Simultaneous Detection of Both Single Nucleotide Variations and Copy Number Alterations by Next-Generation Sequencing in Gorlin Syndrome

• Published in: PloS one Vol. 10; no. 11; p. e0140480
• Main Authors: Morita, Kei-ichi, Naruto, Takuya, Tanimoto, Kousuke, Yasukawa, Chisato, Oikawa, Yu, Masuda, Kiyoshi, Imoto, Issei, Inazawa, Johji, Omura, Ken, Harada, Hiroyuki
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 06.11.2015; Public Library of Science (PLoS)
• Subjects: Adolescent; Adult; Aged; Alterations; Amino acid sequence; Amino acids; Basal Cell Nevus Syndrome - genetics; Biomarkers - analysis; Cancer; Child; Cohort Studies; Copy number; Custom design; Cytogenetics; Deoxyribonucleic acid; DNA; DNA Copy Number Variations - genetics; Exons; Failure analysis; Female; Genes; Genetic testing; Genomes; Genomics; Gorlin syndrome; Hedgehog protein; Hereditary diseases; High-Throughput Nucleotide Sequencing - methods; Humans; Male; Maxillofacial surgery; Medical research; Mutation; Patients; Pedigree; Point mutation; Polymorphism, Single Nucleotide - genetics; Science; Sequences; Signal transduction; Signaling; Skin cancer; Surgery; Tumorigenesis; Tumors; University graduates
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0140480

Gorlin syndrome (GS) is an autosomal dominant disorder that predisposes affected individuals to developmental defects and tumorigenesis, and caused mainly by heterozygous germline PTCH1 mutations. Despite exhaustive analysis, PTCH1 mutations are often unidentifiable in some patients; the failure to detect mutations is presumably because of mutations occurred in other causative genes or outside of analyzed regions of PTCH1, or copy number alterations (CNAs). In this study, we subjected a cohort of GS-affected individuals from six unrelated families to next-generation sequencing (NGS) analysis for the combined screening of causative alterations in Hedgehog signaling pathway-related genes. Specific single nucleotide variations (SNVs) of PTCH1 causing inferred amino acid changes were identified in four families (seven affected individuals), whereas CNAs within or around PTCH1 were found in two families in whom possible causative SNVs were not detected. Through a targeted resequencing of all coding exons, as well as simultaneous evaluation of copy number status using the alignment map files obtained via NGS, we found that GS phenotypes could be explained by PTCH1 mutations or deletions in all affected patients. Because it is advisable to evaluate CNAs of candidate causative genes in point mutation-negative cases, NGS methodology appears to be useful for improving molecular diagnosis through the simultaneous detection of both SNVs and CNAs in the targeted genes/regions.