Marker Information
for
Human Whole Genome STRP Linkage Scans

CIDR performs 10 cM genome scan analysis on human DNA using automated fluorescent microsatellite analysis. The CIDR marker set is composed primarily of trinucleotide and tetranucleotide repeats. The marker set has evolved over the years but was originally based on the Marshfield Genetics version 8 screening set available for purchase from Research Genetics. The current CIDR marker set consists of approximate 400 primer pairs with average spacing of 9 cM throughout the genome. There are no gaps in the map larger than 18 cM. The average marker heterozygosity is 0.76. Approximately 16% of the marker loci are different between the current CIDR marker set and version 8. All reverse primer sequences have been modified from the version 8 sequences in order to reduce '+A' artifacts. The resulting PCR products are sized using a capillary sequencing platform. CIDR multiplexes at both the pre- and post-amplification stages.

The markers are organized into 38 panels (10-fold multiplexing post-amplification). Each primer pair has undergone extensive optimization to improve performance and reliability. Marker optimization is accomplished by varying the type of Taq enzyme (we currently use Taq Gold from Applied Biosystems and Platinum Taq from Invitrogen), the amount of primer, and the thermocycling parameters.

Download the Marker Set

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