The impact of an antibody investigation algorithm emphasizing specificity on reducing potential false-positive warm autoantibody detection at a Canadian tertiary care centre.

BACKGROUND AND OBJECTIVES: To reduce potential false-positive warm autoantibody (WAA) by solid-phase red cell adherence assay (SPRCA), our centre implemented a new antibody investigation algorithm (AIA) by classifying cases with panreactive SPRCA but negative saline-indirect antiglobulin test as 'antibody of undetermined significance' (AUS) after excluding clinically significant antibodies. We assessed the effects of the new AIA and subsequent alloantibody formation in patients with AUS. MATERIALS AND METHODS: Samples from patients with positive SPRCA screens between 1 September 2017 and 31 August 2021 were selected for the study. Frequencies of antibodies classified by the old and new AIAs were compared using Fisher's exact test. Patient demographics, transfusion history and antibody formation in cases of AUS were collected. RESULTS: A significant reduction in potential WAA frequencies from 127/1167 (11%) to 53/854 (6%) was observed (p < 0.001) when compared between the old and new AIAs among 2021 positive SPRCA antibody screens. While no patients with AUS later transitioned to potential WAA using the new AIA, four patients developed alloantibodies, including anti-E, anti-C, both anti-C and anti-E, and anti-Wra . CONCLUSION: A significant reduction in the frequencies of potential false-positive WAA detection at our centre was observed after implementing the new AIA, leading to less resource and phenotypically matched red blood cell (RBC) use. Some patients still developed subsequent RBC alloimmunization, so clinically relevant alloantibodies should be carefully excluded before determining AUS, taking forming or evanescent antibodies into consideration.

The Cedar Project: Racism and its impacts on health and wellbeing among young Indigenous people who use drugs in Prince George and Vancouver, BC.

Racism continues to drive health disparities between Indigenous and non-Indigenous peoples in Canada. This study focuses on racism experienced by young Indigenous people who have used drugs in British Columbia (BC), and predictors of interpersonal racism. Cedar Project is a community-governed cohort study involving young Indigenous people who use drugs in Vancouver and Prince George, BC. This cross-sectional study included data collected between August 2015-October 2016. The Measure of Indigenous Racism Experiences (MIRE) scale was used to assess experiences of interpersonal racism across 9 unique settings on a 5-point Likert scale, collapsing responses into three categories (none/low/high). Multinomial logistic regression models were used to examine associations between key variables and interpersonal racism. Among 321 participants, 79% (n = 255) experienced racism in at least one setting. Thirty two percent (n = 102) experienced high interpersonal racism from police, governmental agencies (child 'welfare', health personnel), and in public settings. Ever having a child apprehended (AOR:2.76, 95%CI:1.14-6.65), probable post-traumatic stress (AOR:2.64; 95%CI:1.08-6.46), trying to quit substances (AOR:3.69; 95%CI:1.04-13.06), leaving emergency room without receiving treatment (AOR:3.05; 95%CI:1.22-7.64), and having a traditional language spoken at home while growing up (AOR:2.86; 95%CI:1.90-6.90) were associated with high interpersonal racism. Among women, experiencing high interpersonal racism was more likely if they lived in Prince George (AOR:3.94; 95%CI:1.07-14.50), ever had a child apprehended (AOR:5.09; 95%CI:1.50-17.30), and had probable post-traumatic stress (AOR:5.21; 95%CI:1.43-18.95). Addressing racism experienced by Indigenous peoples requires immediate structural systemic, and interpersonal anti-racist reforms.

Cango Lyec (Healing the Elephant): HIV Prevalence and Vulnerabilities Among Adolescent Girls and Young Women in Postconflict Northern Uganda.

OBJECTIVES: Adolescent girls and young women younger than 25 years (AGYW) account for disproportionate HIV infections in sub-Saharan Africa. Impacts of war in Northern Uganda continue to affect HIV-related health and wellbeing of young people postconflict. Prevalence and incidence of HIV infection were estimated, and factors associated with HIV prevalence among sexually active AGYW in Northern Uganda were investigated. METHODS: Cango Lyec is a cohort involving conflict-affected populations in Northern Uganda. Nine randomly selected communities in Gulu, Nwoya, and Amuru districts were mapped. House-to-house census was conducted. Consenting participants aged 13-49 years were enrolled over 3 study rounds (2011-2015), of whom 533 were AGYW and had ever had sex. Data were collected on trauma, depression, and sociodemographic-behavioral characteristics. Venous blood was taken for HIV and syphilis serology. Multivariable logistic regression determined baseline factors associated with HIV prevalence. RESULTS: HIV prevalence among AGYW was 9.7% (95% CI: 7.3 to 12.6). AGYW living in Gulu (adjusted risk ratio, aRR: 2.48; 95% CI: 1.12 to 5.51) or Nwoya (aRR: 2.65; 95% CI: 1.03 to 6.83) were more likely than in Amuru to be living with HIV. Having self-reported genital ulcers (aRR: 1.93; 95% CI: 0.97 to 3.85) or active syphilis (aRR: 3.79; 95% CI: 2.35 to 6.12) was associated with increased risk of HIV infection. The likelihood of HIV was higher for those who experienced sexual violence in the context of war (aRR: 2.37; 95% CI: 1.21 to 4.62) and/or probable depression (aRR: 1.95; 95% CI: 1.08 to 3.54). HIV incidence was 8.9 per 1000 person-years. CONCLUSION: Ongoing legacies of war, especially gender violence and trauma, contribute to HIV vulnerability among sexually active AGYW. Wholistic approaches integrating HIV prevention with culturally safe initiatives promoting sexual and mental health in Northern Uganda are essential.

The estimated negative impacts on the red blood cell inventory of reducing shelf-life at two large health authorities in British Columbia, Canada, using a discrete-event simulation model.

BACKGROUND AND OBJECTIVES: Reducing the maximum red blood cell (RBC) shelf-life is under consideration due to potential negative effects of older blood. An assessment of the impacts of this change on blood supply chain management is evaluated. MATERIALS AND METHODS: We performed a simulation study using data from 2017 to 2018 to estimate the outdate rate (ODR), STAT order and non-group-specific RBC transfusion at two Canadian health authorities (HAs). RESULTS: Shortening shelf-life from 42 to 35 and 28 days led to the following: ODRs (in percentage) in both HAs increased from 0.52% (95% confidence interval [CI] 0.50-0.54) to 1.32% (95% CI 1.26-1.38) and 5.47% (95% CI 5.34-5.60), respectively (p < 0.05). The estimated yearly median of outdated RBCs increased from 220 (interquartile range [IQR] 199-242) to 549 (IQR 530-576) and 2422 (IQR 2308-2470), respectively (p < 0.05). The median number of outdated redistributed units increased from 152 (IQR 136-168) to 356 (IQR 331-369) and 1644 (IQR 1591-1741), respectively (p < 0.05). The majority of outdated RBC units were from redistributed units rather than units ordered from the blood supplier. The estimated weekly mean STAT orders increased from 11.4 (95% CI 11.2-11.5) to 14.1 (95% CI 13.1-14.3) and 20.9 (95% CI 20.6-21.1), respectively (p < 0.001). The non-group-specific RBC transfusion rate increased from 4.7% (95% CI 4.6-4.8) to 8.1% (95% CI 7.9-8.3) and 15.6% (95% CI 15.3-16.4), respectively (p < 0.001). Changes in ordering schedules, decreased inventory levels and fresher blood received simulated minimally mitigated these impacts. CONCLUSION: Decreasing RBC shelf-life negatively impacted RBC inventory management, including increasing RBC outdating and STAT orders, which supply modifications minimally mitigate.

Potential for prolongation of fibrinogen concentrates post-reconstitution.

BACKGROUND AND OBJECTIVES: Reconstituted fibrinogen concentrate is considered stable for 8-24 h based on product monographs. Given the long half-life of fibrinogen in vivo (3-4 days), we hypothesized that reconstituted sterile fibrinogen protein would remain stable longer than 8-24 h. Extending the expiry date for reconstituted fibrinogen concentrate could decrease wastage and facilitate reconstitution in advance to minimize turnaround times. We performed a pilot study to define the stability of reconstituted fibrinogen concentrates over time. MATERIALS AND METHODS: Reconstituted Fibryga® (Octapharma AG) from 64 vials was stored in the temperature-controlled refrigerator (4 °C) for up to 7 days with functional fibrinogen concentration measured serially using the automated Clauss method. The samples were frozen, then thawed and diluted with pooled normal plasma in order for them to be batch tested. RESULTS: Reconstituted fibrinogen samples stored in the refrigerator showed no significant reduction in functional fibrinogen concentration for the entire 7-day study period (p = 0.63). Duration of initial freezing had no detrimental effect on functional fibrinogen levels (p = 0.23). CONCLUSION: Fibryga® can be stored at 2-8 °C post-reconstitution for up to one week with no loss in functional fibrinogen activity based on Clauss fibrinogen assay. Further studies with other fibrinogen concentrate formulations and clinical in vivo studies may be warranted.

Evaluation of immunoglobulin replacement therapy in secondary immunodeficiency at three British Columbia hospitals.

BACKGROUND AND OBJECTIVES: Immunoglobulin (Ig) usage has ongoing shortage concerns. Secondary immunodeficiencies (SIDs) account for a major proportion of usage of Igs in Canada. We audited Ig usage in patients with SID at three British Columbia hospitals to determine whether more stringent local guidelines are necessary. MATERIALS AND METHODS: A retrospective chart review was performed for patients who had Ig ordered between 1 January 2018 and 31 December 2019 for any SID indication. Cohorts were stratified into chronic and new users, and the Australian BloodSTAR guidelines were used as the benchmark at the time of conception. Having an eligible primary diagnosis, meeting SID criteria, an appropriate dosage and follow-up immunoglobulin G (IgG) levels encompassed appropriate usage. RESULTS: There were no demographic differences between chronic (N = 81) and new (N = 33) cohorts. The new cohort had a higher rate of appropriate usage (45.7% vs. 66.7%, p = 0.06). The most common reason for inappropriate usage in both groups was the lack of follow-up IgG level at 6 or 12 months. Factors, displayed by relative risk (RR), associated with appropriateness included the dispensing hospital (RR: 6.60), use of subcutaneous Ig (RR: 3.84), having an IgG level before starting therapy (RR: 3.51) and documentation of clinical benefit (RR: 4.70). CONCLUSION: There are high rates of inappropriate Ig usage in SID patients in both new and chronically treated groups. More stringent local guidelines and processes for assessing initial and ongoing Ig replacement are warranted.

Cango Lyec (Healing the Elephant): Probable post-traumatic stress disorder (PTSD) and depression in Northern Uganda five years after a violent conflict.

Background: From 1986 to 2006, Northern Uganda experienced an atrocious civil war between the Lord's Resistance Army (LRA) and the Ugandan government. Acholi people living in the region continue to be impacted by trauma sequelae of the war and a wide range of daily stressors including poverty, hunger, and high rates of HIV infection. To date, there is a dearth of gender-differentiated mental health research in this post-conflict setting. The current study aimed to estimate the prevalence of probable post-traumatic stress disorder (PTSD) and depression in three districts most affected by the Northern Ugandan conflict and examine socio-structural, war-related, and sexual vulnerability factors associated with mental health. Methods: Cango Lyec (Healing the Elephant) is an open cohort study involving participants from eight randomly selected communities in Amuru, Gulu, and Nwoya districts of Northern Uganda. Between November 2011 and July 2012, the baseline cohort (N = 2,458) completed the Harvard Trauma Questionnaire (HTQ) and Hopkins Symptom Checklist-25 (HSCL-25) for screening PTSD and depression, in addition to a detailed questionnaire assessing socio-demographic-behavioral characteristics. Baseline categorical variables were compared between males and females using Fisher's exact test. Multivariate logistic regression was used to model correlates of probable PTSD and depression. All analyses were stratified by gender. Results: The overall prevalence of probable PTSD and depression was 11.7% and 15.2% respectively. Among former abductees, the prevalence was 23.2% for probable PTSD and 26.6% for probable depression. Women were significantly more likely to experience mental distress than men. Factors associated with mental distress included wartime trauma (adjusted odds ratios ranging from 2.80 to 7.19), experiences of abduction (adjusted odds ratios ranging from 1.97 to 3.03), and lack of housing stability and safety (adjusted odds ratios ranging from 1.95 to 4.59). Additional risk factors for women included HIV infection (AOR=1.90; 95% CI: 1.29-2.80), sexual abuse in the context of war (AOR=1.58; 95% CI: 1.02-2.45), and intimate partner violence (AOR=2.45; 95% CI: 1.07-5.63). Conclusion: Cango Lyec participants displayed lower than previously reported yet significant levels of probable PTSD and depression. Based on findings from this study, providing trauma-informed care, ensuring food and housing security, eliminating gender-based violence, and reintegrating former abductees remain important tasks to facilitate post-conflict rehabilitation in Northern Uganda.

The Cedar Project: exploring the role of colonial harms and childhood maltreatment on HIV and hepatitis C infection in a cohort study involving young Indigenous people who use drugs in two Canadian cities.

OBJECTIVES: This study examined associations between childhood maltreatment, colonial harms and sex/drug-related risks for HIV and hepatitis C virus (HCV) infection among young Indigenous people who use drugs. DESIGN: The Cedar Project is a cohort involving young Indigenous people who use drugs in British Columbia (BC), Canada. Indigenous collaborators, collectively known as the Cedar Project Partnership, govern the entire research process. SETTING: Vancouver is a large city on the traditional territory of the Coast Salish peoples. Prince George is a mid-sized city, on the traditional territory of Lheidli T'enneh First Nation. PARTICIPANTS: 420 participants completed the Childhood Trauma Questionnaire and returned for follow-up from 2003 to 2016. PRIMARY/SECONDARY OUTCOME MEASURES: Primary outcomes were HIV and HCV infection over the study period. Secondary outcomes included sex and substance use-related risks. RESULTS: Prevalence of childhood maltreatment was 92.6% experienced any maltreatment; 73.4% experienced emotional abuse; 62.6% experienced physical abuse; 60.3% experienced sexual abuse; 69.5% experienced emotional neglect and 79.1% experienced physical neglect. We observed significant associations between childhood maltreatment and apprehensions into residential schools and foster care. All maltreatment types were associated with higher odds of sex/substance use-related risks; sexual abuse was associated with higher odds of HCV infection (adjusted OR: 1.67; 95% CI 1.05 to 2.66; p=0.031). CONCLUSIONS: Findings reflect high prevalence of childhood maltreatment and their associations with HIV/HCV risk and HCV infection. Public health prevention and treatment initiatives must be trauma informed and culturally safe to support healing, health, and well-being.

The Cedar Project: Relationship between child apprehension and attempted suicide among young Indigenous mothers impacted by substance use in two Canadian cities.

Indigenous leaders are gravely concerned over disproportionate representation of Indigenous children in Canada's child welfare systems. Forced separation from children is deeply traumatizing for mothers and detrimental to the wellbeing of Indigenous families, communities and Nations. This study examined relationships between child apprehension and suicide attempt within a cohort of young Indigenous women impacted by substance use. We utilized data collected every 6 months (2008-2016) by the Cedar Project, an Indigenous-governed cohort study involving young Indigenous people who use drugs in British Columbia, Canada. Recent child apprehension was defined as having a child apprehended by the Ministry of Child and Family Development since last visit. Recurrent event Cox proportional hazards models estimated the independent effect of child apprehension on maternal suicide attempt. Among 293 participants, 78 (27%) reported 136 child apprehensions; incidence of first apprehension was 6.64 (95%CI: 5.25-8.29) per 100 person-years. Forty-seven (16%) participants reported 75 suicide attempts with an incidence of 4.00 (95%CI: 2.94-5.33) per 100 person-years. Participants who reported recent child apprehension (HR: 1.88, 95%CI: 1.00-3.55), had a parent attend residential school (HR: 4.12, 95%CI: 1.63-10.46), experienced recent sexual assault (HR: 4.04, 95%CI: 2.04-7.99), violence (HR: 2.54, 95%CI: 1.52-4.27) or overdose (HR: 4.97, 95%CI: 2.96-8.35) were more likely to attempt suicide. Participants who had a traditional language spoken in the home growing up were half as likely to attempt suicide (HR: 0.49, 95%CI: 0.23-1.01). Results suggest that child welfare systems in Canada perpetuate historical and intergenerational trauma among young Indigenous mothers. Indigenous self-determination over child welfare and culturally safe services are urgently needed to end cycles of child apprehension and support the wellbeing of families, communities and Nations.

Cango Lyec (Healing the Elephant): Chronic Hepatitis B Virus among post-conflict affected populations living in mid-Northern Uganda.

BACKGROUND: The legacy of war in Northern Uganda continues to impact people's health and wellbeing in the Acholi region. Despite increasing attention to Hepatitis B Virus (HBV) in Uganda and globally, concerns remain that unique drivers of infection, and barriers to screening, and treatment, persist among those affected by conflict. METHODS: Cango Lyec (Healing the Elephant) cohort survey involved conflict-affected adults aged 13-49 in three mid-Northern Uganda districts (Gulu, Amuru and Nwoya). Baseline (2011-2012) samples were tested for HBV surface antigen (HBsAg), HBV e-antigen (HBeAg), antibodies to HBV surface antigen (HBsAb), antibodies to HBV e-antigen (HBeAb), and antibodies to HBV core antigen (HBcAb). All HBsAg positive samples were tested for IgM antibodies to HBV B core antigen (HBc-IgM) and where available, >6-month follow-up samples were tested for HBeAg and HBV DNA. Data were analyzed using STATA 15 software. Logistic regression accounted for variance due to complex two-stage sampling that included stratification, unequal selection probabilities and community clustering. Odds ratios measured effect potential risk factors associated with chronic HBV infection. RESULTS: Among 2,421 participants, 45.7% were still susceptible to HBV infection. HBsAg seropositivity was 11.9% (10.9-13.0), chronic HBV was 11.6% (10.4-12.8), acquired immunity resulting from vaccination was 10.9%, and prior natural infection was 31.5%. Older age (OR:0.570; 95%CI:0.368-0.883) and higher education (OR:0.598; 95%CI:0.412-0.868) were associated with reduced odds of chronic HBV infection. Being male (OR:1.639; 95%CI:1.007-2.669) and having been abducted (OR:1.461; 95%CI:1.055-2.023) were associated with increased odds of infection. Among women, having 1 or 2 pregnancies (compared to none or >2) was associated with increased odds of infection (OR:1.764; 95%CI:1.009-3.084). CONCLUSION: Chronic HBV is endemic in Gulu, Amuru and Nwoya districts. Recommended strategies to reduce post-conflict prevalence include establishment of Northern Uganda Liver Wellness Centres, integration of screening and treatment into antenatal care, and roll out of birth-dose vaccination.

The Cedar Project: Historical, structural and interpersonal determinants of involvement in survival sex work over time among Indigenous women who have used drugs in two Canadian cities.

BACKGROUND: Indigenous women involved in survival sex work face multiple layers of discrimination, criminalization and alarming levels of intergenerational and lifetime trauma. This longitudinal study examined historical, structural and interpersonal factors associated with survival sex work involvement among Indigenous women who have used drugs in British Columbia (BC), Canada. METHODS: The Cedar Project is an ongoing cohort study involving young Indigenous people who have used illicit drugs in Vancouver and Prince George, BC. Data was collected every 6 months from 2007 to 2016 . Generalized linear mixed-effects modeling was used to model survival sex work involvement, defined as exchanging sex for money, drugs, food or shelter in the previous six months. RESULTS: Among 292 participants, 34% reported their family always/often lived by traditional culture and 37% reported their family always/often spoke their traditional language. In contrast, 48% had a parent in residential school and 72% were removed from their biological parents. In total, 55% of women were involved in survival sex work at baseline. In adjusted analyses, those who were single (ARR: 1.91; 95% CI: 1.50-2.35), identified as two-spirit (ARR: 2.16; 95% CI: 1.36-2.91), experienced sexual assault (ARR: 1.90; 95% CI: 1.22-2.58), were denied access to shelter (ARR: 1.71; 95% CI: 1.18-2.28), used crack daily (ARR: 2.85; 95% CI: 2.36-3.31), used injection drugs (ARR: 2.52; 95% CI: 1.98-3.07), and were unable to access substance use treatment (ARR: 1.58; 95% CI: 1.15-2.05) were more likely to be involved in sex work. CONCLUSION: Indigenous-governed, wellness-based harm-reduction interventions, and structural reforms addressing housing insecurity and normalization of a culture of violence against Indigenous women, especially those involved in survival sex work, are urgently needed in Canada.

Cango Lyec (Healing the Elephant): HIV incidence in post-conflict Northern Uganda.

BACKGROUND: Civil war in Northern Uganda resulted in widespread atrocities, human rights violations, and death, and caused millions to flee to internally displaced persons camps. War-related traumas combined with difficulties accessing HIV prevention and health services has led to extreme HIV-related vulnerability among conflict-affected people who survived the war. Objectives were to (1) determine HIV incidence among conflict-affected people in Northern Uganda and (2) identify vulnerabilities associated with HIV infection. METHODS: The Cango Lyec (Healing the Elephant) Project is a prospective cohort involving conflict-affected populations in three districts in Northern Uganda. In 2011, eight randomly selected communities were mapped, and a census was conducted. Consenting participants aged 13-49 years were followed over three rounds of follow-up. Longitudinal data collected included war-related experiences, sexual vulnerabilities, and sociodemographics. Blood samples were tested for HIV-1 at baseline and each 12-month follow-up. Multivariable Cox proportional hazard models determined factors associated with HIV incidence. FINDINGS: Overall, 1920 baseline HIV-negative participants with at least one follow-up contributed 3877 person-years (py) for analysis. Thirty-nine (23 female, 16 male) participants contracted HIV during follow-up. Age- and gender-standardised HIV incidence rate was 10•2 per 1000py (95%CI: 7•2-14•0). Stratified by sex, the age-adjusted HIV incidence was 11•0 per 1000py (95%CI: 6•9-16•6) among women and 9•4 per 1000py (95%CI: 5•3-15•3) among men. Adjusting for confounders, factors associated with risk of HIV included: having been abducted (HR: 3•70; 95%CI: 1•87-7•34), experiencing ≥12 war-related traumatic events (HR: 2•91 95%CI: 1•28-6•60), suicide ideation (HR: 2•83; 95%CI: 1•00-8•03), having ≥2 sexual partners (HR: 4•68; 95%CI: 1•36-16•05), inconsistent condom use (HR: 6•75; 95%CI: 2•49-18•29), and self-reported genital ulcers (HR: 4•39; 95%CI: 2•04-9•45). INTERPRETATION: Conflict-affected participants who had experienced abduction and multiple traumas during the war were at greater risk of HIV infection. Trauma-informed HIV prevention and treatment services, and culturally-safe mental health initiatives, are urgent for Northern Uganda.

The Cedar Project: mortality among young Indigenous people who use drugs in British Columbia.

BACKGROUND: Young Indigenous people, particularly those involved in the child welfare system, those entrenched in substance use and those living with HIV or hepatitis C, are dying prematurely. We report mortality rates among young Indigenous people who use drugs in British Columbia and explore predictors of mortality over time. METHODS: We analyzed data collected every 6 months between 2003 and 2014 by the Cedar Project, a prospective cohort study involving young Indigenous people who use illicit drugs in Vancouver and Prince George, BC. We calculated age-standardized mortality ratios using Indigenous and Canadian reference populations. We identified predictors of mortality using time-dependent Cox proportional hazard regression. RESULTS: Among 610 participants, 40 died between 2003 and 2014, yielding a mortality rate of 670 per 100 000 person-years. Young Indigenous people who used drugs were 12.9 (95% confidence interval [CI] 9.2-17.5) times more likely to die than all Canadians the same age and were 7.8 (95% CI 5.6-10.6) times more likely to die than Indigenous people with Status in BC. Young women and those using drugs by injection were most affected. The leading causes of death were overdose (n = 15 [38%]), illness (n = 11 [28%]) and suicide (n = 5 [12%]). Predictors of mortality included having hepatitis C at baseline (adjusted hazard ratio [HR] 2.76, 95% CI 1.47-5.16), previous attempted suicide (adjusted HR 1.88, 95% CI 1.01-3.50) and recent overdose (adjusted HR 2.85, 95% CI 1.00-8.09). INTERPRETATION: Young Indigenous people using drugs in BC are dying at an alarming rate, particularly young women and those using injection drugs. These deaths likely reflect complex intersections of historical and present-day injustices, substance use and barriers to care.

Path: a tool to facilitate pathway-based genetic association analysis.

SUMMARY: Traditional methods of genetic study design and analysis work well under the scenario that a handful of single nucleotide polymorphisms (SNPs) independently contribute to the risk of disease. For complex diseases, susceptibility may be determined not by a single SNP, but rather a complex interplay between SNPs. For large studies involving hundreds of thousands of SNPs, a brute force search of all possible combinations of SNPs associated with disease is not only inefficient, but also results in a multiple testing paradigm, whereby larger and larger sample sizes are needed to maintain statistical power. Pathway-based methods are an example of one of the many approaches in identifying a subset of SNPs to test for interaction. To help determine which SNP-SNP interactions to test, we developed Path, a software application designed to help researchers interface their data with biological information from several bioinformatics resources. To this end, our application brings together currently available information from nine online bioinformatics resources including the National Center for Biotechnology Information (NCBI), Online Mendelian Inheritance in Man (OMIM), Kyoto Encyclopedia of Genes and Genomes (KEGG), UCSC Genome Browser, Seattle SNPs, PharmGKB, Genetic Association Database, the Single Nucleotide Polymorphism database (dbSNP) and the Innate Immune Database (IIDB). AVAILABILITY: The software, example datasets and tutorials are freely available from http://genapha.icapture.ubc.ca/PathTutorial.

A thymic stromal lymphopoietin gene variant is associated with asthma and airway hyperresponsiveness.

BACKGROUND: The epithelial cell-derived protein thymic stromal lymphopoietin stimulates dendritic and mast cells to promote proallergic T(H)2 responses. Studies of transgenic expression of thymic stromal lymphopoietin and its receptor knockout mice have emphasized its critical role in the development of allergic inflammation. Association of genetic variation in thymic stromal lymphopoietin with IgE levels has been reported for human subjects. OBJECTIVE: The aim of this study was to evaluate the relationship between variants of thymic stromal lymphopoietin and asthma and related phenotypes. METHODS: We selected 6 single nucleotide polymorphisms in thymic stromal lymphopoietin and genotyped 5565 individuals from 4 independent asthma studies and tested for association with asthma, atopy, atopic asthma, and airway hyperresponsiveness by using a general allelic likelihood ratio test. P values were corrected for the effective number of independent single nucleotide polymorphisms and phenotypes. RESULTS: The A allele of rs1837253, which is 5.7 kb upstream of the transcription start site of the gene, was associated with protection from asthma, atopic asthma, and airway hyperresponsiveness, with the odds ratios and corrected P values for each being 0.79 and 0.0058; 0.75 and 0.0074; and 0.76 and 0.0094, respectively. Associations between thymic stromal lymphopoietin and asthma-related phenotypes were the most statistically significant observations in our study, which has to date examined 98 candidate genes. Full results are available online at http://genapha.icapture.ubc.ca/. CONCLUSIONS: A genetic variant in the region of the thymic stromal lymphopoietin gene is associated with the phenotypes of asthma and airway hyperresponsiveness.

Analyses of associations with asthma in four asthma population samples from Canada and Australia.

Asthma, atopy, and related phenotypes are heterogeneous complex traits, with both genetic and environmental risk factors. Extensive research has been conducted and over hundred genes have been associated with asthma and atopy phenotypes, but many of these findings have failed to replicate in subsequent studies. To separate true associations from false positives, candidate genes need to be examined in large well-characterized samples, using standardized designs (genotyping, phenotyping and analysis). In an attempt to replicate previous associations we amalgamated the power and resources of four studies and genotyped 5,565 individuals to conduct a genetic association study of 93 previously associated candidate genes for asthma and related phenotypes using the same set of 861 single-nucleotide polymorphisms (SNPs), a common genotyping platform, and relatively harmonized phenotypes. We tested for association between SNPs and the dichotomous outcomes of asthma, atopy, atopic asthma, and airway hyperresponsiveness using a general allelic likelihood ratio test. No SNP in any gene reached significance levels that survived correction for all tested SNPs, phenotypes, and genes. Even after relaxing the usual stringent multiple testing corrections by performing a gene-based analysis (one gene at a time as if no other genes were typed) and by stratifying SNPs based on their prior evidence of association, no genes gave strong evidence of replication. There was weak evidence to implicate the following: IL13, IFNGR2, EDN1, and VDR in asthma; IL18, TBXA2R, IFNGR2, and VDR in atopy; TLR9, TBXA2R, VDR, NOD2, and STAT6 in airway hyperresponsiveness; TLR10, IFNGR2, STAT6, VDR, and NPSR1 in atopic asthma. Additionally we found an excess of SNPs with small effect sizes (OR < 1.4). The low rate of replication may be due to small effect size, differences in phenotypic definition, differential environmental effects, and/or genetic heterogeneity. To aid in future replication studies of asthma genes a comprehensive database was compiled and is available to the scientific community at http://genapha.icapture.ubc.ca/.