Exome sequencing in a family segregating for celiac disease

Celiac disease is a multifactorial disorder caused by an unknown number of genetic factors interacting with an environmental factor. Hence, most patients are singletons and large families segregating with celiac disease are rare. We report on a three-generation family with six patients in which the inheritance pattern is consistent with an autosomal dominant model. To date, 27 loci explain up to 40% of the heritable disease risk. We hypothesized that part of the missing heritability is because of low frequency or rare variants. Such causal variants could be more prominent in multigeneration families where private mutations might co-segregate with the disease. They can be identified by linkage analysis combined with whole exome sequencing. We found three linkage regions on 4q32.3-4q33, 8q24.13-8q24.21 and 10q23.1-10q23.32 that segregate with celiac disease in this family. We performed exome sequencing on two affected individuals to investigate the positional candidate regions and the remaining exome for causal nonsense variants. We identified 12 nonsense mutations with a low frequency (minor allele frequency <10%) present in both individuals, but none mapped to the linkage regions. Two variants in the CSAG1 and KRT37 genes were present in all six affected individuals. Two nonsense variants in the MADD and GBGT1 genes were also present in 5 of 6 and 4 of 6 individuals, respectively; future studies should determine if any of these nonsense variants is causally related to celiac disease.     

Genetic variation in Toll-like receptors and disease susceptibility

Toll-like receptors (TLRs) are key initiators of the innate immune response and promote adaptive immunity. Much has been learned about the role of TLRs in human immunity from studies linking TLR genetic variation with disease. First, monogenic disorders associated with complete deficiency in certain TLR pathways, such as MyD88-IRAK4 or TLR3-Unc93b-TRIF-TRAF3, have demonstrated the specific roles of these pathways in host defense against pyogenic bacteria and herpesviruses, respectively. Second, common polymorphisms in genes encoding several TLRs and associated genes have been associated with both infectious and autoimmune diseases. The study of genetic variation in TLRs in various populations combined with information on infection has demonstrated complex interaction between genetic variation in TLRs and environmental factors. This interaction explains the differences in the effect of TLR polymorphisms on susceptibility to infection and autoimmune disease in various populations.     

Genetics of intracranial aneurysms

Subarachnoid haemorrhage (SAH) is a subtype of stroke caused by the rupture of an intracranial aneurysm. Genetic factors play an important part in the pathogenesis of SAH and intracranial aneurysms. SAH and intracranial aneurysms are complex in origin, involving the interaction of several genes and environmental factors. A disruption of the extracellular matrix of the arterial wall, which provides strength and elasticity to intracranial arteries, is a likely factor in the pathophysiology of intracranial aneurysms. In this review, we discuss the genetic association, linkage, and gene-expression studies of SAH and intracranial aneurysms. At present, four genome-wide linkage studies have identified genetic loci for intracranial aneurysms. Interestingly, three of these loci include functional candidate genes coding for structural proteins of the extracellular matrix. Of these genes, elastin and collagen type 1A2 are the most promising candidates, because allelic association with intracranial aneurysms has also been shown for these genes. However, variation in these two genes only explains a small proportion of the genetic factors involved in intracranial aneurysms. Future studies need to identify new candidate genes to help unravel the pathophysiology of the disorder.     

No association between gluten sensitivity and amyotrophic lateral sclerosis

To examine evidence for a role of gluten sensitivity (GS) or celiac disease (CD) in ALS etiology, we included participants from a population-based case–control study in The Netherlands between January 2006 and December 2015. We compared levels and seroprevalence of IgA antibodies to tissue transglutaminase 6 (TG6) in 359 ALS patients and 359 controls, and to transglutaminase 2 (TG2) and endomysium (EMA) in 199 ALS patients and 199 controls. Questionnaire data on 1829 ALS patients and 3920 controls were examined for CD or gluten-free diets (GFD). Genetic correlation and HLA allele frequencies were analyzed using two genome-wide association studies: one on ALS (12,577 cases, 23,475 controls), and one on CD (4533 cases, 10,750 controls). We found one patient with TG6, TG2 and EMA antibodies who had typical ALS and no symptoms of GS. TG6 antibody concentrations and positivity, CD prevalence and adherence to a GFD were similar in patients and controls (p > 0.66) and in these patients disease progression was compatible with typical ALS. CD and ALS were not found to be genetically correlated (p > 0.37). CD-associated HLA allele frequencies were similar in patients and controls (p > 0.28). In conclusion, we found no serological evidence for involvement of gluten-related antibodies in ALS etiology nor did we observe an association between CD and ALS in medical history or genetic data, indicating that there is no evidence in our data for an association between the two diseases. Hence, a role for a GFD in the ALS treatment seems unlikely.     

WNT2 Locus Is Involved in Genetic Susceptibility of Peyronie's Disease

IntroductionPeyronie's disease (PD) is a fibromatosis of the penis, with a pathology very similar to what is seen in the hand (palmar fascia) in Dupuytren's disease (DD). Recently, we performed a genome‐wide association study and identified nine genetic loci containing common variants associated with DD. Seven of these loci mapped within or near genes of the canonical WNT pathway and each locus yielded relatively large odds ratios (ORs) for DD disease status.AimGiven the clinical overlap between PD and DD, we examined whether the nine DD susceptibility loci are also involved in PD.MethodsAn association study was performed using a case/control design. From 2007 to 2010, we prospectively included 111 men who had been clinically diagnosed with PD. Control subjects (N = 490 males) were randomly drawn from a population‐based cohort from the same region of the Netherlands. Allele frequencies in the 111 PD cases and 490 controls were compared using a 1‐degree‐of‐freedom basic chi‐square test. A P value < 0.05 after Bonferroni correction for the nine tested single nucleotide polymorphisms (SNPs) was considered statistically significant (i.e., P < 0.0056).Main Outcome MeasureAssociation of genetic markers (SNPs) with PD.ResultsWe observed significant association with SNP rs4730775 at the wingless‐type MMTV integration site family member 2 (WNT2) locus on chromosome 7 (P = 0.0015, OR 0.61), but found no evidence for the other eight loci being involved with PD despite the large effect size seen for some of these variants in DD. The WNT2 association was even more significant after we removed 15 patients with comorbid DD.ConclusionsWNT2 is a susceptibility locus for PD and our finding provides evidence for a partly shared genetic susceptibility between PD and DD. Dolmans GH, Werker PM, de Jong IJ, Nijman RJ, LifeLines Cohort Study, Wijmenga C, and Ophoff RA. WNT2 locus is involved in genetic susceptibility of Peyronie's disease. J Sex Med 2012;9:1430–1434.     

Upstream transcription factor 1 (USF1) in risk of type 2 diabetes: association study in 2000 Dutch Caucasians

Type 2 diabetes shares substantial genetic and phenotypic overlap with familial combined hyperlipidemia. Upstream stimulatory factor 1 (USF1), a well-established susceptibility gene for familial combined hyperlipidemia, is postulated to be such a shared genetic determinant. We evaluated two established variants in familial combined hyperlipidemia (rs2073658 and rs3737787) for association with type 2 diabetes in two Dutch case-control samples (N = 2011). The first case-control sample comprised 501 subjects with type 2 diabetes from the Breda cohort and 920 healthy blood bank donors of Dutch Caucasian origin. The second case-control sample included 211 subjects with type 2 diabetes, and 379 normoglycemic controls. SNP rs2073658 and SNP rs3737787 were in perfect linkage disequilibrium. In the first case-control sample, prevalence of the major allele was higher in patients than in controls (75% versus 71%, OR = 1.25, p = 0.018). A similar effect-size and -direction was observed in the second case-control sample (76% versus 72%, OR = 1.22, p = 0.16). A combined analysis strengthened the evidence for association (OR = 1.23, p = 0.006). Notably, the increased risk for type 2 diabetes could be ascribed to the major allele, and its high frequency translated to a substantial population attributable risk of 14.5%.In conclusion, the major allele of rs2073658 in the USF1 gene is associated with a modestly increased risk to develop type 2 diabetes in Dutch Caucasians, with considerable impact at the population level.     

Sequence analysis of 21 genes located in the Kartagener syndrome linkage region on chromosome 15q

Primary ciliary dyskinesia (PCD) is a rare genetic disorder, which shows extensive genetic heterogeneity and is mostly inherited in an autosomal recessive fashion. There are four genes with a proven pathogenetic role in PCD. DNAH5 and DNAI1 are involved in 28 and 10% of PCD cases, respectively, while two other genes, DNAH11 and TXNDC3, have been identified as causal in one PCD family each. We have previously identified a 3.5 cM (2.82 Mb) region on chromosome 15q linked to Kartagener syndrome (KS), a subtype of PCD characterized by the randomization of body organ positioning. We have now refined the KS candidate region to a 1.8 Mb segment containing 18 known genes. The coding regions of these genes and three neighboring genes were subjected to sequence analysis in seven KS probands, and we were able to identify 60 single nucleotide sequence variants, 35 of which resided in mRNA coding sequences. However, none of the variations alone could explain the occurrence of the disease in these patients.     

Molecular genetics of facioscapulohumeral muscular dystrophy

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant neuromuscular disorder. The disease affects specific muscles of the face, shoulder-girdle and upper arm. The biochemical defect underlying FSHD is unknown and there are no specific tests that are diagnostic of FSHD. Genetic linkage studies have mapped the FSHD gene to chromosome 4q35. A DNA marker (p13E-11; D4F104S1, formerly D4S810) has been isolated which recognizes two highly polymorphic loci detectable by EcoRI or HindIII; one locus maps to chromosome 4q35 and shows fragments between about 50 and 320 kb. In FSHD patients deletions occur within this EcoRI/HindIII fragment, yielding fragments that are usually smaller than 28 kb. Characterization of the polymorphic fragments demonstrates that they consist of a 3.2 kb tandem repeat; their number can range between approximately 12 and 96 within the 4q35-specific fragments. In FSHD patients, an integral number of these tandem repeats are deleted, leaving at maximum eight copies.