Framework linkage groups were created by omitting the skewed markers from the data for all the linkage groups except G7, due to the high degree of skewed markers in this group (see Results section).
This population was used to generate the base data for the consensus linkage map for the species (Weeden et al., 1998).
To prepare the cancer data for linkage at the county level and to obtain data on covariates we recorded for each woman's and man's case of cancer, age, race, and year of diagnosis, year of death, and county of residence from the SEER.
We used the Merlin software (Abecasis et al. 2002) and a fully penetrant, recessive model of inheritance to analyze the data for parametric linkage.
Furthermore, we conducted a cohort study and a self-controlled case series (SCCS) analysis in girls from 20 general practitioners (GPs) who agreed to provide data for linkage with the vaccination registry to assess the association between HPV vaccination and migraine.
DNA reports, locus summaries, and final reports were generated for downstream analysis using the BeadStudio software (Illumina Inc .. AFLP, RAPD, SSR, and ESTP marker data previously used for linkage mapping in the two species [ 20, 41, 42] were considered together with the new SNP data for constructing linkage maps.
Presence/absence patterns of RAD alleles furnish the basic data for linkage map construction, SNP variation within the 40-base RAD alleles enables integration of paternally- and maternally-informative linkage maps, and longer sequences adjacent to the RAD alleles provide enough information for cross-species comparisons.
Although methods for the linkage of data within public health agencies to inform health policy are well established [ 12], data linkage is generally not routinely performed to improve the quality of infectious disease surveillance data.
The subgroup characteristics are given in Table S1, and the complete nonparametric linkage data for the Total group and all four subgroups are provided in Text S1, S2, S3, S4 and S5.
High Resolution Melting (HRM) analysis was also used to obtain SNP genotyping data for linkage map construction; the SNPs identified in this way are henceforth referred to as "hrmSNPs".
