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Publication Octet Stream Genome-wide association analysis implicates dysregulation of immunity genes in chronic lymphocytic leukaemia.
by Stephanie McInnis published Feb 21, 2017
Several chronic lymphocytic leukaemia (CLL) susceptibility loci have been reported; however, much of the heritable risk remains unidentified. Here we perform a meta-analysis of six genome-wide association studies, imputed using a merged reference panel of 1,000 Genomes and UK10K data, totalling 6,200 cases and 17,598 controls after replication. We identify nine risk loci at 1p36.11 (rs34676223, P=5.04 × 10(-13)), 1q42.13 (rs41271473, P=1.06 × 10(-10)), 4q24 (rs71597109, P=1.37 × 10(-10)), 4q35.1 (rs57214277, P=3.69 × 10(-8)), 6p21.31 (rs3800461, P=1.97 × 10(-8)), 11q23.2 (rs61904987, P=2.64 × 10(-11)), 18q21.1 (rs1036935, P=3.27 × 10(-8)), 19p13.3 (rs7254272, P=4.67 × 10(-8)) and 22q13.33 (rs140522, P=2.70 × 10(-9)). These new and established risk loci map to areas of active chromatin and show an over-representation of transcription factor binding for the key determinants of B-cell development and immune response.
Located in Platforms / Scientific Publications
Publication backup file Lipid and Alzheimer's disease genes associated with healthy aging and longevity in healthy oldest-old.
by Stephanie McInnis published Feb 21, 2017
Several studies have found that long-lived individuals do not appear to carry lower numbers of common disease-associated variants than ordinary people; it has been hypothesized that they may instead carry protective variants. An intriguing type of protective variant is buffering variants that protect against variants that have deleterious effects. We genotyped 18 variants in 15 genes related to longevity or healthy aging that had been previously reported as having a gene-gene interaction or buffering effect. We compared a group of 446 healthy oldest-old 'Super-Seniors' (individuals 85 or older who have never been diagnosed with cancer, cardiovascular disease, dementia, diabetes or major pulmonary disease) to 421 random population-based midlife controls. Cases and controls were of European ancestry. Association tests of individual SNPs showed that Super-Seniors were less likely than controls to carry an APOEε4 allele or a haptoglobin HP2 allele. Interactions between APOE/FOXO3, APOE/CRYL1, and LPA/CRYL1 did not remain significant after multiple testing correction. In a network analysis of the candidate genes, lipid and cholesterol metabolism was a common theme. APOE, HP, and CRYL1 have all been associated with Alzheimer's Disease, the pathology of which involves lipid and cholesterol pathways. Age-related changes in lipid and cholesterol maintenance, particularly in the brain, may be central to healthy aging and longevity.
Located in Platforms / Scientific Publications
Publication Kollector: transcript-informed, targeted de novo assembly of gene loci.
by Stephanie McInnis published Feb 21, 2017
Motivation: Despite considerable advancements in sequencing and computing technologies, de novo assembly of whole eukaryotic genomes is still a time-consuming task that requires a significant amount of computational resources and expertise. A targeted assembly approach to perform local assembly of sequences of interest remains a valuable option for some applications. This is especially true for gene-centric assemblies, whose resulting sequence can be readily utilized for more focused biological research. Here we describe Kollector, an alignment-free targeted assembly pipeline that uses thousands of transcript sequences concurrently to inform the localized assembly of corresponding gene loci. Kollector robustly reconstructs introns and novel sequences within these loci, and scales well to large genomes – properties that makes it especially useful for researchers working on non-model eukaryotic organisms. Results: We demonstrate the performance of Kollector for assembling complete or near-complete Caenorhabditis elegans and Homo sapiens gene loci from their respective, input transcripts. In a time- and memory-efficient manner, the Kollector pipeline successfully reconstructs respectively 99% and 80% (compared to 86% and 73% with standard de novo assembly techniques) of C. elegans and H. sapiens transcript targets in their corresponding genomic space using whole genome shotgun sequencing reads. We also show that Kollector outperforms both established and recently released targeted assembly tools. Finally, we demonstrate three use cases for Kollector, including comparative and cancer genomics applications. Availability: Kollector is implemented as a bash script, and is available at https://github.com/bcgsc/kollector. Contact:ibirol@bcgsc.ca
Located in Platforms / Scientific Publications
Publication RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.
by Stephanie McInnis published Feb 21, 2017
Background. Chronic fatigue syndrome (CFS) remains poorly understood. Although infections are speculated to trigger the syndrome, a specific infectious agent and underlying pathophysiological mechanism remain elusive. In a previous study, we described similar clinical phenotypes in CFS patients and alternatively diagnosed chronic Lyme syndrome (ADCLS) patients—individuals diagnosed with Lyme disease by testing from private Lyme specialty laboratories but who test negative by reference 2-tiered serologic analysis. Methods. Here, we performed blinded RNA-seq analysis of whole blood collected from 25 adults diagnosed with CFS and 13 ADCLS patients, comparing these cases to 25 matched controls and 11 patients with well-controlled systemic lupus erythematosus (SLE). Samples were collected at patient enrollment and not during acute symptom flares. RNA-seq data were used to study host gene expression, B-cell/T-cell receptor profiles (BCR/TCR), and potential viral infections. Results. No differentially expressed genes (DEGs) were found to be significant when CFS or ADCLS cases were compared to controls. Forty-two DEGs were found when SLE cases were compared to controls, consistent with activation of interferon signaling pathways associated with SLE disease. BCR/TCR repertoire analysis did not show significant differences between CFS and controls or ADCLS and controls. Finally, viral sequences corresponding to anelloviruses, human pegivirus 1, herpesviruses, and papillomaviruses were detected in RNA-seq data, but proportions were similar (P = .73) across all genus-level taxonomic categories. Conclusions. Our observations do not support a theory of transcriptionally mediated immune cell dysregulation in CFS and ADCLS, at least outside of periods of acute symptom flares.
Located in Platforms / Scientific Publications
Scientific Publications from the Personalized Oncogenomics study
by Stephanie McInnis published Feb 21, 2017 last modified Oct 09, 2017 09:26 PM
Located in Projects / Personalized Oncogenomics
Northern biobank will fill health knowledge gaps in rural, First Nations communities
by Stephanie McInnis published Feb 21, 2017
Nadine Caron, associate professor at the University of B.C.’s department of surgery and an academic physician at the University of Northern B.C. was interviewed by Randy Shore, in a recent article in The Province newspaper highlighting the Northern Biobank, Prince George, BC.
Located in About / News Releases
BC scientists play major role in international effort to map the human epigenome
by Stephanie McInnis published Feb 21, 2017
BC scientists and their colleagues from across the globe have made a major leap forward in understanding how the human body’s trillions of cells develop from a single genetic template, and how those genes interact with the environment. A collection of 41 coordinated papers has been published by scientists involved in the International Human Epigenome Research Consortium (IHEC) which shed light on epigenomic processes.
Located in About / News Releases
"Cracking Cancer" on The Nature of Things with David Suzuki, CBC
by Stephanie McInnis published Feb 21, 2017 last modified Feb 23, 2017 04:41 PM
"Cracking Cancer" will debut on February 23rd at 8 PM. With exclusive and rare access, Cracking Cancer follows a group of patients, all with incurable cancer, through the highly experimental clinical trial at the BC Cancer Agency, a trial that holds the promise of personalized cancer diagnosis and treatment.
Located in About / News Releases
Image Flow Cell
by Stephanie McInnis last modified Feb 18, 2017 04:13 PM
Flow Cell used in next Gen DNA sequencing
Located in About / News Releases
Image object code Canada's Genomics Enterprise logo
by Stephanie McInnis last modified Feb 06, 2017 04:31 PM
CGEn logo
Located in About / News Releases