HLA associations with cervical cancer histopathological type, and HPV genotype, for alleles scoring <i>P<</i>0.005 in at least one sub-analysis.

<p>HLA associations with cervical cancer histopathological type, and HPV genotype, for alleles scoring <i>P<</i>0.005 in at least one sub-analysis.</p

Characteristics of cervical neoplasia cases in participating study populations following quality control steps.

<p>Characteristics of cervical neoplasia cases in participating study populations following quality control steps.</p

Conditional logistic regression analysis of imputed HLA alleles for the overall dataset for alleles scoring <i>P<</i>10⁻⁵ in either the primary analysis or after conditioning on stated variants.

<p>Conditional logistic regression analysis of imputed HLA alleles for the overall dataset for alleles scoring <i>P<</i>10⁻⁵ in either the primary analysis or after conditioning on stated variants.</p

Accuracy of HLA typing by imputation compared with directly genotyped findings at two–and four-digit resolution.

<p>Accuracy of HLA typing by imputation compared with directly genotyped findings at two–and four-digit resolution.</p

Pairwise linkage disequilibrium (<i>r</i>²) plot of HLA alleles associated with cervical cancer.

<p>HLA alleles have been clustered according to their pairwise linkage disequilibrium on both the x- and y-axes. On the left-hand y-axis they are labelled as to whether they are risk or protective alleles in the overall cervical cancer dataset, and on the top x-axis according to whether they are HLA Class I or II alleles.</p

Zoom plot of the MHC showing association with cervical neoplasia.

<p>SNP associations are reported as filled-in dots, HLA amino-acid associations as hollow diamonds (<i>P</i>-values are for omnibus test of association at specific amino-acid positions). Colours represent extent of linkage disequilibrium with the HLA amino-acid(s) or SNP stated in the figure. (A) The linkage disequilibrium with amino acids at positions 13 and 71 that form part of the p4-pocket of HLA-DRB1. Reading from the p-telomere the HLA loci at which amino-acid constituents have been imputed are <i>HLA-A</i>, <i>-C</i>, <i>-B</i>, <i>-DRB1</i>, <i>-DQA1</i>, <i>-DQB1</i>, <i>-DPA1</i> and–<i>DPB1</i>. Allele-specific HLA type associations are given in the right hand plot. (B) Cervical neoplasia MHC association results having conditioned on amino acid positions 13 and 71 in HLA-DRB1. Linkage disequilibrium with the next largest association amino acid position 156 at HLA-B is shown. (C) Cervical neoplasia MHC association results having conditioned on amino acid positions 13 and 17 in HLA-DRB1 and 156 in HLA-B. No significant association remains.</p

Manhattan plot of genome-wide association study of cervical neoplasia.

<p>Manhattan plot of genome-wide association study of cervical neoplasia.</p

Conditional logistic regression analysis of imputed HLA amino acids at HLA-B position 156 (B_156), HLA-DRB1 position 13 (DRB1_13) and 71 (DRB1_71).

<p>Conditional logistic regression analysis of imputed HLA amino acids at HLA-B position 156 (B_156), HLA-DRB1 position 13 (DRB1_13) and 71 (DRB1_71).</p

Positive and negative predictive values for cervical neoplasia for centiles of genetic risk scores.

<p>Error Bars denote 2 standard deviations based on 10-fold cross validation.</p