Additional file 1:

Chromosome 16 banding nomenclature and signal localization of clone WI2-1621D20 in anthropoids. Indicated are the FISH signal localizations of clone WI2-1621D20 (red) on chromosome 16 in great apes and human. Human chromosome 16 nomenclature according to ISCN (2005). Chromosome 16 banding pattern of great apes (PTR, GGO and PPY) according to Goidts et al. (2005). Chromosome 16 banding nomenclature of great apes according to ISCN (1985) and adjusted to the human chromosome 16 banding nomenclature. Black bars represent the evolutionary breakpoints as described by Goidts et al. (2005). References: ISCN (2005): An international system for human cytogenetic nomenclature. Shaffer LG, Tommerup N (eds): S. Karger, Basel 2005. ISCN (1985): An international system for human cytogenetic nomenclature. Harnden DG, Klinger HP (eds): S. Karger, Basel 1985. Goitds V, Szamalek JM, de Jong PJ, Cooper DN, Chuzhanova N, Hameister H, Kehrer-Sawatzki H.: Independent intrachromosomal recombination events underlie the pericentromeric inversion of chimpanzee and gorilla chromosomes homologous to human chromosome 16, Genome Res 2005, 15(9): 1232–42

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Additional file 2:

Evolutionary distances overview. Based on the Kimura two-parameter model the average number of nucleotide substitutions per site (K) were calculated for outgroup distances: all human sequences to macaque sequences (HSA to MMU), all human non-ancestral paralogs to the macaque outgroup (MMU to Para) and the human ancestral duplicon to the macaque outgroup (MMU to Anc). Comparison of these values with two human interparalog distances, i.e. human ancestral to all human paralogs (Anc to Para) and the average K of all human paralogs (all Para), provides information on the timing of the initial duplicationevent (Macaque Seed) and the onset of secondary duplications (Macaque Swaps). We calculated locus-specific effective nucleotide substitution rates (r = K/2 T) based on an estimated divergence time of 25 million years between the human and the Old World monkeys. In addition, all calculations were performed replacing the human lineage by the chimpanzee lineage.

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Additional file 3:

Sequence Identity Matrix of sequences used for the phylogenetic analysis. We created a sequence identity matrix of all sequences, which were used for our phylogenetic analysis. Multi-sequence alignments were composed of 1951 basepairs derived from two loci within the CHEK2 duplicons. The proximal sequence is located upstream of exon 1 of TTC28 (NT_011520: 8465388–8465900) and the distal sequence is located within intron 14 of CHEK2 (NT_011520: 8478430–8480219). The sequence identity matrix of these sequence alignments was generated with the BioEdit software (version 7.0.0).

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Additional file 4:

qPCR predicted CN calculations. qPCR reactions were performed in duplicate. Copy number mean, standard deviation (SD) and standard error (SE) were calculated for all analysed human (HSA), chimpanzee (PTR), gorilla (GGO), orangutan (PPY), rhesus macaque (MMU), pig-tailed macaque (MNE) and baboon (PHA) normalised samples. Standard errors of the normalised CHEK2 copy numbers were calculated from the standard deviations of the values of the CFTR and CHEK2 genes using the formula provided by the user menu (ABI Prism 7700 Sequence Detection System, User Bulletin no.2 1997, p.34). P-values were calculated by a 2-tailed Student t-test.

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