A Decade of Next-generation Sequencing in Genodermatoses

The Impact on Gene Discovery and Clinical Diagnostics

F.P.-C. Chiu; B.J. Doolan; J.A. McGrath; A. Onoufriadis

Disclosures

The British Journal of Dermatology. 2021;184(4):606-616. 

In This Article

Abstract and Introduction

Abstract

Background: Discovering the genetic basis of inherited skin diseases is fundamental to improving diagnostic accuracy and genetic counselling. In the 1990s and 2000s, genetic linkage and candidate gene approaches led to the molecular characterization of several dozen genodermatoses, but over the past decade the advent of next-generation sequencing (NGS) technologies has accelerated diagnostic discovery and precision.

Objectives: This review examines the application of NGS technologies from 2009 to 2019 that have (i) led to the initial discovery of gene mutations in known or new genodermatoses and (ii) identified involvement of more than one contributing pathogenic gene in individuals with complex Mendelian skin disorder phenotypes.

Methods: A comprehensive review of the PubMed database and dermatology conference abstracts was undertaken between January 2009 and December 2019. The results were collated and cross-referenced with OMIM.

Results: We identified 166 new disease–gene associations in inherited skin diseases discovered by NGS. Of these, 131 were previously recognized, while 35 were brand new disorders. Eighty-five were autosomal dominant (with 43 of 85 mutations occurring de novo), 78 were autosomal recessive and three were X-linked. We also identified 63 cases harbouring multiple pathogenic mutations, either involving two coexisting genodermatoses (n = 13) or an inherited skin disorder in conjunction with other organ system phenotypes (n = 50).

Conclusions: NGS technologies have accelerated disease–gene discoveries in dermatology over the last decade. Moreover, the era of NGS has enabled clinicians to split complex Mendelian phenotypes into separate diseases. These genetic data improve diagnostic precision and make feasible accurate prenatal testing and better-targeted translational research.

Introduction

Currently, there are approximately 9000 distinct Mendelian conditions, of which more than 1000 involve skin pathology.[1,2] Moreover, inherited skin diseases are often protean in their clinical manifestations, with many harbouring systemic manifestations and potentially overlapping syndromic phenotypes.[3] Apart from characterized genodermatoses, patients may have clinically recognizable disorders that still lack a genetic basis, or they may have new uncharacterized diseases, or complex phenotypes that are the result of mutations in more than one gene in an individual. On top of these presentations, there may be further manipulation of the phenotype by genetic modifiers or epigenetic influences. Therefore, fundamentally, accurate diagnosis can be difficult, but it is essential to allow dermatologists to offer effective genetic counselling and optimal clinical management.[4]

Over the last 35 years the molecular bases of inherited skin diseases have been partially elucidated, with some initial discoveries driven by genetic linkage and candidate gene approaches.[5] Genetic linkage approaches typically involved analysing large pedigrees to identify and subsequently refine genomic loci that segregated with a disease phenotype, until a specific region with several candidate genes was identified that was sufficiently small to undertake Sanger sequencing of those genes.[6] In clinical genetics, this technique was first used successfully in 1986 to identify CYBB as the gene underlying chronic granulomatous disease.[7,8] In dermatology, genetic linkage first contributed to delineating the genetic basis of X-linked ichthyosis, with STS identified in 1987.[9,10]

For autosomal recessive diseases, an alternative approach was to identify candidate genes by detecting loss of protein expression or structural differences within the skin of affected individuals, using techniques such as immunohistochemistry or transmission electron microscopy.[11] Mutations in candidate genes were then confirmed by Sanger sequencing. For example, this approach led to the discovery of biallelic loss-of-function mutations in COL17A1 (encoding type XVII collagen, also known as the 180-kDa bullous pemphigoid antigen) in generalized atrophic benign epidermolysis bullosa (now known as intermediate junctional epidermolysis bullosa).[12]

Further spurring Mendelian gene discovery was the development of dense, genome-wide linkage maps and the knowledge gleaned from the Human Genome Project during the 1990s and early 2000s.[5,13] The number of discoveries increased from approximately 40 disease-associated genes prior to the identification of CYBB in 1986,[5] to having over 1000 disease genes documented in the Online Mendelian Inheritance in Man (OMIM) database by early 2000.[14] However, despite these successes genetic linkage and candidate gene studies were costly and laborious. Moreover, the genetic basis of many Mendelian phenotypes proved to be intractable to these approaches.[4,9,15]

Indeed, reports of novel gene discoveries somewhat stalled until the advent of new unbiased methods for the interrogation of the genome using next-generation sequencing (NGS) technologies, particularly whole-exome sequencing (WES).[5,16,17] Unlike whole-genome sequencing (WGS), which analyses around 3·2 billion nucleotides of human DNA, WES allows the analysis of the roughly 1·5% of the human genome that encompasses most exons of all ~20 000 human genes, revealing around 25 000 variants in any individual.[18] Given that roughly 85% of the reported pathogenic mutations in monogenic diseases reside within protein-coding regions, at present WES represents a useful innovation for both gene discovery and molecular diagnostics.[16] Furthermore, WES offers the opportunity to interrogate diseases that were previously intractable to gene identification given their rarity, clinical and genetic heterogeneity, and paucity of multiplex families.[16,19]

Regarding clinically relevant testing, the first successful application of WES was performed in 2009, identifying a single candidate gene, DHODH, responsible for Miller syndrome in four affected, unrelated individuals.[20,21] Since this development, there has been a steady growth in the identification of new genes, with a reported trajectory of 263 novel discoveries per year (Figure 1).[22] Despite these advances, only 20% (4081 of around 20 000) of identified human protein-coding genes have an established association with one or more disease traits.[23] On average, each person is found to carry approximately 250–300 loss-of-function variants in annotated genes,[24] harbouring 50–100 de novo single-nucleotide mutations that may potentially cause damaging mutations to the coding sequence.[25,26] It has also been noted that multiple gene mutations in the same individual are recognized to account for at least 4% of cases for which molecular testing is diagnostic,[27] with a diagnostic rate that is even higher (12%) in cohorts of selected phenotypes.[23,28] Therefore, genetic variation and/or multiple genetic mutations may have the potential to exhibit manifestations that can complicate or confuse clinical interpretation of the genotype–phenotype relationship, but that the new methodologies can identify and assess.

Figure 1.

Selected significant annual highlights in next-generation sequencing-based gene discoveries for inherited skin diseases since the first successful application of whole-exome sequencing (WES) in 2009. PLACK syndrome: peeling, leuconychia, acral keratoses, cheilitis and knuckle pads; SAM syndrome: severe skin dermatitis, multiple allergies and metabolic wasting. For the full list of gene discoveries, see Table S1 in the Supporting Information.

NGS has also been integral towards developing our understanding of mosaic disorders, which harbour genotype–phenotype associations that were previously difficult to assess with traditional sequencing techniques due to the somatic nature of their causative mutations. This includes the identification of AKT1 mutations as the underlying genetic basis for Proteus syndrome,[29] and, more recently, mutations in RHOA underlying a novel mosaic neuroectodermal syndrome.[30] For the purposes of this review, we do not explore use of NGS for mosaic disorders, and for this information the reader is directed elsewhere.[31]

The main aim of this review is to document the impact of NGS on gene discovery for inherited skin diseases and dissection of complex Mendelian disorders that include skin abnormalities. We hope the tabulated data (comprehensively listed in Table S1, Table S2 and Table S3; see Supporting Information) will provide a useful reference resource for recent history in the era of molecular diagnostics in dermatology and NGS.

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