Molecular Diagnosis of Intellectual Disability
Molecular Diagnosis of Intellectual Disability
Background Intellectual disability (ID) is characterised by an extreme genetic heterogeneity. Several hundred genes have been associated to monogenic forms of ID, considerably complicating molecular diagnostics. Trio-exome sequencing was recently proposed as a diagnostic approach, yet remains costly for a general implementation.
Methods We report the alternative strategy of targeted high-throughput sequencing of 217 genes in which mutations had been reported in patients with ID or autism as the major clinical concern. We analysed 106 patients with ID of unknown aetiology following array-CGH analysis and other genetic investigations. Ninety per cent of these patients were males, and 75% sporadic cases.
Results We identified 26 causative mutations: 16 in X-linked genes (ATRX, CUL4B, DMD, FMR1, HCFC1, IL1RAPL1, IQSEC2, KDM5C, MAOA, MECP2, SLC9A6, SLC16A2, PHF8) and 10 de novo in autosomal-dominant genes (DYRK1A, GRIN1, MED13L, TCF4, RAI1, SHANK3, SLC2A1, SYNGAP1). We also detected four possibly causative mutations (eg, in NLGN3) requiring further investigations. We present detailed reasoning for assigning causality for each mutation, and associated patients' clinical information. Some genes were hit more than once in our cohort, suggesting they correspond to more frequent ID-associated conditions (KDM5C, MECP2, DYRK1A, TCF4). We highlight some unexpected genotype to phenotype correlations, with causative mutations being identified in genes associated to defined syndromes in patients deviating from the classic phenotype (DMD, TCF4, MECP2). We also bring additional supportive (HCFC1, MED13L) or unsupportive (SHROOM4, SRPX2) evidences for the implication of previous candidate genes or mutations in cognitive disorders.
Conclusions With a diagnostic yield of 25% targeted sequencing appears relevant as a first intention test for the diagnosis of ID, but importantly will also contribute to a better understanding regarding the specific contribution of the many genes implicated in ID and autism.
Intellectual disability (ID) is a common neurodevelopmental disorder reported in 1.5–2% of children and adolescents. ID is defined by significant limitations in both intellectual functioning and adaptative behaviour with onset before the age of 18. Different classes of ID are conventionally defined upon IQ values (severe or profound, <35; moderate, 35–49 and mild, 50–70). However, in routine genetic practice, clinical assessment mainly based on records of developmental history, speech acquisition and patients' autonomy is used for classification in such subcategories.
Causes of ID can be environmental, genetic or multifactorial. Single genetic events are thought to account for a majority of cases, varying from large chromosomal anomalies or copy number variants (CNVs) affecting several genes to point mutations in single genes. These latter monogenic forms are characterised by an extreme genetic heterogeneity, with a hundred genes described as implicated in X-linked ID (XLID), and more associated to autosomal-recessive or autosomal-dominant forms. Altogether there are more than 500 genes proposed to cause ID with high penetrance when mutated underlying a phenotypic heterogeneity of the same extent in both severity and associated symptoms. This genetic heterogeneity has long limited the diagnostic offer for patients and families, which was often restricted to fragile-X (MIM 300624) testing, array-CGH (comparative genomic hybridization) analysis and generic metabolic tests (see online supplementary figure S1 http://jmg.bmj.com/content/51/11/724/suppl/DC1). It may be complemented by sequencing a few genes associated to a specific syndrome evoked by patients' phenotype, yet the diagnostic yield remains low (1–2% for the recurrent fragile-X mutation; 10–15% for array-CGH and chromosomal analyses, higher in highly syndromic patients). A majority of patients remain therefore without molecular diagnosis, while it is of crucial importance for establishing recurrence risks and providing genetic counselling in the family. Moreover, such diagnosis often has direct consequences for the medical prognosis of patients or their optimised healthcare, and even (yet in still a minority of cases) can indicate specific therapeutic options.
To obviate this low diagnostic yield, we developed the simultaneous targeted sequencing of protein-coding exons of 217 genes associated with ID or autism spectrum disorders (ASDs) as primary clinically significant feature: 99 located on the X-chromosome, 118 on the autosomes. We report here the results of such strategy on a cohort of 106 ID patients with or without associated autistic-like features, negative for array-CGH, fragile-X and other specific genetic analyses. A causal mutation was detected in 25% of these patients, regardless the severity of their cognitive impairment. We illustrate cases in which the molecular diagnosis was immediately established, as well as other more complex situations. This highlights the challenge of interpreting variants generated by NGS technologies, already from targeted approaches restricted to a few hundred genes. This work demonstrates that a targeted sequencing approach is highly efficient for the diagnosis of ID, but also allows refining the clinical spectrum associated with mutations in certain genes, and confirming or questioning the involvement of other genes in cognitive disorders.
Abstract and Introduction
Abstract
Background Intellectual disability (ID) is characterised by an extreme genetic heterogeneity. Several hundred genes have been associated to monogenic forms of ID, considerably complicating molecular diagnostics. Trio-exome sequencing was recently proposed as a diagnostic approach, yet remains costly for a general implementation.
Methods We report the alternative strategy of targeted high-throughput sequencing of 217 genes in which mutations had been reported in patients with ID or autism as the major clinical concern. We analysed 106 patients with ID of unknown aetiology following array-CGH analysis and other genetic investigations. Ninety per cent of these patients were males, and 75% sporadic cases.
Results We identified 26 causative mutations: 16 in X-linked genes (ATRX, CUL4B, DMD, FMR1, HCFC1, IL1RAPL1, IQSEC2, KDM5C, MAOA, MECP2, SLC9A6, SLC16A2, PHF8) and 10 de novo in autosomal-dominant genes (DYRK1A, GRIN1, MED13L, TCF4, RAI1, SHANK3, SLC2A1, SYNGAP1). We also detected four possibly causative mutations (eg, in NLGN3) requiring further investigations. We present detailed reasoning for assigning causality for each mutation, and associated patients' clinical information. Some genes were hit more than once in our cohort, suggesting they correspond to more frequent ID-associated conditions (KDM5C, MECP2, DYRK1A, TCF4). We highlight some unexpected genotype to phenotype correlations, with causative mutations being identified in genes associated to defined syndromes in patients deviating from the classic phenotype (DMD, TCF4, MECP2). We also bring additional supportive (HCFC1, MED13L) or unsupportive (SHROOM4, SRPX2) evidences for the implication of previous candidate genes or mutations in cognitive disorders.
Conclusions With a diagnostic yield of 25% targeted sequencing appears relevant as a first intention test for the diagnosis of ID, but importantly will also contribute to a better understanding regarding the specific contribution of the many genes implicated in ID and autism.
Introduction
Intellectual disability (ID) is a common neurodevelopmental disorder reported in 1.5–2% of children and adolescents. ID is defined by significant limitations in both intellectual functioning and adaptative behaviour with onset before the age of 18. Different classes of ID are conventionally defined upon IQ values (severe or profound, <35; moderate, 35–49 and mild, 50–70). However, in routine genetic practice, clinical assessment mainly based on records of developmental history, speech acquisition and patients' autonomy is used for classification in such subcategories.
Causes of ID can be environmental, genetic or multifactorial. Single genetic events are thought to account for a majority of cases, varying from large chromosomal anomalies or copy number variants (CNVs) affecting several genes to point mutations in single genes. These latter monogenic forms are characterised by an extreme genetic heterogeneity, with a hundred genes described as implicated in X-linked ID (XLID), and more associated to autosomal-recessive or autosomal-dominant forms. Altogether there are more than 500 genes proposed to cause ID with high penetrance when mutated underlying a phenotypic heterogeneity of the same extent in both severity and associated symptoms. This genetic heterogeneity has long limited the diagnostic offer for patients and families, which was often restricted to fragile-X (MIM 300624) testing, array-CGH (comparative genomic hybridization) analysis and generic metabolic tests (see online supplementary figure S1 http://jmg.bmj.com/content/51/11/724/suppl/DC1). It may be complemented by sequencing a few genes associated to a specific syndrome evoked by patients' phenotype, yet the diagnostic yield remains low (1–2% for the recurrent fragile-X mutation; 10–15% for array-CGH and chromosomal analyses, higher in highly syndromic patients). A majority of patients remain therefore without molecular diagnosis, while it is of crucial importance for establishing recurrence risks and providing genetic counselling in the family. Moreover, such diagnosis often has direct consequences for the medical prognosis of patients or their optimised healthcare, and even (yet in still a minority of cases) can indicate specific therapeutic options.
To obviate this low diagnostic yield, we developed the simultaneous targeted sequencing of protein-coding exons of 217 genes associated with ID or autism spectrum disorders (ASDs) as primary clinically significant feature: 99 located on the X-chromosome, 118 on the autosomes. We report here the results of such strategy on a cohort of 106 ID patients with or without associated autistic-like features, negative for array-CGH, fragile-X and other specific genetic analyses. A causal mutation was detected in 25% of these patients, regardless the severity of their cognitive impairment. We illustrate cases in which the molecular diagnosis was immediately established, as well as other more complex situations. This highlights the challenge of interpreting variants generated by NGS technologies, already from targeted approaches restricted to a few hundred genes. This work demonstrates that a targeted sequencing approach is highly efficient for the diagnosis of ID, but also allows refining the clinical spectrum associated with mutations in certain genes, and confirming or questioning the involvement of other genes in cognitive disorders.
