Familial cosegregation of rare genetic variants with disease in complex disorders

The role of copy number variants in the genetic architecture of common familial epilepsies

OBJECTIVE

Copy number variants (CNVs) contribute to genetic risk and genetic etiology of both rare and common epilepsies. Whereas many studies have explored the role of CNVs in sporadic or severe cases, fewer have been done in familial generalized and focal epilepsies.

METHODS

We analyzed exome sequence data from 267 multiplex families and 859 first-degree relative pairs with a diagnosis of genetic generalized epilepsies or nonacquired focal epilepsies to predict CNVs. Validation and segregation studies were performed using an orthogonal method when possible.

RESULTS

We identified CNVs likely to contribute to epilepsy risk or etiology in the probands of 43 of 1116 (3.9%) families, including known recurrent CNVs (16p13.11 deletion, 15q13.3 deletion, 15q11.2 deletion, 16p11.2 duplication, 1q21.1 duplication, and 5-Mb duplication of 15q11q13). We also identified CNVs affecting monogenic epilepsy genes, including four families with CNVs disrupting the DEPDC5 gene, and a de novo deletion of HNRNPU in one affected individual from a multiplex family. Several large CNVs (>500 kb) of uncertain clinical significance were identified, including a deletion in 18q, a large duplication encompassing the SCN1A gene, and a 15q13.3 duplication (BP4-BP5).

SIGNIFICANCE

The overall CNV landscape in common familial epilepsies is similar to that of sporadic epilepsies, with large recurrent deletions at 15q11, 15q13, and 16p13 contributing in 2.5%-3% of families. CNVs that interrupt known epilepsy genes and rare, large CNVs were also identified. Multiple etiologies were found in a subset of families, emphasizing the importance of genetic testing for multiple affected family members. Rare CNVs found in a single proband remain difficult to interpret and require larger cohorts to confirm their potential role in disease. Overall, our work indicates that CNVs contribute to the complex genetic architecture of familial generalized and focal epilepsies, supporting the role for clinical testing in affected individuals.

Basic Research Protocol: Exome Sequencing in Adults With Loin Pain Hematuria Syndrome: A Pilot Study

Background

Loin pain hematuria syndrome (LPHS) is a poorly understood clinical syndrome characterized by hematuria and either unilateral or bilateral severe kidney pain in the absence of identifiable urological disease. Loin pain hematuria syndrome imposes a significant health and economic impact with a loss of productivity and quality of life in a young population. Owing to an incomplete understanding of its pathophysiology, treatment has been limited to nonspecific pain management. Nearly 60 years after its initial description, we are no further ahead in understanding the molecular pathways involved in LPHS.

Objective

To outline the study design for exome sequencing in adults with LPHS and their families.

Methods

In this single-center case series, 24 patients with LPHS and 2 additional first-degree family members per participant will be recruited. DNA extracted from venous blood samples will undergo exome sequencing on the Illumina NovaSeq 6000 System at 100× depth and will be assessed for pathogenic variants in genes associated with hematuria (number of genes in: glomerular endothelium [n = 10] and basement membrane [n = 8]), and pain pathways (number of genes in: pain transduction [n = 17], conduction [n = 8], synaptic transmission [n = 37], and modulation [n = 27]). We will further examine identified potentially pathogenic variants that co-segregate with LPHS features among affected families.

Conclusions

This pilot study may identify new directions for an investigation into the molecular mechanisms underlying LPHS.

Rare and common variant discovery in complex disease: the IBD case study

Complex diseases such as inflammatory bowel disease (IBD), which consists of ulcerative colitis and Crohn's disease, are a significant medical burden-70 000 new cases of IBD are diagnosed in the United States annually. In this review, we examine the history of genetic variant discovery in complex disease with a focus on IBD. We cover methods that have been applied to microsatellite, common variant, targeted resequencing and whole-exome and -genome data, specifically focusing on the progression of technologies towards rare-variant discovery. The inception of these methods combined with better availability of population level variation data has led to rapid discovery of IBD-causative and/or -associated variants at over 200 loci; over time, these methods have grown exponentially in both power and ascertainment to detect rare variation. We highlight rare-variant discoveries critical to the elucidation of the pathogenesis of IBD, including those in NOD2, IL23R, CARD9, RNF186 and ADCY7. We additionally identify the major areas of rare-variant discovery that will evolve in the coming years. A better understanding of the genetic basis of IBD and other complex diseases will lead to improved diagnosis, prognosis, treatment and surveillance.

Two high-risk susceptibility loci at 6p25.3 and 14q32.13 for Waldenström macroglobulinemia

Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a rare, chronic B-cell lymphoma with high heritability. We conduct a two-stage genome-wide association study of WM/LPL in 530 unrelated cases and 4362 controls of European ancestry and identify two high-risk loci associated with WM/LPL at 6p25.3 (rs116446171, near EXOC2 and IRF4; OR = 21.14, 95% CI: 14.40-31.03, P = 1.36 × 10-54) and 14q32.13 (rs117410836, near TCL1; OR = 4.90, 95% CI: 3.45-6.96, P = 8.75 × 10-19). Both risk alleles are observed at a low frequency among controls (~2-3%) and occur in excess in affected cases within families. In silico data suggest that rs116446171 may have functional importance, and in functional studies, we demonstrate increased reporter transcription and proliferation in cells transduced with the 6p25.3 risk allele. Although further studies are needed to fully elucidate underlying biological mechanisms, together these loci explain 4% of the familial risk and provide insights into genetic susceptibility to this malignancy.

Exome sequencing reveals a novel MFN2 missense mutation in a Chinese family with Charcot-Marie-Tooth type 2A

Charcot-Marie-Tooth (CMT) is a group of inherited peripheral neuropathies. To date, mutations in >80 genes are reportedly associated with CMT. Protein mitofusin 2 encoded by MFN2 serves an essential role in mitochondrial fusion and regulation of apoptosis, which has previously been reported to be highly associated with an axonal form of neuropathy (CMT2A). In the present study, a large Chinese family with severe CMT was reported and a genetic analysis of the disease was performed. A detailed physical examination for CMT was performed in 13 family members and electrophysiological examinations were performed in 3 affected family members. Whole-exome sequencing was performed on the proband, and the suspected variants were identified by Sanger sequencing. The pathogenicity of mutation was verified by restriction fragment length polymorphism analysis in the family followed by a bioinformatics analysis. A novel c.1190G>C; p.(R397P) mutation in the MFN2 gene was identified in the proband, and co-segregated between genotype and phenotype in the family. The substituted amino acid changed the hydrophobicity and charge characteristics of the mitofusin 2 coiled-coiled domain; thus it may affect its biological function. In summary, a novel pathogenic mutation was identified in a Chinese family with CMT, which expands the phenotypic and mutational spectrum of CMT2A, and provides evidence for prenatal interventions and more precise pharmacological treatments to this family.

Advancing epilepsy genetics in the genomic era

Epilepsy is a group of disorders characterized by recurrent seizures, and is one of the most common neurological conditions. The genetic basis of epilepsy is clear from epidemiological studies and from rare gene discoveries in large families. The three major classes of epilepsy disorders are genetic generalized, focal and encephalopathic epilepsies, with several specific disorders within each class. Advances in genomic technologies that facilitate genome-wide discovery of both common and rare variants have led to a rapid increase in our understanding of epilepsy genetics. Copy number variant and genome-wide association studies have contributed to our understanding of the complex genetic architecture of generalized epilepsy, while genetic insights into the focal epilepsies and epileptic encephalopathies have come primarily from exome sequencing. It is increasingly clear that epilepsy is genetically heterogeneous, and novel gene discoveries have moved the field beyond the known contribution of ion channels to implicate chromatin remodeling, transcriptional regulation and regulation of the mammalian target of rapamycin (mTOR) protein in the etiology of epilepsy. Such discoveries pave the way for new therapeutics, some of which are already being studied. In this review, we discuss the rapid pace of gene discovery in epilepsy, as facilitated by genomic technologies, and highlight several novel genes and potential therapies.

Robust and Powerful Affected Sibpair Test for Rare Variant Association

Advances in DNA sequencing technology facilitate investigating the impact of rare variants on complex diseases. However, using a conventional case-control design, large samples are needed to capture enough rare variants to achieve sufficient power for testing the association between suspected loci and complex diseases. In such large samples, population stratification may easily cause spurious signals. One approach to overcome stratification is to use a family-based design. For rare variants, this strategy is especially appropriate, as power can be increased considerably by analyzing cases with affected relatives. We propose a novel framework for association testing in affected sibpairs by comparing the allele count of rare variants on chromosome regions shared identical by descent to the allele count of rare variants on nonshared chromosome regions, referred to as test for rare variant association with family-based internal control (TRAFIC). This design is generally robust to population stratification as cases and controls are matched within each sibpair. We evaluate the power analytically using general model for effect size of rare variants. For the same number of genotyped people, TRAFIC shows superior power over the conventional case-control study for variants with summed risk allele frequency f < 0.05; this power advantage is even more substantial when considering allelic heterogeneity. For complex models of gene-gene interaction, this power advantage depends on the direction of interaction and overall heritability. In sum, we introduce a new method for analyzing rare variants in affected sibpairs that is robust to population stratification, and provide freely available software.

Genetic testing preferences in families containing multiple individuals with epilepsy

OBJECTIVE

To examine genetic testing preferences in families containing multiple individuals with epilepsy.

METHODS

One hundred forty-three individuals with epilepsy and 165 biologic relatives without epilepsy from families containing multiple affected individuals were surveyed using a self-administered questionnaire. Four genetic testing scenarios were presented, defined by penetrance (100% vs. 50%) and presence or absence of clinical utility. Potential predictors of genetic testing preferences were evaluated using generalized estimating equations with robust Poisson regression models. The influence of 21 potential testing motivations was also assessed.

RESULTS

For the scenario with 100% penetrance and clinical utility, 85% of individuals with epilepsy and 74% of unaffected relatives responded that they would definitely or probably want genetic testing. For the scenario with 100% penetrance but without clinical utility, the proportions who responded that they would want testing were significantly lower in both affected individuals (69%) and unaffected relatives (57%). Penetrance (100% vs. 50%) was not a significant predictor of genetic testing interest. The highest-ranking motivations for genetic testing were the following: the possibility that the results could improve health or health care, the potential to know if epilepsy in the family is caused by a gene, and the possibility of changing behavior or lifestyle to prevent seizures.

SIGNIFICANCE

Interest in epilepsy genetic testing may be high in affected and unaffected individuals in families containing multiple individuals with epilepsy, especially when testing has implications for improving clinical care.

Genetics of the epilepsies: where are we and where are we going?

PURPOSE OF REVIEW

We aim to review the most recent advances in the field of epilepsy genetics with particular focus on the progress in gene discovery in monogenic epilepsies, identification of risk genes in complex genetic epilepsies and recent findings in the field of epilepsy pharmacogenomics.

RECENT FINDINGS

During the last 12 months, the use of massive parallel sequencing technologies has allowed for the discovery of several genes for monogenic epilepsies. Most importantly, PRRT2 was identified as the long-sought gene for benign familial infantile seizures. Mutations in KCNT1 were found in two seemingly unrelated monogenic epilepsies including malignant migrating partial seizures of infancy and severe autosomal dominant nocturnal frontal lobe epilepsy. A genome-wide association study in idiopathic generalized epilepsy revealed the first common risk variants for human seizure disorders including variants in VRK2, PNPO and SCN1A. Furthermore, a landmark study provided evidence that screening for the HLA-B1502 variant may prevent carbamazepine CBZ-induced side effects in the Taiwanese population. Also, HLA-A3101 variants were identified as a risk factor for carbamazepine side effects in Europeans.

SUMMARY

Novel technologies and an unprecedented level of international collaboration have resulted in identification of novel genes for monogenic and complex genetic epilepsies as well as risk factors for side effects of antiepileptic drugs. This review provides an overview of the most relevant studies in the last year and highlights the future direction of the field.