title: A highly informative SNP linkage panel for human genetic studies.
abstract: We have developed a highly informative set of single-nucleotide polymorphism (SNP) assays designed for linkage mapping of the human genome. These assays were developed on a robust multiplexed assay system to provide a combination of very high accuracy and data completeness with high throughput for linkage studies. The linkage panel is comprised of approximately 4,700 SNPs with 0.39 average minor allele frequency and 624-kb average spacing. Based on almost 2 million genotypes, data quality was shown to be extremely high, with a 99.94% call rate, >99.99% reproducibility and 99.995% genotypes consistent with mendelian inheritance. We constructed a genetic map with an average 1.5-cM resolution using series of 28 CEPH pedigrees. The relative information content of this panel was higher than those of commonly used STR marker panels. The potent combination of this SNP linkage panel with the multiplexed assay system provides a previously unattainable level of performance for linkage studies.
authors.affiliation: Illumina, Inc., 9885 Towne Centre Drive, San Diego, California 92121-1975, USA. smurray@illumina.com
authors.forename: Sarah Shaw
authors.initials: SS
authors.lastname: Murray
authors.forename: Arnold
authors.initials: A
authors.lastname: Oliphant
authors.forename: Richard
authors.initials: R
authors.lastname: Shen
authors.forename: Celeste
authors.initials: C
authors.lastname: McBride
authors.forename: Rhoberta J
authors.initials: RJ
authors.lastname: Steeke
authors.forename: Stuart G
authors.initials: SG
authors.lastname: Shannon
authors.forename: Todd
authors.initials: T
authors.lastname: Rubano
authors.forename: Bahram G
authors.initials: BG
authors.lastname: Kermani
authors.forename: Jian-Bing
authors.initials: JB
authors.lastname: Fan
authors.forename: Mark S
authors.initials: MS
authors.lastname: Chee
authors.forename: Mark S T
authors.initials: MS
authors.lastname: Hansen
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D005820:Genetic Testing / Q000379:methods; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid