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Following PCR, multiplex genotyping was performed with pyrosequencing analysis.

For SNP and functional markers, multiplex genotyping was conducted using the SNPstream system (Beckman Coulter, California, USA).

Multiplex genotyping was performed at 15 loci as in (Milinkovitch et al. 2004) using three fluorescent dyes and 'HotStarTaq Plus' polymerase (Qiagen, Venlo, the Netherlands) with the following thermal profile: 95°C 5-min activation step, followed by 28 cycles of denaturation at 95°C for 30 s, annealing at 60 or 62°C for 90 s, and extension at 72°C for 30 s.

Multiplex SNP genotyping was carried out using the Illumina Golden Gate™ assay on custom BeadChips (Illumina Inc., San Diego, CA, USA).

Multiplex SNP genotyping was carried out with the Illumina Golden Gate™ assay on the Sentrix Array Matrix scanned with the Bead Array Reader (Illumina Inc., San Diego, CA, USA).

As a result, the majority of primers used in the multiplex for genotyping were also used for sequencing due to difficulty in finding effective sequencing primers.

(1 -(4): different multiplex PCRs (See Materials and Methods) Genotyping was performed using the SNaPShot multiplex genotyping method described earlier [ 28].

The HPV genotyping was done by multiplex-HPV-genotyping kit (Multimetrix, Progen Biotechnik GmbH, Heidelberg, Germany) as outlined in our recent study [ 20].

Multiplex genotyping assays were then developed for these genes so they could be analysed on an ABI 3130 × l Genetic Analyser (Applied Biosystems, Australia).

High-throughput genotyping was performed by multiplex PCR, as described by Bell et al. (2002) with certain modifications.

Single nucleotide polymorphism genotyping: Genotyping was performed by multiplex PCR of amplicons containing the 52 SNPs followed by the ligase detection reaction (LDR) method of Bruse et al. [16] on a Luminex 200 Multiplex Bio-Assay Analyzer.