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Highly conserved extended haplotypes of the major histocompatibility complex and their relationship to multiple sclerosis susceptibility

S. Goodin. Data curation: Douglas S. Goodin. Formal analysis: Douglas S. Goodin, Pouya Khankhanian, Nicolas Vince. Investigation: Douglas S. Goodin. Methodology: Douglas S. Goodin, Pouya ... Khankhanian, Pierre-Antoine Gourraud, Nicolas Vince. 20 / 23 Software: Douglas S. Goodin, Pouya Khankhanian. Supervision: Douglas S. Goodin. Visualization: Douglas S. Goodin. Writing ± original draft

Single Nucleotide Polymorphism (SNP)-Strings: An Alternative Method for Assessing Genetic Associations

Background Genome-wide association studies (GWAS) identify disease-associations for single-nucleotide-polymorphisms (SNPs) from scattered genomic-locations. However, SNPs frequently reside on several different SNP-haplotypes, only some of which may be disease-associated. This circumstance lowers the observed odds-ratio for disease-association. Methodology/Principal Findings Here...

Genetic contribution to multiple sclerosis risk among Ashkenazi Jews

Background Multiple sclerosis (MS) is an autoimmune disease of the central nervous system, with a strong genetic component. Over 100 genetic loci have been implicated in susceptibility to MS in European populations, the most prominent being the 15:01 allele of the HLA-DRB1 gene. The prevalence of MS is high in European populations including those of Ashkenazi origin, and low in...

Sequencing of the IL6 gene in a case–control study of cerebral palsy in children

Background Cerebral palsy (CP) is a group of nonprogressive disorders of movement and posture caused by abnormal development of, or damage to, motor control centers of the brain. A single nucleotide polymorphism (SNP), rs1800795, in the promoter region of the interleukin-6 (IL6) gene has been implicated in the pathogenesis of CP by mediating IL-6 protein levels in amniotic fluid...

iCTNet: A Cytoscape plugin to produce and analyze integrative complex traits networks

Background The speed at which biological datasets are being accumulated stands in contrast to our ability to integrate them meaningfully. Large-scale biological databases containing datasets of genes, proteins, cells, organs, and diseases are being created but they are not connected. Integration of these vast but heterogeneous sources of information will allow the systematic and...

HLA Diversity in the 1000 Genomes Dataset

The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation by sequencing at a level that should allow the genome-wide detection of most variants with frequencies as low as 1%. However, in the major histocompatibility complex (MHC), only the top 10 most frequent haplotypes are in the 1% frequency range whereas thousands of haplotypes are...

In depth comparison of an individual’s DNA and its lymphoblastoid cell line using whole genome sequencing

Background A detailed analysis of whole genomes can be now achieved with next generation sequencing. Epstein Barr Virus (EBV) transformation is a widely used strategy in clinical research to obtain an unlimited source of a subject’s DNA. Although the mechanism of transformation and immortalization by EBV is relatively well known at the transcriptional and proteomic level, the...

Blood RNA profiling in a large cohort of multiple sclerosis patients and healthy controls

Multiple sclerosis (MS) is the most common autoimmune disease of the central nervous system (CNS). It is characterized by the infiltration of autoreactive immune cells into the CNS, which target the myelin sheath, leading to the loss of neuronal function. Although it is accepted that MS is a multifactorial disorder with both genetic and environmental factors influencing its...

Genetic variation in the odorant receptors family 13 and the mhc loci influence mate selection in a multiple sclerosis dataset

Background When selecting mates, many vertebrate species seek partners with major histocompatibility complex (MHC) genes different from their own, presumably in response to selective pressure against inbreeding and towards MHC diversity. Attempts at replication of these genetic results in human studies, however, have reached conflicting conclusions. Results Using a multi...