Post-mortem genetic analysis of sudden unexplained death in a young cohort: a whole-exome sequencing study

Sudden unexplained death (SUD) constitutes a considerable portion of unexpected sudden death in the young. Molecular autopsy has proved to be an efficient diagnostic tool in the multidisciplinary management of SUD. Yet, many cases remain undiagnosed using the widely adopted targeted genetic screening strategies. Here, we investigated the genetic substrates of a young SUD cohort (18-40 years old) from China using whole-exome sequencing (WES), with the primary aim to identify novel SUD susceptibility genes. Within 255 previously acknowledged SUD-associated genes, 21 variants with likely functional effects (pathogenic/likely pathogenic) were identified in 51.9% of the SUD cases. More importantly, a set of 33 candidate genes associated with myopathy were identified to be novel susceptibility genes for SUD. Comparative analysis of the cumulative PHRED-scaled CADD score and polygenetic burden score showed that the amount and deleteriousness of variants in the 255 SUD-associated genes and the 33 candidate genes identified by this study were significantly higher compared with 289 randomly selected genes. A significantly higher genetic burden of rare variants (MAF < 0.1%) in the 33 candidate genes also highlighted putative roles of these genes in SUD. After incorporating these novel genes, the genetic testing yields of the current SUD cohort elevated from 51.9 to 66.7%. Our study expands understanding of the genetic variants underlying SUD and presents insights that improve the utility of genetic screenings.

Differential Effect of Genetic Burden on Disease Phenotypes in Crohn's Disease and Ulcerative Colitis in a Canadian Cohort

Background and Aims

Crohn’s disease (CD) and ulcerative colitis (UC) demonstrate considerable phenotypic heterogeneity and course. Accurate predictors of disease behaviour are lacking. The contribution of genetics and specific polymorphisms is widely appreciated; however, their cumulative effect(s) upon disease behaviour remains poorly understood. Here, we investigate the relationship between genetic burden and disease phenotype in a Canadian inflammatory bowel disease (IBD) Cohort.

Methods

We retrospectively examined a cohort of CD and UC patients recruited from a single tertiary referral center genotyped using a Goldengate Illumina platform. A genetic risk score (GRS) incorporating strength of association (log odds ratio) and allele dose for 151 IBD-risk loci was calculated and evaluated for phenotypic associations.

Results

Among CD patients, higher GRS was associated with earlier onset of disease (regression coefficient −2.19, 95% confidence interval [CI] −3.77 to −0.61, P = 0.007), ileal disease (odds ratio [OR] 1.45), stricturing/penetrating disease (OR 1.72), perianal disease (OR 1.57) and bowel resection (OR 1.66). Higher GRS was associated with use of anti-tumor necrosis factor (TNF) (P < 0.05) but not immunomodulators. Interestingly, we could not demonstrate an association between higher GRS and family history of IBD (OR 1.27, P = 0.07). Onset of disease remained statistically significant for never smokers (P = 0.03) but not ever smokers (P = 0.13). For UC, having a higher GRS did not predict the age of diagnosis nor was it predictive of UC disease extent (P = 0.18), the need for surgery (P = 0.74), nor medication use (immunomodulators P = 0.53, anti-TNF P = 0.49). We could not demonstrate an association between increased GRS and having a family history of IBD in the UC group.

Conclusions

Increasing genetic burden is associated with early age of diagnosis in CD and may be useful in predicting disease behaviour in CD but not UC.

Familial multiple sclerosis in Greece: Distinct clinical and imaging characteristics in comparison with the sporadic disease

OBJECTIVE

Few studies are available worldwide concerning clinical, imaging and genetic/immunogenetic profile of familial multiple sclerosis (fMS). Recent but not systematic data concerning fMS, without direct comparison to sporadic MS (sMS) drove our aim towards further research in the field, given the total lack of information for the Greek population as well. Thus, in this case-control study we examined the clinical and imaging characteristics of 102 fMS-patients, compared to 282 patients suffering sMS.

PATIENTS AND METHODS

Patients recruited underwent medical interview (demographic, clinical and family history data collected). They were also assessed for disability and their MRI-scans were analyzed for lesion distribution. Statistical analyses were performed using SPSS v.21.0 software.

RESULTS

49% of unrelated fMS cases had at least one 1^st degree relative affected, while the rest had also at least one relative with MS, 3^rd degree or closer. Only the former subgroup (1^st degree relative) and not the entire fMS sample, had significantly younger age at onset (AAO) compared to sMS cases (mean AAO 28.08 vs 31.33 years, p = 0.036). AAO anticipation was noted in younger generation fMS patients (mean AAO 24.67 years in younger generation vs 37 years in older generation, p = 0.001). With regard to our MRI findings, subcortical lesions were less frequent in fMS (71% in fMS vs 81.9% in sMS patients, p = 0.028), whereas cervical cord lesions more frequent (93% in fMS vs 79.9% in sMS patients, p = 0.033, only in the 1^st degree relative subgroup). Double vision was a less common first symptom in fMS (4.1% in fMS vs 14.8% in sMS patients, p = 0.005). 1^st degree relatives of fMS patients were more often diagnosed with Hashimoto's (8.9% in fMS relatives vs 3.3% in sMS relatives, p = 0.033).

CONCLUSION

Younger AAO and different lesion distribution in brain and possibly spinal cord was observed in fMS in comparison to sMS patients. The hypothesis of increased genetic burden in fMS could offer some explanation for these differences, which needs though further validation as a next step, through genetic/immunogenetic testing in larger cohorts, of different ethnic groups.

Germline and somatic variations influence the somatic mutational signatures of esophageal squamous cell carcinomas in a Chinese population

BACKGROUND

Esophageal squamous cell carcinomas (ESCC) is the fourth most lethal cancer in China. Previous studies reveal several highly conserved mutational processes in ESCC. However, it remains unclear what are the true regulators of the mutational processes.

RESULTS

We analyzed the somatic mutational signatures in 302 paired whole-exome sequencing data of ESCC in a Chinese population for potential regulators of the mutational processes. We identified three conserved subtypes based on the mutational signatures with significantly different clinical outcomes. Our results show that patients of different subpopulations of Chinese differ significantly in the activity of the "NpCpG" signature (FDR = 0.00188). In addition, we report ZNF750 and CDC27, of which the somatic statuses and the genetic burdens consistently influence the activities of specific mutational signatures in ESCC: the somatic ZNF750 status is associated with the AID/APOBEC-related mutational process (FDR = 0.0637); the somatic CDC27 copy-number is associated with the "NpCpG" (FDR = 0.00615) and the AID/APOBEC-related mutational processes (FDR = 8.69 × 10- 4). The burdens of germline variants in the two genes also significantly influence the activities of the same somatic mutational signatures (FDR < 0.1).

CONCLUSIONS

We report multiple factors that influence the mutational processes in ESCC including: the subpopulations of Chinese; the germline and somatic statuses of ZNF750 and CDC27 and exposure to alcohol and tobacco. Our findings based on the evidences from both germline and somatic levels reveal potential genetic regulators of the somatic mutational processes and provide insights into the biology of esophageal carcinogenesis.

Genetic burden of MS risk variants distinguish patients from healthy individuals but are not associated with disease activity

Weighted genetic risk score (wGRS) was analysed for association with disease activity in more than 500 MS patients before and during interferon-beta treatment. The wGRS was higher in MS patients than in healthy controls when analysing eight HLA - and 109 non-HLA MS risk gene variants. No significant associations were observed between number of relapses prior to or during treatment with interferon-beta, both with and without HLA risk alleles included in the wGRS. In conclusion, among Danes the wGRS was higher in MS patients than controls but was not associated with the overall disease activity or response to treatment with interferon-beta.