Lessons Learned from Whole Exome Sequencing in Multiplex Families Affected by a Complex Genetic Disorder, Intracranial Aneurysm

Abstract

Genetic risk factors for intracranial aneurysm (IA) are not yet fully understood. Genomewide association studies have been successful at identifying common variants; however, the role of rare variation in IA susceptibility has not been fully explored. In this study, we report the use of whole exome sequencing (WES) in seven densely-affected families (45 individuals) recruited as part of the Familial Intracranial Aneurysm study. WES variants were prioritized by functional prediction, frequency, predicted pathogenicity, and segregation within families. Using these criteria, 68 variants in 68 genes were prioritized across the seven families. Of the genes that were expressed in IA tissue, one gene (TMEM132B) was differentially expressed in aneurysmal samples (n=44) as compared to control samples (n=16) (false discovery rate adjusted p-value=0.023). We demonstrate that sequencing of densely affected families permits exploration of the role of rare variants in a relatively common disease such as IA, although there are important study design considerations for applying sequencing to complex disorders. In this study, we explore methods of WES variant prioritization, including the incorporation of unaffected individuals, multipoint linkage analysis, biological pathway information, and transcriptome profiling. Further studies are needed to validate and characterize the set of variants and genes identified in this study.

A Review of the Genetics of Intracranial Berry Aneurysms and Implications for Genetic Counseling

“…Yasuno et al (2010) and Yasuno et al (2011) analyzed the same discovery and replication cohorts, which were expanded on from the cohort studied in Bilguvar et al (2008) in GSTCD, DUSP16, LMBR1L, HAL and TSC2, segregated fully with disease in one family and were present in the affected individuals of a second FIA family. None of the variants found in this study overlapped with any GWAS flagged loci (Farlow et al 2015). This is presumably because rare, highly-penetrant pathogenic variants that result in a Mendelian inheritance pattern in a multiplex family tend not to spread through to the general population (unless some sort of balancing selection occurs).…”

“…Initially, WES was carried out on 50 affected and unaffected individuals from these families, and analysis identified 96 candidate genes (Foroud for the FIA Study Investigators 2013). In their second publication (Farlow et al 2015), the FIA Study researchers analyzed WES data from 36 affected and 9 unaffected family members. Unaffected family members were only included if they were above 45 years of age and had received a negative screen by MRA.…”

“…It is of course possible that some of the family members who were scored as unaffected may yet develop an IBA in their lifetime. For this analysis, Farlow et al (2015) employed six biological filters on their WES data to generate a list of 68 candidate variants in 68 genes. These filters examined the variant type (non-synonymous SNVs or exonic and splice site indels), variants with a minor allele frequency (MAF) of <0.01, the segregation within families, and the predicted effect on protein (via CADD score ≥ 10, and predicted damaging by Polyphen2 or SIFT).…”

Intracranial Aneurysm Pathophysiology: To Bleed, or not To Bleed, That Is the Question

“…However, it did not consider other possible factors implicated in the mechanisms of sIA rupture and it was not validated in independent series of unruptured sIA. It was also supposed that the genetic profile could contribute to IA rupture susceptibility; emerging evidence, in fact, suggests that a positive family history represents the strongest known risk factor for SAH from ruptured IA, indicating that heritable DNA variation may influence IA susceptibility (6,21).…”

“…There are some limitations that the authors honestly recognized, related to the retrospective design of the study, the lack of data about familial history of IA and aortopathy and the bias of selection only patients with available data on echocardiography. In addition, the number of fusiform compared to saccular aneurysms is small and thus a large multicentric study, maybe incorporating other aspects of aortopathy M A N U S C R I P T A C C E P T E D ACCEPTED MANUSCRIPT 6 and also including and analyzing ruptured and unruptured IA, would be required to confirm this association and possibly exploring causality too.…”