Targeted exome sequencing and chromosomal microarray for the molecular diagnosis of nevoid basal cell carcinoma syndrome.
BACKGROUND
Nevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant disorder mainly caused by heterozygous mutations of PTCH1. In addition to characteristic clinical features, detection of a mutation in causative genes is reliable for the diagnosis of NBCCS; however, no mutations have been identified in some patients using conventional methods.


OBJECTIVE
To improve the method for the molecular diagnosis of NBCCS.


METHODS
We performed targeted exome sequencing (TES) analysis using a multi-gene panel, including PTCH1, PTCH2, SUFU, and other sonic hedgehog signaling pathway-related genes, based on next-generation sequencing (NGS) technology in 8 cases in whom possible causative mutations were not detected by previously performed conventional analysis and 2 recent cases of NBCCS. Subsequent analysis of gross deletion within or around PTCH1 detected by TES was performed using chromosomal microarray (CMA).


RESULTS
Through TES analysis, specific single nucleotide variants or small indels of PTCH1 causing inferred amino acid changes were identified in 2 novel cases and 2 undiagnosed cases, whereas gross deletions within or around PTCH1, which are validated by CMA, were found in 3 undiagnosed cases. However, no mutations were detected even by TES in 3 cases. Among 3 cases with gross deletions of PTCH1, deletions containing the entire PTCH1 and additional neighboring genes were detected in 2 cases, one of which exhibited atypical clinical features, such as severe mental retardation, likely associated with genes located within the 4.3Mb deleted region, especially.


CONCLUSIONS
TES-based simultaneous evaluation of sequences and copy number status in all targeted coding exons by NGS is likely to be more useful for the molecular diagnosis of NBCCS than conventional methods. CMA is recommended as a subsequent analysis for validation and detailed mapping of deleted regions, which may explain the atypical clinical features of NBCCS cases.
Department of Dermatology, Tokushima University Graduate School of Medical Science, Tokushima, Japan.
Yoshihiro
Y
Matsudate
Department of Human Genetics, Tokushima University Graduate School of Medical Science, Tokushima, Japan.
Takuya
T
Naruto
Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan.
Yumiko
Y
Hayashi
Divisions of Dermatology, Matsuyama Red Cross Hospital, Matsuyama, Japan.
Mitsuyoshi
M
Minami
Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan.
Mikiko
M
Tohyama
Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
Kenji
K
Yokota
Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan.
Daisuke
D
Yamada
Department of Human Genetics, Tokushima University Graduate School of Medical Science, Tokushima, Japan.
Issei
I
Imoto
Department of Dermatology, Tokushima University Graduate School of Medical Science, Tokushima, Japan. Electronic address: kubo@tokushima-u.ac.jp.
Yoshiaki
Y
Kubo
D000293:Adolescent; D000328:Adult; D001478:Basal Cell Nevus Syndrome / Q000175:diagnosis / Q000235:genetics*; D014408:Biomarkers, Tumor / Q000235:genetics*; D002877:Chromosomes, Human; D019295:Computational Biology; D056915:DNA Copy Number Variations; D004252:DNA Mutational Analysis; D059472:Exome; D005260:Female; D018628:Gene Dosage; D020022:Genetic Predisposition to Disease; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011237:Predictive Value of Tests; D015203:Reproducibility of Results; D055815:Young Adult
D014408:Biomarkers, Tumor
Chromosomal microarray; Nevoid basal cell carcinoma syndrome; Next-generation sequencing; PTCH1; Targeted exome sequencing