Mapping 250K/500K SNP assay

4 GeneChip ® Mapping 500K Assay Manual
Appendix B: Thermal Cycler Programs Required for 96-Well
Plate Protocol: Includes a list of the thermal cycler programs
required for the 96-Well Plate Protocol.
Appendix C: Low Throughput Protocol: Detailed, step-by-step
protocol for low throughput human genomic DNA sample processing.
Included is a description of quality control checkpoints at various
stages of the protocol which enable array performance to be monitored.
Appendix D: Reagents, Instruments, and Supplies Required for
Low Throughput Protocol: A complete list of the equipment and
reagents required to run the Low Throughput Protocol.
About Whole Genome Sampling Analysis
Long before the completion of the sequence of the human genome, it
was clear that sites of genetic variation could be used as markers to
identify disease segregation patterns among families. This approach
successfully led to the identification of a number of genes involved in
rare, monogenic disorders [1]. Now that the genome sequence has
been completed and is publicly available [2, 3], attention has turned
to the challenge of identifying genes involved in common, polygenic
diseases [4, 5]. The markers of choice that have emerged for wholegenome
linkage scans and association studies are single nucleotide
polymorphisms (SNPs). Although there are multiple sources of
genetic variation that occur among individuals, SNPs are the most
common type of sequence variation and are powerful markers due to
their abundance, stability, and relative ease of scoring [6]. Current
estimates of the total human genetic variation suggest that there are
over 7 million SNPs with a minor allele frequency of at least 5% [7].
The ongoing international effort to build a haplotype map will
identify a standard set of common-allele SNPs that are expected to
provide the framework for new genome-wide studies designed to
identify the underlying genetic basis of complex diseases, pathogen
susceptibility, and differential drug responses [8, 9]. Genome-wide
association studies, which are based on the underlying principle of
linkage disequilibrium (LD) in which a disease predisposing allele cosegregates
with a particular allele of a SNP, have been hampered by
the lack of whole-genome genotyping methodologies [10]. As new
genotyping technologies develop, coupled with ongoing studies into