The development of participatory health research among incarcerated women in a Canadian prison

This paper describes the development of a unique prison participatory research project, in which incarcerated women formed a research team, the research activities and the lessons learned. The participatory action research project was conducted in the main short sentence minimum/medium security women's prison located in a Western Canadian province. An ethnographic multi-method approach was used for data collection and analysis. Quantitative data was collected by surveys and analysed using descriptive statistics. Qualitative data was collected from orientation package entries, audio recordings, and written archives of research team discussions, forums and debriefings, and presentations. These data and ethnographic observations were transcribed and analysed using iterative and interpretative qualitative methods and NVivo 7 software. Up to 15 women worked each day as prison research team members; a total of 190 women participated at some time in the project between November 2005 and August 2007. Incarcerated women peer researchers developed the research processes including opportunities for them to develop leadership and technical skills. Through these processes, including data collection and analysis, nine health goals emerged. Lessons learned from the research processes were confirmed by the common themes that emerged from thematic analysis of the research activity data. Incarceration provides a unique opportunity for engagement of women as expert partners alongside academic researchers and primary care workers in participatory research processes to improve their health

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved