1 ) we first selected snps to represent variation among 25 widely used classical laboratory strains . the genome was divided into non - overlapping 40 kb intervals and , in each interval , three snps with high minor allele frequency and low missing rate were selected . next we selected snps based on local phylogenetic trees constructed on 100 kb non - overlapping intervals using the 15 niehs strains7 plus c57bl/6j . first , for intervals with > 20 snps in which 30% or more have complete genotypes , we constructed local phylogenetic trees and corrected branch lengths to account for sampling bias in the snp discovery data6(supplementary fig.6 , online ) . in each window , we selected one snp corresponding to each branch in the local tree until either 98% of the variation was represented or a maximum of 22 snps were selected . the threshold of 22 snps allowed us to capture over 98% of the variation in 90% of the intervals , and 95% of the variation in the remaining 10% of intervals ( supplementary fig.7 , online ) . next , for intervals having > 20 niehs snps7 but with less than 30% having complete genotypes , we used the same procedure but used imputed snp genotypes12 . these snps represent 4.9% ( 21,138 ) of the total snps in this strategy . finally , for windows having fewer than 20 niehs snps7 , we selected snps from other sources . therefore , we identified private c57bl/6j snps by comparing the genotypes of six strains used in other snp discovery experiments,27 c57bl/6j , a / j , dba/2j,129x1/svj , 129s1/svimj , and msm / ms . we selected three c57bl/6j singletons in every 1 mb interval . the wild derived strains pwd / phj and molf / eij used in the niehs study7 each carry substantial genomic regions of m. m. domesticus origin6 . in order to identify non - domesticus snps in these regions and to include additional m. m. molossinus variants , we aligned the bac end sequences from msm / ms27 with strains c57bl/6j , a / j , dba/2j , 129x1/svj , and 129s1/svimj . we note that the representative m. m castaneus strain in the niehs panel7 , cast / eij , also has substantial introgression regions but there are no comparable resources to help make up for this deficiency . additional snps were identified by small scale resequencing of other mus species ( m. spretus , m. spicilegus and m. macedonicus ) and m. m. musculus subspecies . snps identified in the niehs study7 that represent the main branches of the chromosome y phylogenetic tree6 were selected . in addition we searched the ncbi database for y chromosome sequences from m. spretus , m. spicilegus and m. macedonicus , snps present in the niehs data7 were eliminated . snps identified in resequencing studies that represent the main branches of the mitochondrial phylogenetic tree were selected . ultraconserved elements ( uce ) are short non - genic sequences with exceptionally high degree of sequence conservation between species . among the 481 uces identified between human and mouse16 we tiled the entire sequence of 238 that were chippable in the c57bl/6j genome . for every annotated exon we selected three probes spanning the proximal , intermediate and distal regions . the majority of exons ( 58% ) ( denoted exon 1 probes ) have probes that are chippable according to affymetrix specifications . we selected probes in most of the remaining exons with unique sequences ( 35% ) , regardless of whether they were chippable using the same procedure ( denoted as exon 2 probes ) . we included probes from sequence reads of msm / ms bac ends that had no corresponding sequence in the c57bl/6j genome . we selected three probes per bac end from the proximal , middle and distal regions . the majorities of these were contiguous and fell into genome regions known to contain segmental duplications17 . this is consistent with the absence of niehs data7 and the failure of probes to satisfy the selection criteria for unique sequences . for these intervals , we identified all chippable probes , either unique or nonspecific , and selected one or two probes per nspi or styi fragment . to identify chippable probes we used the following criteria : 1 ) snp should be on nspi or styi fragments with sizes of 50bp to 1 kb , computed on c57bl/6j reference genome ; 2 ) snp should be at least 10bp away from cut site ; 3 ) there should be no other known snps in  12bp flanking sequences around target snp ; and 4 ) the 33mer centered on the snp must blat as unique with no alignments which have > 28bp matches against c57bl/6j genome . we used the brlmm - p algorithm11 implemented in affymetrix power tools to obtain genotype calls . we then applied a transformation that converts intensities of the a - allele ( sa ) and b - allele ( sb ) into contrast ( as in(k(sasb)/(sa+sb ) ) and strength ( log ( sa + sb ) ) values . the parameter k in this transformation can be adjusted to optimize the contrast between a and b allele intensities . we used k=2 for the test arrays and k=4 for the final mouse diversity array . for genotyping we used only the contrast value , although there is clearly additional information in the strength value . we used the silhouette score18 to assess genotype class separation and we used variance of intensity as a measure of within cluster consistency to guide probe selection . we used 116 samples , including 76 f1 hybrids , many with known genotypes , to train the brlmm - p algorithm . we have observed that performance continues to improve as more samples are added to the training set . we have extensively annotated the mouse diversity array to help users interpret results , integrate array data with other genomic resources , and develop new uses for the array . annotation and information regarding probe performance can be obtained from the center for genome dynamics website ( http://genomedynamics.org/tools/diversityarray.shtml ) . probe contrast , silhouette scores and heterozygous genotype calls in inbred strains are important indicators of individual snp performance . we have flagged poorly performing snps in the annotation files on the basis of their performance . these snps should be ignored or used with caution . in the future , we will annotate snp and igp for performance in additional samples , including wild derived strains from different m. musculus subspecies and other mus species . to identify chippable probes we used the following criteria : 1 ) snp should be on nspi or styi fragments with sizes of 50bp to 1 kb , computed on c57bl/6j reference genome ; 2 ) snp should be at least 10bp away from cut site ; 3 ) there should be no other known snps in  12bp flanking sequences around target snp ; and 4 ) the 33mer centered on the snp must blat as unique with no alignments which have > 28bp matches against c57bl/6j genome . we used the brlmm - p algorithm11 implemented in affymetrix power tools to obtain genotype calls . we then applied a transformation that converts intensities of the a - allele ( sa ) and b - allele ( sb ) into contrast ( as in(k(sasb)/(sa+sb ) ) and strength ( log ( sa + sb ) ) values . the parameter k in this transformation can be adjusted to optimize the contrast between a and b allele intensities . we used k=2 for the test arrays and k=4 for the final mouse diversity array . for genotyping we used only the contrast value , although there is clearly additional information in the strength value . we used the silhouette score18 to assess genotype class separation and we used variance of intensity as a measure of within cluster consistency to guide probe selection . we used 116 samples , including 76 f1 hybrids , many with known genotypes , to train the brlmm - p algorithm . we have observed that performance continues to improve as more samples are added to the training set . we have extensively annotated the mouse diversity array to help users interpret results , integrate array data with other genomic resources , and develop new uses for the array . annotation and information regarding probe performance can be obtained from the center for genome dynamics website ( http://genomedynamics.org/tools/diversityarray.shtml ) . probe contrast , silhouette scores and heterozygous genotype calls in inbred strains are important indicators of individual snp performance . we have flagged poorly performing snps in the annotation files on the basis of their performance . these snps should be ignored or used with caution . in the future , we will annotate snp and igp for performance in additional samples , including wild derived strains from different m. musculus subspecies and other mus species .
we designed a high - density mouse genotyping array containing 623,124 snps that capture the known genetic variation present in the laboratory mouse . 
 the array also contains 916,269 invariant genomic probes that are targeted to functional elements and regions known to harbor segmental duplications . 
 the array opens the door to the characterization of genetic diversity , copy number variation , allele specific gene expression and dna methylation and will extend the successes of human genome - wide association studies to the mouse .