Non-Hodgkin’s lymphoma (NHL) is a group of B-cell malignancies that is the 5th most common cancer in males and the 4th most common cancer in females. Three of the four most common histological subtypes of NHL are Diffuse Large B-cell Lymphoma (DLBCL), Follicular Lymphoma (FL) and B-cell Chronic Lymphocytic Leukemia (B-CLL), which together make up over 60% of NHL cases. These diseases vary in both aetiology and aggressiveness, with patient prognosis predicted using indices that rely on biological surrogates in order to predict disease behavior. This results in a large degree of heterogeneity within prognostic groups, with some high-risk patients demonstrating long survival and low-risk patients undergoing rapid transformation and succumbing to an early death. The use of molecular profiling allows interrogation of genetic and transcriptional features of tumor samples that are directly indicative of cellular mechanisms of disease pathogenesis. This is therefore an attractive option for more accurately predicting patient prognosis and thereby allowing design of risk-adapted therapeutic regimes in order to increase survival rates. In this work whole-genome gene expression and single nucleotide polymorphism (SNP) microarrays have been employed in order to interrogate the transcriptome and genome of NHL tumor samples. In order to allow informed analysis of genomic data-sets within the context of gene networks, novel bioinformatic methods were required. This work therefore included the development of novel methods for informed analysis of genome-wide SNP microarray data, visualization of the subsequent gene-set enrichment analysis (GSEA) results, as well as bioinformatic methods for mapping loss-of-heterozygosity without the need for patient-matched control samples. Following development, the utility of these genome-wide approaches for the elucidation of pathogenic mechanisms with the use of small sample sizes was investigated by the interrogation of a novel immunodeficiency disorder. This resulted in our characterization of the first described case of immunodeficiency linked with a chromosomal duplication of the IL25 locus at 14q11.2 and an aberrant Th2-switching mechanism. It also provided proof that whole-genome analyses could be used to determine pathogenic mechanisms of disease.