Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips

The Brassica napus 60K Illumina Infinium™ SNP array has had huge international uptake in the rapeseed community due to the revolutionary speed of acquisition and ease of analysis of this high-throughput genotyping data, particularly when coupled with the newly available reference genome sequence. However, further utilization of this valuable resource can be optimized by better understanding the promises and pitfalls of SNP arrays. We outline how best to analyze Brassica SNP marker array data for diverse applications, including linkage and association mapping, genetic diversity and genomic introgression studies. We present data on which SNPs are locus-specific in winter, semi-winter and spring B. napus germplasm pools, rather than amplifying both an A-genome and a C-genome locus or multiple loci. Common issues that arise when analyzing array data will be discussed, particularly those unique to SNP markers and how to deal with these for practical applications in Brassica breeding applications

The Socioeconomic Impact of Living with Multiple Sclerosis in New Zealand

Multiple sclerosis (MS) is a disease where the majority of people are diagnosed in early adulthood however they experience a long sequela, with chronic progressive deterioration in most cases and a median survival time of 35-42 years. The increasing levels of disability reduce the individual’s potential to work fully and in time their ability to perform their activities of daily living. As these patients are affected in their most productive years the resulting impact on their health, employment and social status means that there is likely to be a large socioeconomic cost to the individual, their families, and those countries with a high prevalence of multiple sclerosis. In 2006 the New Zealand National MS Prevalence Study (NZNMSPS) was undertaken to ascertain the prevalence, distribution and profile of MS in New Zealand (NZ). In conjunction with the prevalence study, demographic features, disease characteristics and socioeconomic markers of people living with MS were investigated by this study to characterise the effects of the disease process on the socioeconomic status (SES) of the working age (25-64 years) MS population. The overriding objective was to identify the predictors of change in work, income and socioeconomic status for people with MS, thereby enabling targeting of disease modifying therapies, and allied health support to increase and prolong workforce participation. Capture-recapture methods estimated that over 96% of the clinically definite MS population in NZ had been identified. Data was collected through a postal survey sent to all people with MS, with a response rate of 71.1% (2073 individuals). The NZNMSPS confirmed the high prevalence of MS in NZ, and the presence of a latitudinal gradient below 370 South. A novel finding was that the latitudinal gradient was mostly driven by females with the relapsing remitting MS (RRMS) phenotype indicating that genetic and/or environmental factors do not affect all MS cases equally. This study found MS had a profound impact on work status, income and socioeconomic status which occurred early in the disease course and at low levels of disability. Both males and females were affected however the effect was significantly greater for females. On prevalence day 54.6% of the working age MS population were not working. People with MS who were not working were more likely to report an income below both the NZ and MS median annual personal incomes. Income loss occurred early with increased effect in the older age groups. Results highlight the significant difference in median annual personal income for people with MS when compared with their age stratified NZ peers. The New Zealand Socioeconomic Index (NZSEI) was used to evaluate the impact of MS on the SES of people living with the disease. Change in SES occurred early in the disease course with an apparent cumulative effect over the working age time-span, with the oldest age group most affected by loss of SES. Notably, people who remained in the workforce, whether full time or part time, were most likely to retain their SES. The major original contributions of this work are the descriptive epidemiology of the work, income, and socioeconomic status of people living with MS in NZ. Recommendations include review of government policy on timely access to disease modifying therapy to prevent disability accumulation and delay disease progression enabling people with MS to continue working and contributing to society. Furthermore improved planning, with both workplace and social support services, will maximise opportunities for people with MS to remain employed and living in the community

The Socioeconomic Impact of Living with Multiple Sclerosis in New Zealand

Multiple sclerosis (MS) is a disease where the majority of people are diagnosed in early adulthood however they experience a long sequela, with chronic progressive deterioration in most cases and a median survival time of 35-42 years. The increasing levels of disability reduce the individual’s potential to work fully and in time their ability to perform their activities of daily living. As these patients are affected in their most productive years the resulting impact on their health, employment and social status means that there is likely to be a large socioeconomic cost to the individual, their families, and those countries with a high prevalence of multiple sclerosis. In 2006 the New Zealand National MS Prevalence Study (NZNMSPS) was undertaken to ascertain the prevalence, distribution and profile of MS in New Zealand (NZ). In conjunction with the prevalence study, demographic features, disease characteristics and socioeconomic markers of people living with MS were investigated by this study to characterise the effects of the disease process on the socioeconomic status (SES) of the working age (25-64 years) MS population. The overriding objective was to identify the predictors of change in work, income and socioeconomic status for people with MS, thereby enabling targeting of disease modifying therapies, and allied health support to increase and prolong workforce participation. Capture-recapture methods estimated that over 96% of the clinically definite MS population in NZ had been identified. Data was collected through a postal survey sent to all people with MS, with a response rate of 71.1% (2073 individuals). The NZNMSPS confirmed the high prevalence of MS in NZ, and the presence of a latitudinal gradient below 370 South. A novel finding was that the latitudinal gradient was mostly driven by females with the relapsing remitting MS (RRMS) phenotype indicating that genetic and/or environmental factors do not affect all MS cases equally. This study found MS had a profound impact on work status, income and socioeconomic status which occurred early in the disease course and at low levels of disability. Both males and females were affected however the effect was significantly greater for females. On prevalence day 54.6% of the working age MS population were not working. People with MS who were not working were more likely to report an income below both the NZ and MS median annual personal incomes. Income loss occurred early with increased effect in the older age groups. Results highlight the significant difference in median annual personal income for people with MS when compared with their age stratified NZ peers. The New Zealand Socioeconomic Index (NZSEI) was used to evaluate the impact of MS on the SES of people living with the disease. Change in SES occurred early in the disease course with an apparent cumulative effect over the working age time-span, with the oldest age group most affected by loss of SES. Notably, people who remained in the workforce, whether full time or part time, were most likely to retain their SES. The major original contributions of this work are the descriptive epidemiology of the work, income, and socioeconomic status of people living with MS in NZ. Recommendations include review of government policy on timely access to disease modifying therapy to prevent disability accumulation and delay disease progression enabling people with MS to continue working and contributing to society. Furthermore improved planning, with both workplace and social support services, will maximise opportunities for people with MS to remain employed and living in the community

Assessing possible selection bias in a national voluntary MS longitudinal study in Australia

Background: Surveying volunteer members of a multiple sclerosis registry is a very cost-effective way of assessing the impact of the disease on life outcomes. However, whether the data from such a study can be generalised to the whole population of perso

Assessing possible selection bias in a national voluntary MS longitudinal study in Australia

Background: Surveying volunteer members of a multiple sclerosis registry is a very cost-effective way of assessing the impact of the disease on life outcomes. However, whether the data from such a study can be generalised to the whole population of persons living with MS in a country or region is unclear. Methods: Here we compare the demographic and disease characteristics of participants in one such study, the Australian Multiple Sclerosis Longitudinal Study (AMSLS), with two well-characterised MS prevalence studies with near-complete ascertainment of MS in their study regions. Results: Although some differences were found, these largely represented the effects of geography (sex ratios) and local factors (national immunomodulatory therapy prescribing requirements), and the cohorts were otherwise comparable. Overall, despite comprising only 12–16% of MS cases in Australia, the AMSLS is highly representative of the MS population. Conclusions: Therefore with some minor caveats, the AMSLS data can be generalised to the whole Australasian MS population. Volunteer disease registries such as this can be highly representative and provide an excellent convenience sample when studying rare conditions such as MS. </jats:sec