT projects , *SEQUENCE analysis , *GENETIC testing , *PEDIATRICS , *PRESERVATION of organs, tissues, etc. , *PEPTIDES , *ONCOLOGY - Abstract
Background: Disorders in the PIK3CA-related overgrowth spectrum because of somatic mosaicism are associated with segmental overgrowth of the body in conjunction with vascular, skeletal, and brain malformations such as hemimegalencephaly. A pathogenic variant may only be detectable in affected tissue and not in peripheral blood or saliva samples; therefore archival tissue may be the only relevant available specimen for testing. Although this is a common approach for cancer testing, it is not typically used for constitutional genetic disorders.Methods: PIK3CA mosaicism was assessed with a custom pediatric oncology next-generation sequencing panel (OncoKids) designed to capture somatic mutations in pediatric malignancies. The panel covers a wide range of targets including PIK3CA and AKT1 hotspots. We used OncoKids on archival formalin-fixed, paraffin-embedded or frozen samples from seven patients with facial hemihypertrophy and lipomas, hemimegalencephaly, or hemihypertrophy with a lymphovascular malformation. The age of the archival tissue examined by next-generation sequencing ranged from two to 13 years (median 5 years). Every patient had clinical manifestations within the PIK3CA-related overgrowth spectrum and had a sample of an affected tissue available for testing from a prior surgical intervention.Results: PIK3CA mosaicism was detected in all seven patients and the mutant allele fraction was lower in the lymphovascular malformation tissues (8% to 11%) than in brain (20% to 32%) and lipomatous (16% to 23%) tissues.Conclusions: Our study highlights the clinical utility of using a robust, oncology-focused next-generation sequencing assay to identify PIK3CA mosaicism in noncancer cases. It is feasible to use archival samples that are more than a decade old to obtain a molecular diagnosis, which can then be used to improve health care management. [ABSTRACT FROM AUTHOR]- Published
- 2021
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