The Newfoundland population: a unique resource for genetic investigation of complex diseases

"Unnatural resources?": parallels and distinctions between the Newfoundland Genome and traditional resource sectors

Newfoundland and Labrador (NL) has a long history of resource development, exploitation, and frequent mismanagement. Even before joining the Canadian confederation in 1949, industries such as mining, fishing, and forestry had significantly shaped the province. Recently, a new "resource" has been recognized: NL's genetic data, often described as a "genetic gold mine" and "the new oil." These analogies reflect the perception of genetic data as a valuable resource, resonating in a province historically reliant on resource extraction. Since the early 2000s, NL's genetic data has been recognized as a unique asset, prompting provincial reports on its management. Renewed interest has emerged with a local biotechnology company aiming to leverage NL's unique genetic architecture. This paper examines the implications of conceptualizing genetic information as a resource, exploring how this fits within existing resource development frameworks and policies, and considering its potential to shape policies for managing the benefits and burdens of genetic data exploitation. I conclude that while the NL genome is not a natural resource in the traditional sense, the province nevertheless needs to take more direct responsibility for its development and to ensure that any potential benefits from exploiting it are shared with the population.

Genomic heterozygosity is associated with a lower risk of osteoarthritis

BACKGROUND

Genomic heterozygosity has been shown to confer a health advantage in humans and play a protective role in complex diseases. Given osteoarthritis (OA) is a highly polygenic disease, we set out to determine if an association exists between OA and genomic heterozygosity.

RESULTS

End-stage knee and hip OA patients and healthy controls were recruited from the Newfoundland and Labrador (NL) population. The Arthritis Research UK Osteoarthritis Genetics (arcOGEN) consortium database was utilized as a replication cohort. DNA was extracted from blood samples and genotyped. Individual rates of observed heterozygosity (HetRate) and heterozygosity excess (HetExcess) relative to the expected were mathematically derived, and standardized to a z-score. Logistic regression modeling was used to examine the association between OA and HetRate or HetExcess. A total of 559 knee and hip OA patients (mean age 66.5 years, body mass index (BMI) 33.7 kg/m2, and 55% females) and 118 healthy controls (mean age 56.4 years, BMI 29.5 kg/m2, and 59% female) were included in the NL cohort analysis. We found that OA had an inverse relationship with HetRate and HetExcess with odds ratios of 0.64 (95% CI: 0.45-0.91) and 0.65 (95% CI: 0.45-0.93) per standard deviation (SD), respectively. The arcOGEN data included 2,019 end-stage knee and hip OA patients and 2,029 healthy controls, validating our findings with HetRate and HetExcess odds ratios of 0.60 (95% CI: 0.56-0.64) and 0.44 (95% CI: 0.40-0.47) per SD, respectively.

CONCLUSIONS

Our results are the first to clearly show evidence, from two separate cohorts, that reduced genomic heterozygosity confers a risk for the future development of OA.

A Population Description of Young Women with Breast Cancer in Newfoundland and Labrador

It has been well established in the literature that young women tend to carry more aggressive subtypes of breast cancer than their older-aged counterparts. The objective of this study was to describe the characteristics and outcomes of young women with breast cancer. In this retrospective analysis, data were collected for women under the age of 40 years who were diagnosed with breast cancer between 2008 and 2018 in the province of Newfoundland and Labrador. Specifically, data were collected on demographics, staging, pathological characteristics, treatment, and survival outcomes for young women with this disease. Results demonstrate that most of these women were diagnosed between the age of 35 and 39 years (91.2%). Most women presented with early-stage disease (stage I and II-66.4%), while 24% were stage III and 9.6% presented with stage IV metastatic disease. The prevalence of hormone-receptor-positive disease represented 41.9% of the cohort, with triple-negative and HER2+ measuring 27.7% and 30.4%, respectively. Five-year disease-free survival was 80.5% and overall survival was 82.7%. These findings provoke discussion regarding the intersecting roles of genetics, environment, and lifestyle in a region with some of the highest rates of malignancy in the country.

A partitioned 88-loci psoriasis genetic risk score reveals HLA and non-HLA contributions to clinical phenotypes in a Newfoundland psoriasis cohort

Psoriasis is an immune-mediated inflammatory skin disease typically characterized by erythematous and scaly plaques. It affects 3% of the Newfoundland population while only affecting 1.7% of the general Canadian population. Recent genome-wide association studies (GWAS) in psoriasis have identified more than 63 genetic susceptibility loci that individually have modest effects. Prior studies have shown that a genetic risk score (GRS) combining multiple loci can improve psoriasis disease prediction. However, these prior GRS studies have not fully explored the association of GRS with patient clinical characteristics. In this study, we calculated three types of GRS: one using all known GWAS SNPs (GRS-ALL), one using a subset of SNPs from the HLA region (GRS-HLA), and the last using non-HLA SNPs (GRS-noHLA). We examined the relationship between these GRS and a number of psoriasis features within a well characterized Newfoundland psoriasis cohort. We found that both GRS-ALL and GRS-HLA were significantly associated with early age of psoriasis onset, psoriasis severity, first presentation of psoriasis at the elbow or knee, and the total number of body locations affected, while only GRS-ALL was associated with a positive family history of psoriasis. GRS-noHLA was uniquely associated with genital psoriasis. These findings clarify the relationship of the HLA and non-HLA components of GRS with important clinical features of psoriasis.

The Newfoundland and Labrador mosaic founder population descends from an Irish and British diaspora from 300 years ago

The founder population of Newfoundland and Labrador (NL) is a unique genetic resource, in part due to its geographic and cultural isolation, where historical records describe a migration of European settlers, primarily from Ireland and England, to NL in the 18th and 19th centuries. Whilst its historical isolation, and increased prevalence of certain monogenic disorders are well appreciated, details of the fine-scale genetic structure and ancestry of the population are lacking. Understanding the genetic origins and background of functional, disease causing, genetic variants would aid genetic mapping efforts in the Province. Here, we leverage dense genome-wide SNP data on 1,807 NL individuals to reveal fine-scale genetic structure in NL that is clustered around coastal communities and correlated with Christian denomination. We show that the majority of NL European ancestry can be traced back to the south-east and south-west of Ireland and England, respectively. We date a substantial population size bottleneck approximately 10-15 generations ago in NL, associated with increased haplotype sharing and autozygosity. Our results reveal insights into the population history of NL and demonstrate evidence of a population conducive to further genetic studies and biomarker discovery.

Genetic Analyses of Discrete Geographic Samples of a Golden Chanterelle in Canada Reveal Evidence for Recent Regional Differentiation

The wild edible mushroom Cantharellus enelensis is a recently described species of the golden chanterelles found in eastern North America. At present, the genetic diversity and population structure of C. enelensis are not known. In this study, we analyzed a total of 230 fruiting bodies of C. enelensis that were collected from three regions of Canada: near the east and west coasts of Newfoundland (NFLD), with 110 fruiting bodies each, and around Hamilton, Ontario (10 fruiting bodies). Among the 110 fruiting bodies from each coast in NFLD, 10 from 2009 were without specific site information, while 100 sampled in 2010 were from each of five patches separated by at least 100 m from each other. Each fruiting body was genotyped at three microsatellite loci. Among the total 28 multilocus genotypes (MLGs) identified, 2 were shared among all three regions, 4 were shared between 2 of the t3hree regions, and the remaining 22 were each found in only 1 region. Minimal spanning network analyses revealed several region-specific MLG clusters, consistent with geographic specific mutation and expansion. Though the most frequently observed MLGs were shared among local (patch) and regional populations, population genetic analyses revealed that both local and regional geographic separations contributed significantly to the observed genetic variation in the total sample. All three regional populations showed excess heterozygosity; for the eastern NFLD population, we reject the null hypothesis of Hardy–Weinberg equilibrium (HWE) at all three loci. However, the analyses of clone-corrected samples revealed that most loci were in HWE. Together, our results suggest that the three discrete regional populations of C. enelensis were likely colonized from a common refugium since the last ice age. However, the local and regional populations are diverging from each other through mutation, drift, and selection at least partly due to heterozygous advantage.

A founder effect in hemophilia A patients from Russian Ural region with a new p.(His634Arg) variant in F8 gene

Hemophilia A is a clotting disease caused by defects in the F8 gene. A lot of them are described and most are unique or have polyphyletic origin. We here study the origin of a pathogenic variant found in a few patients. We sequenced F8 gene for seven hemophilia A patients from the Ural region, Sverdlovskaya oblast, Russia. We constructed haplotypes for them and for 21 hemophilia A patients with other defects from the same area as a control group using four previously described X-chromosome loci associated with F8 gene. We identified a new missense variant p.(His634Arg) in seven apparently unrelated patients with mild hemophilia A from Sverdlovskaya oblast. The haplotype analysis showed that all patients share the same haplotype, absent in the other patients, suggesting a founder effect. The most recent common ancestor for the p.(His634Arg) patients is estimated to exist around the end of XVII century; however, the 95% confidence interval spans from XII to early XX century. The Ural region did not suffer from the recent bottlenecks or isolation. Therefore, the founder effect could be a natural consequence of population structuring in a relatively stable population. We identified a founder effect mutation in hemophilia A, which is a quite rare event for this disease.

Language and Geographical Location influences the Incidence of Chronic Cough in the Canadian Longitudinal Study on Aging (CLSA)

The prevalence of chronic cough is highly variable globally ranging from 2% to 18% [1]. The prevalence was higher in Australia, Europe, America (11–18%) and much lower in Asia (4%) and Africa (2%), even after adjusting for smoking. The majority of the studies used the 3-month chronic bronchitis definition, but even in studies using the same 8-week cut-off, variations still persist: UK (12%) [2], Finland (7.2%) [3], Germany (5%) [4], Denmark (4%) [5], South Korea (2.6%) [6], Japan (2.2%) [7], Nigeria (1.1%) [8]. The reasons for these variations, even in geographically similar countries, are unclear.

French speakers have a 4% lower incidence of chronic cough than English speakers in the CLSA, but English speakers from Quebec, Newfoundland and Labrador, and Nova Scotia also have a lower risk of developing chronic coughhttps://bit.ly/3qAd3Mf

The Association of Upper Body Obesity with Insulin Resistance in the Newfoundland Population

Body-fat distribution is a primary risk factor for insulin resistance and cardiovascular disease. Visceral fat explains only a portion of this risk. The link between upper-body fat and insulin resistance is uncertain. Furthermore, upper-body fat is not clearly defined. Dual-energy X-ray absorptiometry (DXA) can accurately quantify body fat. In this study, we explored the relationship between non-visceral upper-body adiposity and insulin resistance and other markers of metabolic syndrome. Fat proportions in the upper body, leg, and visceral regions were quantified by using DXA in 2547 adult Newfoundlanders aged 19 and older. Adjusting for remaining fat regions, we performed partial correlation analysis for each body region and insulin resistance defined by the Homeostatic Model of Assessment (HOMA). Similarly, partial correlation analysis was also performed between each fat region and other markers of metabolic syndrome, including high-density lipoprotein cholesterol (HDL), triglycerides (TG), body mass index (BMI), and blood pressure. Major confounding factors, including age, caloric intake, and physical activity, were statistically controlled by using partial correlation analysis. Interactions between sex, menopausal status, and medication status were also tested. Arm adiposity was correlated with HOMA-IR (R = 0.132, p < 0.001) and HOMA-β (R = 0.134, p < 0.001). Visceral adiposity was correlated with HOMA-IR (R = 0.230, p < 0.001) and HOMA-β (R = 0.160, p < 0.001). No significant correlation between non-visceral trunk adiposity and insulin resistance was found. Non-visceral trunk adiposity was negatively correlated with HDL in men (R = −0.110, p < 0.001) and women (R = −0.117, p < 0.001). Non-visceral trunk adiposity was correlated with TG (total: R = 0.079, p < 0.001; men: R = 0.105, p = 0.012; women: R = 0.078, p = 0.001). In menopausal women, leg adiposity was negatively correlated with HOMA-IR (R = −0.196, p < 0.001) and HOMA-β (R = −0.101, p = 0.012). Upper-body adiposity in the arms is an independent contributor to insulin resistance. Upper-body adiposity in the non-visceral trunk region is an independent contributor to metabolic syndrome. Leg adiposity is protective against metabolic syndrome in women.

Familial Intracranial Aneurysm in Newfoundland: Clinical and Genetic Analysis

Objective:

Intracranial aneurysm (IA) is an expansion of the weakened arterial wall that is often asymptomatic until rupture, resulting in subarachnoid hemorrhage. Here we describe the high prevalence of familial IA in a cohort of Newfoundland ancestry. We began to investigate the genetic etiology of IA in affected family members, as the inheritance of this disease is poorly understood.

Methods:

Whole exome sequencing was completed for a cohort of 12 affected individuals from two multiplex families with a strong family history of IA. A filtering strategy was implemented to identify rare, shared variants. Filtered variants were prioritized based on validation by Sanger sequencing and segregation within the families.

Results:

In family R1352, six variants passed filtering; while in family R1256, 68 variants remained, so further filtering was pursued. Following validation by Sanger sequencing, top candidates were investigated in a set of population controls, namely,C4orf6c.A1G (p.M1V) andSPDYE4c.C103T (p.P35S). Neither was detected in 100 Newfoundland control samples.

Conclusion:

Rare and potentially deleterious variants were identified in both families, though incomplete segregation was identified for all filtered variants. Alternate methods of variant prioritization and broader considerations regarding the interplay of genetic and environmental factors are necessary in future studies of this disease.

Surgical treatment choices for breast cancer in Newfoundland and Labrador: a retrospective cohort study

BACKGROUND

Mastectomy is often chosen by women for treatment of breast cancer, even when breast-conserving surgery (BCS) is an option. Newfoundland and Labrador has a high mastectomy rate. We documented the number of breast cancers over a given period in the province and their related surgical treatments, and explored the impact of several variables on surgical choice.

METHODS

A retrospective cohort design linked diagnosis data from the Newfoundland and Labrador tumour registry to surgery data from the Canadian Institute for Health Information Discharge Abstract Database. Data were extracted for all women aged 19 years or more in whom breast cancer was diagnosed in 2009-2014.

RESULTS

A total of 2346 cases of breast cancer with a linked surgical procedure were included. Most operations (1605 [68.4%]) were mastectomy procedures, with the remainder being BCS. Logistic regression analysis revealed that women were 1.82 times (95% confidence interval [CI] 1.64-2.02) more likely to have mastectomy for each unit of stage increase from 0 to IV and 1.15 times (95% CI 1.11-1.21) more likely for each unit of driving time increase.

CONCLUSION

Tumour stage and driving time to a radiation facility significantly predicted Newfoundland and Labrador women's surgical treatment choices for breast cancer. Notably, mastectomy was the favoured choice across all age groups, tumour stages and geographical regions of the province. We hope that these results will galvanize efforts to better understand local surgical practices and assist in improving the quality of surgical care of women with breast cancer.

Genetic associations in community context: a mixed model approach identifies a functional variant in the RBP4 gene associated with HDL-C dyslipidemia

Background

The objective of this study was to examine individual and community factors that influence high-density lipoprotein cholesterol (HDL-C) dyslipidemia in Newfoundland and Labrador (NL), a genetically isolated population in Canada with a high prevalence of HDL-C dyslipidemia.

Methods

First, a group of single nucleotide polymorphisms from 10 metabolic trait candidate genes was tested using a multivariate logistic regression model. The significant SNPs were entered into the second phase, where a mixed logistic model incorporated the community disease risk factors together with the individual factors as the fixed part of the model and the geographic region as a random effect.

Results

Analysis of 1489 subjects (26.9% HDL-C dyslipidemia) identified rs3758539, a non-coding variant in the 5’UTR of RBP4, to be associated with HDL-C dyslipidemia (odds ratio = 1.45, 95% confidence interval = 1.08–1.97, p = 0.01). The association remained significant, and the effect size did not change after the incorporation of individual and community risk factors from 17 geographic regions (odds ratio: 1.41, 95% confidence interval = 1.03–1.93, p = 0.03) in NL. Besides this variant, sex, BMI, and smoking also showed significant associations with HDL-C dyslipidemia, whereas no role was identified for the community factors.

Conclusions

This study demonstrates the use of community-level data in a genetic association testing. It reports a functional variant in the promoter of RBP4, a gene directly involved in lipoprotein metabolism, to be associated with HDL-C dyslipidemia. These findings indicate that individual factors are the main reason for a higher prevalence of HDL-C dyslipidemia in the NL population.

Evidence for GALNT12 as a moderate penetrance gene for colorectal cancer

Characterizing moderate penetrance susceptibility genes is an emerging frontier in colorectal cancer (CRC) research. GALNT12 is a strong candidate CRC-susceptibility gene given previous linkage and association studies, and inactivating somatic and germline alleles in CRC patients. Previously, we found rare segregating germline GALNT12 variants in a clinic-based cohort (N = 118) with predisposition for CRC. Here, we screened a new population-based cohort of incident CRC cases (N = 479) for rare (MAF ≤1%) deleterious germline GALNT12 variants. GALNT12 screening revealed eight rare variants. Two variants were previously described (p.Asp303Asn, p.Arg297Trp), and additionally, we found six other rare variants: five missense (p.His101Gln, p.Ile142Thr, p.Glu239Gln, p.Thr286Met, p.Val290Phe) and one putative splice-altering variant (c.732-8 G>T). Sequencing of population-matched controls (N = 400) revealed higher burden of these variants in CRC cases compared with healthy controls (P = 0.0381). We then functionally characterized the impact of substitutions on GALNT12 enzyme activity using in vitro-derived peptide substrates. Three of the newly identified GALNT12 missense variants (p.His101Gln, p.Ile142Thr, p.Val290Phe) demonstrated a marked loss (>2-fold reduction) of enzymatic activity compared with wild-type (P ≤ 0.05), whereas p.Glu239Gln exhibited a ∼2-fold reduction in activity (P = 0.077). These findings provide strong, independent evidence for the association of GALNT12 defects with CRC-susceptibility; underscoring implications for glycosylation pathway defects in CRC.

Six-year time-trend analysis of dyslipidemia among adults in Newfoundland and Labrador: findings from the laboratory information system between 2009 and 2014

Background

Dyslipidemia, an increased level of total cholesterol (TC), triglycerides (TG), low-density-lipoprotein cholesterol (LDL-C) and decreased level of high-density-lipoprotein cholesterol (HDL-C), is one of the most important risk factors for cardiovascular disease. We examined the six-year trend of dyslipidemia in Newfoundland and Labrador (NL), a Canadian province with a historically high prevalence of dyslipidemia.

Methods

A serial cross-sectional study on all of the laboratory lipid tests available from 2009 to 2014 was performed. Dyslipidemia for every lipid component was defined using the Canadian Guidelines for the Diagnosis and Treatment of Dyslipidemia. The annual dyslipidemia rates for each component of serum lipid was examined. A fixed and random effect model was applied to adjust for confounding variables (sex and age) and random effects (residual variation in dyslipidemia over the years and redundancies caused by individuals being tested multiple times during the study period).

Results

Between 2009 and 2014, a total of 875,208 records (mean age: 56.9 ± 14.1, 47.6% males) containing a lipid profile were identified. The prevalence of HDL-C and LDL-C dyslipidemia significantly decreased during this period (HDL-C: 35.8% in 2009 [95% CI 35.5-36.1], to 29.0% in 2014 [95% CI: 28.8-29.2], P = 0.03, and LDL-C: 35.2% in 2009 [95% CI: 34.9-35.4] to 32.1% in 2014 [95% CI: 31.9-32.3], P = 0.02). A stratification by sex, revealed no significant trend for any lipid element in females; however, in men, the previously observed trends were intensified and a new decreasing trend in dyslipidemia of TC was appeared (TC: 34.1% [95% CI 33.7-34.5] to 32.3% [95%CI: 32.0-32.6], p < 0.02, HDL-C: 33.8% (95%CI: 33.3-34.2) to 24.0% (95% CI: 23.7-24.3)], P < 0.01, LDL-C: 32.9% (95%CI:32.5-33.3) to 28.6 (95%CI: 28.3-28.9), P < 0.001). Adjustment for confounding factors and removing the residual noise by modeling the random effects did not change the significance.

Conclusion

This study demonstrates a significant downward trend in the prevalence of LDL-C, HDL-C, and TC dyslipidemia, exclusively in men. These trends could be the result of males being the primary target for cardiovascular risk management.

Embodying a New Meaning of Being At Risk: Living With an Implantable Cardioverter Defibrillator for Arrhythmogenic Right Ventricular Cardiomyopathy

Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia (ARVC/D) is a genetic condition that can cause fatal arrhythmias. The implantable cardioverter defibrillation (ICD) is a primary treatment for ARVC/D. Using a grounded theory approach, this study examines the experiences of 15 individuals living with an ICD. The ability to cope with and adjust to having an ICD is influenced by the acceptance of the ICD as something needed to survive, an understanding of the ICD's function, existing support networks, and ones' ability to manage everyday challenges. Coping well requires reshaping ideas about the meaning of being at risk and understanding how the ICD fits into that changing personal risk narrative. A thorough understanding of the unique needs of individuals with ARVC/D and of the specific factors contributing to the psychosocial distress related to having an ICD (vs. having the disease itself) is needed. Nurses must be prepared to provide ongoing support and education to this population.

How Two Small Pharmacy Schools' Competency Standards Compare with an International Competency Framework and How Well These Schools Prepare Students for International Placements

International standards of pharmacy curricula are necessary to ensure student readiness for international placements. This paper explores whether curricula from two pharmacy programs, in Australia and Canada, are congruent with international standards and if students feel prepared for international placements. Nationally prescribed educational standards for the two schools were compared to each other and then against the International Pharmaceutical Federation (FIP) Global Competency Framework. Written student reflections complemented this analysis. Mapping results suggested substantial agreement between the FIP framework and Australia and Canada, with two gaps being identified. Moreover, the students felt their programs prepared them for their international placements. Despite differences in countries, pharmacy programs, and health-systems all students acclimatized to their new practice sites. Implications are that if pharmacy programs align well with FIP, pharmacists should be able to integrate and practise in other jurisdictions that also align with the FIP. This has implications for the mobility of pharmacy practitioners to countries not of their origin of training.

Assessing the Causality Factors in the Association between (Abdominal) Obesity and Physical Activity among the Newfoundland Population-A Mendelian Randomization Analysis

A total of 1,263 adults from Newfoundland and Labrador were studied in the research. Body mass index (BMI) and percent trunk fat (PTF) were analyzed as biomarkers for obesity. The Mendelian randomization (MR) approach with two single-nucleotide polymorphisms in the fat-mass and obesity (FTO) gene as instruments was employed to assess the causal effect. In both genders, increasing physical activity significantly reduced BMI and PTF when adjusted for age and the FTO gene. The effect of physical activity was stronger on PTF than BMI. Direct observational analyses showed significant increase in BMI/PTF when physical activity decreased. A similar association in MR analyses was not significant. The association between physical activity and BMI/PTF could be due to reversed causality or common confounding factors. Our study provides insights into the causal contributions of obesity to physical activity in adults. Health intervention strategies to increase physical activity among adults should include some other plans such as improving diet for reducing obesity.

Genetic structure of the Newfoundland and Labrador population: founder effects modulate variability

The population of the province of Newfoundland and Labrador (NL) has been a resource for genetic studies because of its historical isolation and increased prevalence of several monogenic disorders. Controversy remains regarding the genetic substructure and the extent of genetic homogeneity, which have implications for disease gene mapping. Population substructure has been reported from other isolated populations such as Iceland, Finland and Sardinia. We undertook this study to further our understanding of the genetic architecture of the NL population. We enrolled 494 individuals randomly selected from NL. Genome-wide SNP data were analyzed together with that from 14 other populations including HapMap3, Ireland, Britain and Native American samples from the Human Genome Diversity Project. Using multidimensional scaling and admixture analysis, we observed that the genetic structure of the NL population resembles that of the British population but can be divided into three clusters that correspond to religious/ethnic origins: Protestant English, Roman Catholic Irish and North American aboriginals. We observed reduced heterozygosity and an increased inbreeding coefficient (mean=0.005), which corresponds to that expected in the offspring of third-cousin marriages. We also found that the NL population has a significantly higher number of runs of homozygosity (ROH) and longer lengths of ROH segments. These results are consistent with our understanding of the population history and indicate that the NL population may be ideal for identifying recessive variants for complex diseases that affect populations of European origin.

GENLIB: an R package for the analysis of genealogical data

BACKGROUND

Founder populations have an important role in the study of genetic diseases. Access to detailed genealogical records is often one of their advantages. These genealogical data provide unique information for researchers in evolutionary and population genetics, demography and genetic epidemiology. However, analyzing large genealogical datasets requires specialized methods and software. The GENLIB software was developed to study the large genealogies of the French Canadian population of Quebec, Canada. These genealogies are accessible through the BALSAC database, which contains over 3 million records covering the whole province of Quebec over four centuries. Using this resource, extended pedigrees of up to 17 generations can be constructed from a sample of present-day individuals.

RESULTS

We have extended and implemented GENLIB as a package in the R environment for statistical computing and graphics, thus allowing optimal flexibility for users. The GENLIB package includes basic functions to manage genealogical data allowing, for example, extraction of a part of a genealogy or selection of specific individuals. There are also many functions providing information to describe the size and complexity of genealogies as well as functions to compute standard measures such as kinship, inbreeding and genetic contribution. GENLIB also includes functions for gene-dropping simulations. The goal of this paper is to present the full functionalities of GENLIB. We used a sample of 140 individuals from the province of Quebec (Canada) to demonstrate GENLIB's functions. Ascending genealogies for these individuals were reconstructed using BALSAC, yielding a large pedigree of 41,523 individuals. Using GENLIB's functions, we provide a detailed description of these genealogical data in terms of completeness, genetic contribution of founders, relatedness, inbreeding and the overall complexity of the genealogical tree. We also present gene-dropping simulations based on the whole genealogy to investigate identical-by-descent sharing of alleles and chromosomal segments of different lengths and estimate probabilities of identical-by-descent sharing.

CONCLUSIONS

The R package GENLIB provides a user friendly and flexible environment to analyze extensive genealogical data, allowing an efficient and easy integration of different types of data, analytical methods and additional developments and making this tool ideal for genealogical analysis.

Does the Prevalence of Dyslipidemias Differ between Newfoundland and the Rest of Canada? Findings from the Electronic Medical Records of the Canadian Primary Care Sentinel Surveillance Network

Introduction: Newfoundland and Labrador (NL) has the highest prevalence of cardiovascular disease (CVD) in Canada. Dyslipidemia is a risk factor for CVD. This study compares the prevalence of dyslipidemia in the NL population with the rest of Canada.

Methods: A cross-sectional study, using data from the Canadian Primary Care Sentinel Surveillance Network (CPCSSN), was undertaken. The study population included adults, excluding pregnant women, aged 20 years and older. Canadian guidelines were used for classifying dyslipidemia. Univariate and multivariate analyses were conducted to compare the lipid levels and prevalence of dyslipidemia between NL and the rest of Canada.

Results: About 128,825 individuals (NL: 7,772; rest of Canada: 121,053) were identified with a mean age of 59 years (55% females). Mean levels of total cholesterol (4.96 vs. 4.93, p = 0.03), low-density lipoprotein (LDL) (3.00 vs. 2.90 mmol/L, p < 0.0001), triglyceride (1.47 vs. 1.41 mmol/L, p < 0.0001), and high-density lipoprotein (HDL) (1.29 vs. 1.39 mmol/L, p < 0.0001) were significantly different in NL compared to the rest of Canada. Dyslipidemias of LDL (29 vs. 25% p < 0.0001), HDL (38 vs. 27%, p < 0.0001), and triglyceride (29 vs. 26%, p < 0.0001) were significantly more common in NL. After adjustment for confounding variables, NL inhabitants were more likely to have dyslipidemia of total cholesterol (OR: 1.16, 95% CI: 1.10–1.23, p < 0.0001), HDL (OR: 1.52, 95% CI: 1.44–1.60, p < 0.0001), LDL (OR: 1.38, 95% CI: 1.30–1.46, p < 0.0001), and ratio (OR: 1.53, 95% CI: 1.42–1.60, p < 0.0001).

Conclusion: The NL population has a significantly higher rate of dyslipidemia compared to the rest of Canada, and the mean levels of all lipid components are worse in NL. Distinct cultural and genetic features of the NL population may explain this, accounting for a higher rate of CVD in NL.

"Awakening to" a new meaning of being at-risk for arrhythmogenic right ventricular cardiomyopathy: a grounded theory study

Efforts of social scientists to understand how individuals living in a family at risk for a genetically linked condition make health care decisions, having brought to the forefront the contextual nature of risk perception. Using a grounded theory approach, this study examines the experiences of 29 individuals living in families at risk for arrhythmogenic right ventricular cardiomyopathy (ARVC). Attention is paid to how individuals (re)construct the meaning of being at risk in relation to the developing science of gene discovery. Findings highlight that individuals living in a family at risk for ARVC juxtapose existing scientific knowledge against experiential knowledge as they "awaken to" the fact that they or a family member are at risk. This process is pragmatic and fluid and contingent upon whether and how symptoms are aligned with the constructed image of the at-risk relative.

Multiple Sclerosis in Newfoundland and Labrador - A Model for Disease Prevalence

Background:

Newfoundland and Labrador, Canada, have been almost exclusively populated by immigrants from southwest England and southeast Ireland. The province’s population grew largely by natural increase from 20,000 people in 1835 to half a million at present. Very little interregional migration occurred within the province. This uniquely-populated region and its subsequent founder effect provide the basis to develop models of disease prevalence.

Objectives:

To develop a model for the regional prevalence of multiple sclerosis (MS), accounting for settlement patterns and geographic location (latitude).

Methods:

All living MS patients with confirmed addresses (438 patients) in the province were mailed a survey requesting their place of birth. Regional prevalences were calculated from a 75% rate of return of the survey. Theoretical regional prevalences were proportionally calculated from the source prevalences of southwest England, southeast Ireland, Scotland and the Channel Islands based on settlement patterns. These theoretical regional prevalences were corrected for geographical variations of latitude based on observations in the United Kingdom. Theoretical and actual regional prevalences were compared.

Results:

When actual regional prevalences were compared with theoretical prevalences, very little variation was noted, especially after correcting for variation in latitude.

Conclusion:

A regional variation in MS prevalence is noted in the island portion of Newfoundland and Labrador. This regional variation can be modeled by using both migration patterns and latitudinal position. This model demonstrates that the prevalence of MS is influenced by both genetic and environmental contributions.

Incidence and Prevalence of Multiple Sclerosis in Newfoundland and Labrador

Background:

The incidence and prevalence of multiple sclerosis (MS) in Newfoundland and Labrador (NL) had been reported in 1984 and was considered to be relatively low at that time. This study revisits the incidence and prevalence of MS in NL for the year 2001.

Methods:

Case searches through patient files of neurologists in NL were conducted. A complete list of patients billed for MS in NL between 1996 and 2003 was obtained and all cases were confirmed via chart review.

Results:

There were 493 living MS patients yielding a prevalence of 94.4/100,000 which is significantly higher than previously reported. Of the living patients, 330 had relapsing remitting (RRMS), 94 had secondary progressive, 66 had primary progressive (PPMS) and three had unspecified MS. The total female to male ratio was 2.7:1. There was no difference between the female to male ratios for RRMS vs PPMS. Patients with PPMS had a later onset compared to RRMS (p<0.00001). Yearly incidences were relatively constant from 1994 to 2001 (5.6/100,000). Significant delays between first symptoms and final diagnosis were common and the delay time has not changed over the past 15 years. A prevalence of 88.9/100,000 was estimated from survival and incidence trends and was not significantly different than the measured prevalence (p=0.38).

Conclusion:

The increase in incidence and prevalence are accounted for through both better access to diagnostic facilities and more practicing neurologists. The revised prevalence and incidence are more in keeping with recently reported values throughout Canada.

Conclusion:

L’augmentation de l’incidence et de la prÉvalence se justifient par une plus grande accessibilitÉ aux moyens diagnostiques et par la prÉsence d’un plus grand nombre de neurologues. La prÉvalence et l’incidence que nous rapportons sont plus conformes à celles rapportÉes rÉcemment à travers le Canada.

Darwinian medicine and psoriasis

Darwinian medicine, or evolutionary medicine, regards some pathological conditions as attempts by the organism to solve a problem or develop defense mechanisms. At certain stages of human evolution, some diseases may have conferred a selective advantage. Psoriasis is a high-penetrance multigenic disorder with prevalence among whites of up to 3%. Psoriatic lesions have been linked with enhanced wound-healing qualities and greater capacity to fight infection. Leprosy, tuberculosis, and infections caused by viruses similar to human immunodeficiency virus have been postulated as environmental stressors that may have selected for psoriasis-promoting genes in some human populations. The tendency of patients with severe psoriasis to develop metabolic syndrome may reflect the body's attempt to react to environmental stresses and warning signs by triggering insulin resistance and fat storage.

Effect of FTO Gene and Physical Activity Interaction on Trunk Fat Percentage Among the Newfoundland Population

OBJECTIVE

To explore the effect of FTO gene and physical activity interaction on trunk fat percentage.

DESIGN AND METHODS

Subjects are 3,004 individuals from Newfoundland and Labrador whose trunk fat percentage and physical activity were recorded, and who were genotyped for 11 single-nucleotide polymorphisms (SNPs) in the FTO gene. Subjects were stratified by gender. Multiple tests and multiple regressions were used to analyze the effects of physical activity, variants of FTO, age, and their interactions on trunk fat percentage. Dietary information and other environmental factors were not considered.

RESULTS

Higher levels of physical activity tend to reduce trunk fat percentage in all individuals. Furthermore, in males, rs9939609 and rs1421085 were significant (α = 0.05) in explaining central body fat, but no SNPs were significant in females. For highly active males, trunk fat percentage varied significantly between variants of rs9939609 and rs1421085, but there is no significant effect among individuals with low activity. The other SNPs examined were not significant in explaining trunk fat percentage.

CONCLUSIONS

Homozygous male carriers of non-obesity risk alleles at rs9939609 and rs1421085 will have significant reduction in central body fat from physical activity in contrast to homozygous males of the obesity-risk alleles. The additive effect of these SNPs is found in males with high physical activity only.

Functional modelling of a novel mutation in BBS5

Background

Bardet-Biedl syndrome (BBS) is an autosomal recessive ciliopathy disorder with 18 known causative genes (BBS1-18). The primary clinical features are renal abnormalities, rod-cone dystrophy, post-axial polydactyly, learning difficulties, obesity and male hypogonadism.

Results

We describe the clinical phenotype in three Saudi siblings in whom we have identified a novel mutation in exon 12 of BBS5 (c.966dupT; p.Ala323CysfsX57). This single nucleotide duplication creates a frame shift results in a predicted elongated peptide. Translation blocking Morpholino oligonucleotides were used to create zebrafish bbs5 morphants. Morphants displayed retinal layering defects, abnormal cardiac looping and dilated, cystic pronephric ducts with reduced cilia expression. Morphants also displayed significantly reduced dextran clearance via the pronephros compared to wildtype embryos, suggesting reduced renal function in morphants. The eye, kidney and heart defects reported in morphant zebrafish resemble the human phenotype of BBS5 mutations. The pathogenicity of the novel BBS5 mutation was determined. Mutant mRNA was unable to rescue pleiotropic phenotypes of bbs5 morphant zebrafish and in cell culture we demonstrate a mislocalisation of mutant BBS5 protein which fails to localise discretely with the basal body.

Conclusions

We conclude that this novel BBS5 mutation has a deleterious function that accounts for the multisystem ciliopathy phenotype seen in affected human patients.

Native American admixture in the Quebec founder population

For years, studies of founder populations and genetic isolates represented the mainstream of genetic mapping in the effort to target genetic defects causing Mendelian disorders. The genetic homogeneity of such populations as well as relatively homogeneous environmental exposures were also seen as primary advantages in studies of genetic susceptibility loci that underlie complex diseases. European colonization of the St-Lawrence Valley by a small number of settlers, mainly from France, resulted in a founder effect reflected by the appearance of a number of population-specific disease-causing mutations in Quebec. The purported genetic homogeneity of this population was recently challenged by genealogical and genetic analyses. We studied one of the contributing factors to genetic heterogeneity, early Native American admixture that was never investigated in this population before. Consistent admixture estimates, in the order of one per cent, were obtained from genome-wide autosomal data using the ADMIXTURE and HAPMIX software, as well as with the fastIBD software evaluating the degree of the identity-by-descent between Quebec individuals and Native American populations. These genomic results correlated well with the genealogical estimates. Correlations are imperfect most likely because of incomplete records of Native founders' origin in genealogical data. Although the overall degree of admixture is modest, it contributed to the enrichment of the population diversity and to its demographic stratification. Because admixture greatly varies among regions of Quebec and among individuals, it could have significantly affected the homogeneity of the population, which is of importance in mapping studies, especially when rare genetic susceptibility variants are in play.

High mammographic density in women of Ashkenazi Jewish descent

Introduction

Percent mammographic density (PMD) adjusted for age and body mass index is one of the strongest risk factors for breast cancer and is known to be approximately 60% heritable. Here we report a finding of an association between genetic ancestry and adjusted PMD.

Methods

We selected self-identified Caucasian women in the California Pacific Medical Center Research Institute Cohort whose screening mammograms placed them in the top or bottom quintiles of age-adjusted and body mass index-adjusted PMD. Our final dataset included 474 women with the highest adjusted PMD and 469 with the lowest genotyped on the Illumina 1 M platform. Principal component analysis (PCA) and identity-by-descent analyses allowed us to infer the women's genetic ancestry and correlate it with adjusted PMD.

Results

Women of Ashkenazi Jewish ancestry, as defined by the first principal component of PCA and identity-by-descent analyses, represented approximately 15% of the sample. Ashkenazi Jewish ancestry, defined by the first principal component of PCA, was associated with higher adjusted PMD (P = 0.004). Using multivariate regression to adjust for epidemiologic factors associated with PMD, including age at parity and use of postmenopausal hormone therapy, did not attenuate the association.

Conclusions

Women of Ashkenazi Jewish ancestry, based on genetic analysis, are more likely to have high age-adjusted and body mass index-adjusted PMD. Ashkenazi Jews may have a unique set of genetic variants or environmental risk factors that increase mammographic density.

The functional MICA-129 polymorphism is associated with skin but not joint manifestations of psoriatic disease independently of HLA-B and HLA-C

A methionine/valine polymorphism at amino acid 129 of the major histocompatibility complex class I chain-related gene A (MICA-129) categorizes alleles into strong and weak binders of the natural killer (NK) and T-cell receptor NKG2D. We investigated whether MICA-129 is differentially associated with skin and joint manifestations of psoriatic disease (PsD) independently of human leukocyte antigen (HLA)-C and HLA-B in patients and controls from Toronto and St. John's. The MICA-129 methionine (Met) allele, particularly Met/Met homozygosity, was strongly associated with both cutaneous psoriasis (PsC) and psoriatic arthritis (PsA) independently of HLA-B and HLA-C in Toronto patients, and was also associated with PsA in St. John's patients, but with no additional effect of Met/Met homozygosity. No association remained after adjustment for HLA alleles in St. John's patients. MICA-129 was not associated with PsA when compared with PsC. We conclude that MICA-129 is a marker of skin manifestations of PsD that is independent of HLA class I in Toronto patients.

Identification of a novel in-frame deletion in KCNQ4 (DFNA2A) and evidence of multiple phenocopies of unknown origin in a family with ADSNHL

Autosomal dominant sensorineural hearing loss (ADSNHL) is extremely genetically heterogeneous, making it difficult to molecularly diagnose. We identified a multiplex (n=28 affected) family from the genetic isolate of Newfoundland, Canada with variable SNHL and used a targeted sequencing approach based on population-specific alleles in WFS1, TMPRSS3 and PCDH15; recurrent mutations in GJB2 and GJB6; and frequently mutated exons of KCNQ4, COCH and TECTA. We identified a novel, in-frame deletion (c.806_808delCCT: p.S269del) in the voltage-gated potassium channel KCNQ4 (DFNA2), which in silico modeling predicts to disrupt multimerization of KCNQ4 subunits. Surprisingly, 10/23 deaf relatives are non-carriers of p.S269del. Further molecular characterization of the DFNA2 locus in deletion carriers ruled out the possibility of a pathogenic mutation other than p.S269del at the DFNA2A/B locus and linkage analysis showed significant linkage to DFNA2 (maximum LOD=3.3). Further support of genetic heterogeneity in family 2071 was revealed by comparisons of audio profiles between p.S269del carriers and non-carriers suggesting additional and as yet unknown etiologies. We discuss the serious implications that genetic heterogeneity, in this case observed within a single family, has on molecular diagnostics and genetic counseling.

High prevalence of psoriatic arthritis in a cohort of patients with psoriasis seen in a dermatology practice

BACKGROUND/OBJECTIVES

The prevalence of psoriatic arthritis (PsA) is expected to range from 5 to 40% in individuals with psoriasis. The objective of this study was to quantify the prevalence of PsA in psoriasis patients seen in a dermatology practice and to define their characteristics using the validated Psoriatic Arthritis Screening Questionnaire (PASQ).

METHODS

Patients with definite plaque psoriasis (as determined by a dermatologist) completed the self-administered PASQ tool, and patients with a score ≥ 7 or ≥ 9 were assessed by a rheumatologist to ascertain the diagnosis of PsA according to the CASPAR (Classification Criteria for Psoriatic Arthritis) criteria.

RESULTS

Using a PASQ cutoff of 7, the estimated prevalence (95% CI) of PsA was 40.9% (29.0-52.8%), whereas a prevalence (95% CI) of 36.4% (24.8-48.0%) was estimated when a PASQ cutoff of 9 was used.

CONCLUSION

Our estimated prevalence of PsA in psoriasis patients from a population of patients drawn from a dermatology practice is greater than most previous estimates. This finding illustrates the importance of screening for PsA in psoriasis patients as this comorbidity may affect the course of treatment and, if left untreated, may have a profound effect on the disability and quality of life of a large number of psoriasis patients.

Privacy protection and public goods: building a genetic database for health research in Newfoundland and Labrador

Objective

To provide a legal and ethical analysis of some of the implementation challenges faced by the Population Therapeutics Research Group (PTRG) at Memorial University (Canada), in using genealogical information offered by individuals for its genetics research database.

Materials and methods

This paper describes the unique historical and genetic characteristics of the Newfoundland and Labrador founder population, which gave rise to the opportunity for PTRG to build the Newfoundland Genealogy Database containing digitized records of all pre-confederation (1949) census records of the Newfoundland founder population. In addition to building the database, PTRG has developed the Heritability Analytics Infrastructure, a data management structure that stores genotype, phenotype, and pedigree information in a single database, and custom linkage software (KINNECT) to perform pedigree linkages on the genealogy database.

Discussion

A newly adopted legal regimen in Newfoundland and Labrador is discussed. It incorporates health privacy legislation with a unique research ethics statute governing the composition and activities of research ethics boards and, for the first time in Canada, elevating the status of national research ethics guidelines into law. The discussion looks at this integration of legal and ethical principles which provides a flexible and seamless framework for balancing the privacy rights and welfare interests of individuals, families, and larger societies in the creation and use of research data infrastructures as public goods.

Conclusion

The complementary legal and ethical frameworks that now coexist in Newfoundland and Labrador provide the legislative authority, ethical legitimacy, and practical flexibility needed to find a workable balance between privacy interests and public goods. Such an approach may also be instructive for other jurisdictions as they seek to construct and use biobanks and related research platforms for genetic research.

A Newfoundland cohort of familial and sporadic idiopathic pulmonary fibrosis patients: clinical and genetic features

BACKGROUND

Idiopathic pulmonary fibrosis (IPF) is an adult-onset Idiopathic Interstitial Pneumonia (IIP) usually diagnosed between age 50 to 70 years. Individuals with Familial Pulmonary Fibrosis (FPF) have at least one affected first or second-degree relative and account for 0.5-20% of cases.

METHODS

We ascertained and collected DNA samples from a large population-based cohort of IPF patients from Newfoundland, Canada. For each proband, a family history was documented and medical records were reviewed. Each proband was classified as familial (28 patients) or sporadic (50 patients) and all 78 probands were screened for variants in four highly penetrant, adult-onset PF genes (SFTPC, SFTPA2, TERT,TERC).

RESULTS

Seventy-eight IPF probands were enrolled of whom 28 (35.9%) had a positive family history. These 28 familial patients led to the recruitment of an additional 49 affected relatives (total of 77 FPF patients). By age 60 years, 42% of the familial cohort had been diagnosed with PF compared with only 16% of the sporadic patient collection (χ2 = 8.77, p = 0.003). Mean age of diagnosis in the familial group was significantly younger than the sporadic group (61.4 years vs. 66.6 yrs, p = 0.012) with a wider age range of diagnosis (19-92 years compared with 47-82 years). Thirty-three of 77 (42.8%) FPF patients had a tissue diagnosis and all but five had usual interstitial pneumonia histology. Compared with other published case series, the familial IIP histologies were more homogeneous. Three of 28 familial probands (10.7%) and none of the 50 sporadic probands had pathogenic variants in the four genes tested. All three familial probands had mutations in TERT. Other phenotypes associated with telomerase deficiency were present in these families including cirrhosis, bone marrow hypoplasia and premature graying. Telomere length assays were performed on mutation carriers from two families and confirmed telomere-related deficiency.

CONCLUSION

The proportion of familial cases in our cohort is higher than any previously reported estimate and we suggest that this is due to the fact that Newfoundland cohort is ethnically homogeneous and drawn from a founder population. In our patient collection, diagnosis with IPF prior to age 45 years predicted familial disease. In two of the three TERT mutation families, the pedigree appearance is consistent with genetic anticipation. In the other 25 FPF families negative for mutations in known PF genes, we did not identify other telomerase associated medical problems (bone marrow dysfunction, cirrhosis) and we hypothesize that there are novel PF genes segregating in our population.

Interest in newborn genetic testing: a survey of prospective parents and the general public

PURPOSE

Newborn screening (NBS) panels continue to expand, yet there are too few data on public attitudes toward testing in the newborn period to indicate whether there is support for such testing. We measured interest in newborn testing for several autosomal recessive disorders and reasons for interest.

METHODS

A cross-sectional, pen and paper survey was administered to the general public and prospective parents attending prenatal classes in Eastern Canada between April and December, 2010.

RESULTS

A total of 648 individuals completed surveys. Interest in newborn testing for inherited hearing loss, vision loss, and neurological disorders was high (over 80% would have their newborn tested). The attitudes of prospective parents and students were positive, but somewhat less so than members of the general public. Across all disorders, interest in testing was driven by the desire to be prepared for the birth of a child with a genetic disorder. Significantly more people would use the information from testing for fatal neurological disorders in future reproductive decisions than the information generated by newborn testing for inherited hearing or vision loss.

CONCLUSION

Interest is high in newborn testing for a variety of conditions, including those for which no effective treatment exists. Findings lend support to the expansion of NBS panels to include those disorders currently lacking treatment and highlight the value of including the views of diverse stakeholders, including prospective parents, in screening policies.

High incidence of pediatric idiopathic epilepsy is associated with familial and autosomal dominant disease in Eastern Newfoundland

PURPOSE

To describe the incidence and epidemiology of pediatric idiopathic epilepsy (IE) in Newfoundland and Labrador.

METHODS

All children in Newfoundland and Labrador aged 0-15 years with IE were ascertained through the provincial neurology clinic at the Janeway Child Health Centre. Family history, medical history and blood samples were obtained from probands and relatives. Two genes, SCN1A and KCNQ2, were screened for mutations by direct sequencing.

RESULTS

The mean annual incidence of IE for the population of children living in the Avalon region of Newfoundland from 2000 to 2004 was 107 per 100,000. This rate is approximately three-fold greater than rates reported in other developed countries. Of 117 families with IE eligible for study, 86 (74%) provided detailed pedigree data. Multiple different epilepsy phenotypes were identified. Fifty-five families (64%) had a positive family history. Eight of these had family histories compatible with autosomal dominant (AD) inheritance and these families lived in five different geographic isolates. DNA was obtained from 21 families (79 individuals). The two previously identified mutations in Newfoundland families with epilepsy were sequenced and excluded as pathogenic sites in all but one family which had a mutation in SCN1A.

CONCLUSION

The incidence of IE is high in the Avalon Peninsula of Newfoundland and the rate of familial disease is high throughout the province of Newfoundland and Labrador. The distribution of familial and AD IE in different geographic isolates, together with the clinical heterogeneity of disease suggests substantial genetic heterogeneity. It is likely that other novel mutations will be identified in this population.

Mitogenomic and microsatellite variation in descendants of the founder population of Newfoundland: high genetic diversity in an historically isolated population

The island of Newfoundland, the first of England's overseas colonies, was settled from the 17th century onward by restricted numbers of English, Irish, and French immigrants, in small "outport" communities that have maintained geographic, religious, and linguistic isolation to the latest generations. To measure the extent of modification and loss of genetic variation through founder effect, drift, and inbreeding in this historically isolated population, we analyzed the complete mitochondrial DNA (mtDNA) genomes and 14 microsatellite loci from each of 27 individuals with matrilineal ancestries extending to the colonial period. Every individual has a unique mtDNA genome sequence. All but one of these genomes are assignable to one of five major (H,J,K,T, and U) or minor (I) European haplogroups. The possibility of homoplasy at single nucleotide polymorphism (SNP) sites that define subtypes within the H haplogroup is discussed. Observed haplogroup proportions do not differ significantly from those of western Europeans or between English and Irish Newfoundlanders. The exceptional individual is a member of haplogroup A2, who appears to be the descendant of a Mi'kmaq First Nations mother and a French father, a common marriage pattern in the early settlement of Newfoundland. Microsatellite diversity is high (HE = 0.763), unstructured with respect to mtDNA haplotype or ethnicity, and there is no evidence of linkage disequilibrium. There is a small but significant degree of inbreeding (FIS = 0.0174). Collection of whole mtDNA genome data was facilitated by the use of microarray sequencing, and we describe a simple algorithm that is 99.67% efficient for sequence recovery.

The geospatial relation between UV solar radiation and type 1 diabetes in Newfoundland

Type 1 diabetes (T1DM) has been previously associated with northern latitude and vitamin D insufficiency. This study investigates the geospatial association between average daily ultraviolet B (UVB) irradiance and T1DM across the province of Newfoundland (NL), Canada. NL has one of the highest documented incidences of T1DM worldwide. A complete list of patients diagnosed (1987-2005) with T1DM in the province of Newfoundland and Labrador (NL) was constructed using multiple sources. All places of habitation at diagnosis were ascertained. Ecological analysis using Bayesian estimation was performed employing both NASA UVB data and latitude. Correlation of T1DM to both UVB irradiation and latitude was measured. A statistically significant correlation of erythemal UVB irradiance was observed (-0.0284: 95% CI -0.0542 to -0.0096). A more significant correlation of T1DM was observed with erythemal UVB irradiance than with latitude. This study suggests that erythemal UVB radiation may be geospatially associated with the incidence of T1DM in NL.

Of founder populations, long QT syndrome, and destiny

Founder populations, characterized by a single ancestor affected by long QT syndrome (LQTS) and by a large number of individuals and families who all are related to the ancestor and thereby carry the same disease-causing mutation, represent the ideal human model for studying the role of "modifier genes" in LQTS. This article reviews some of the fundamental concepts related to founder populations and provides the necessary historical background to understand why so many can be found in South Africa. The focus then moves to a specific LQT1 founder population, carrier of the A341V mutation, that has been studied extensively during the last 10 years and has provided a significant amount of previously unforeseen information. These novel findings range from an unusually high clinical severity not explained by the electrophysiologic characteristics of the mutation, to the importance of tonic and reflex control of heart rate for risk stratification, to the identification of the first modifier genes for clinical severity of LQTS.

Vitamin D insufficiency common in newborns, children and pregnant women living in Newfoundland and Labrador, Canada

Vitamin D deficiency is associated with poor bone health, colorectal cancer, type 1 diabetes and multiple sclerosis. Two national health-related societies in Canada have made recommendations for vitamin D supplementation, yet little research has been reported on the vitamin D status of Canadians. Lifestyle changes, such as sunscreen use, spending less time outdoors and insufficient intake of vitamin D-containing foods as well as northern latitude, may be affecting human vitamin D status. A cross-sectional analysis of 25-hydroxyvitamin D [25-(OH)D] was conducted in pregnant women, newborns (umbilical cord blood) and children. Samples were analysed by liquid chromatography mass spectrometry. Published ranges for 25-(OH)D were used to determine vitamin D status. The prevalence of 25-(OH)D deficiency for the three groups studied revealed most concentrations in the 25-(OH)D deficiency or insufficiency ranges. There were significant differences in all groups studied between seasons, with the exception of maternal blood and female cord blood samples. 25-(OH)D insufficiency was common in all groups for winter and summer, more so in winter. 25-(OH)D insufficiency was common in the three groups studied. The Newfoundland and Labrador population may be at increased risk for vitamin D insufficiency because of factors such as northern latitude and lifestyle issues. Further research on the vitamin D status of this population is important, considering the potential adverse health-related outcomes and the recommendations on supplementation being made.

Profound, prelingual nonsyndromic deafness maps to chromosome 10q21 and is caused by a novel missense mutation in the Usher syndrome type IF gene PCDH15

We studied a consanguineous family (Family A) from the island of Newfoundland with an autosomal recessive form of prelingual, profound, nonsyndromic sensorineural hearing loss. A genome-wide scan mapped the deafness trait to 10q21-22 (max LOD score of 4.0; D10S196) and fine mapping revealed a 16 Mb ancestral haplotype in deaf relatives. The PCDH15 gene was mapped within the critical region and was an interesting candidate because truncating mutations cause Usher syndrome type IF (USH1F) and two missense mutations have been previously associated with isolated deafness (DFNB23). Sequencing of the PCDH15 gene revealed 33 sequencing variants. Three of these variants were homozygous exclusively in deaf siblings but only one of them was not seen in ethnically matched controls. This novel c.1583 T>A transversion predicts an amino-acid substitution of a valine with an aspartic acid at codon 528 (V528D). Like the two DFNB23 mutations, the V528D mutation in Family A occurs in a highly conserved extracellular cadherin (EC) domain of PCDH15 and is predicted to be more deleterious than the previously identified DFNB23 missense mutations (R134G and G262D). Physical assessment, vestibular and visual function testing in deaf adults ruled out syndromic deafness because of Usher syndrome. This study validates the DFNB23 designation and supports the hypothesis that missense mutations in conserved motifs of PCDH15 cause nonsyndromic hearing loss. This emerging genotype-phenotype correlation in USH1F is similar to that in several other USH1 genes and cautions against a prognosis of a dual sensory loss in deaf children found to be homozygous for hypomorphic mutations at the USH1F locus.

Association of interleukin-23 receptor variants with ankylosing spondylitis

OBJECTIVE

Recent studies have shown that a nonsynonymous single-nucleotide polymorphism (SNP) (Arg381Gln; rs11209026) in the interleukin-23 receptor (IL-23R) gene on chromosome 1p31 is associated with Crohn's disease and psoriasis. Given the clinical and immunologic overlap between ankylosing spondylitis (AS) and these diseases, and the potential function of this candidate SNP, this study was undertaken to examine the association of IL-23R variants with AS in multiple Canadian populations.

METHODS

We examined 3 cohorts of AS patients from established rheumatic disease centers in Canada. The majority of AS patients were Caucasians of northern European descent, and all patients satisfied the modified New York classification criteria for AS or for juvenile spondylarthritis. We examined 424 AS probands and 401 controls from Alberta, 251 AS probands and 122 controls from Toronto, and 121 AS probands and 219 controls from Newfoundland. Ten IL-23R SNPs were genotyped, 9 of which were incorporated in the haplotype analysis. Allele and haplotype associations were calculated using the WHAP software package. P values for haplotype associations were calculated using a permutation test.

RESULTS

The primary SNP of interest in a previous study of inflammatory bowel disease (IBD) (Arg381Gln; rs11209026) was found to be protective against AS in the Newfoundland population (P=0.04) and in the Toronto population (P=0.04) in single-marker univariate analysis. The strongest association, however, was with SNP rs11465804 (P=0.007 for the Newfoundland population and P=0.0007 for the Toronto population). A 3-marker sliding window omnibus test revealed a significant association with markers rs10489629, rs2201841, and rs11465804 in both the Newfoundland population (P=0.04) and the Alberta population (P=0.034). Our results were independent of the IBD and psoriasis status of the AS patients.

CONCLUSION

This concurrent analysis of 3 distinct AS populations and their regional controls demonstrates a disease association with the IL-23R locus and implicates the same polymorphisms associated with IBD and psoriasis.

The relation of ultraviolet radiation and multiple sclerosis in Newfoundland

BACKGROUND

It has been thought that the occurrence of multiple sclerosis (MS) could be associated with daily ultraviolet exposure. In this study we investigated the geospatial association between average daily ultraviolet B (UVB) irradiance and MS prevalence in Newfoundland and Labrador (NL), Canada.

METHODS

A complete list of patients diagnosed with MS in the province of NL was constructed. Places of habitation from birth to diagnosis were ascertained by mailout survey.

RESULTS

A 74% rate of return on the survey results was obtained. A plot of the average daily erythemal UV over the available five years (1998-2002) shows that the distribution of MS follow a north-south gradient. Average daily UVB measurements are lower in the higher latitudes. A statistically significant negative correlation of MS incidence with erythemal UVB was found that is stronger than the correlation using latitude. This correlation appears to be strongest in the first year of life and declines when subsequent years are examined up to age ten. No significant correlation was found for the subjects' locale of habitation at the time of their first MS attack.

CONCLUSIONS

This study suggests that UVB radiation may contribute to the pathogenesis of MS.