D888 Nucleic Acids Research, 2012, Vol. 40, Database issue strains (7,8). Taken together with high-quality phenotype data, transcriptome and dense genotypic data enable the identiﬁcation of regions of the genome that may be causal to a phenotype of interest through correlative analyses. Sanger SNPs, indels and structural variants will be added to MPD and made available in the coming months. MPD history, standards, schema and other topics have been presented elsewhere (9–11). Here, we review a few salient points regarding MPD contents. The recommended basic study design is a strain survey format, e.g. 10 females and 10 males of a large number of genetically stable, re- producible strains (such as inbred strains). Acquired data sets are annotated and formatted to meet a set of deﬁned MPD standards. Each data set is accompanied by a detailed protocol; health status and environmental param- eters of the test animals; and any other information essen- tial to understanding and evaluating the data. Data and documentation are then bundled together into an MPD ‘project’, which is given a descriptive title and annotated with submitter information, references and funding acknowledgements. MPD phenotypic data sets are typically quantitative, although we do house categorical data such as MHC haplotypes and a growing collection of annotated images. Data from microarray gene expression studies are considered a special class of phenotype data and handled accordingly. Summary statistics are computed as part of the MPD accessioning process, where the unit of analysis is an MPD ‘measurement’ with strain (by sex) being the analysis group. Each measurement in a data set is classiﬁed and integrated in the MPD phenotype category structure. Male and female data are not combined. Data from different MPD measurements are not averaged together although these data may be dis- played in the same plot for comparison (composite/con- sensus view). As part of the accessioning process, regression analysis is performed on all measurements (pair-wise) to identify compelling correlations, which may indicate common genetic determinants or overlapping biological pathways. Results are stored to optimize and support queries based on correlations. Strain genotypes are collected and stored in MPD so that phenotypic and genotypic data can be linked or visually juxtaposed, facilitating the ability to determine how allele-speciﬁc variations translate to variation in mouse phenotype. Our last NAR update was published in 2009 (11). Here, we summarize new data and data types, and describe major improvements in MPD functionality. This update refers to Supplementary Data. CONTENTS ‘MPD current contents’ are summarized in Table 1, and a snapshot of ‘What’s New’ is shown in Table 2. Users can search the database by our keyword search, or browse by strain, phenotype category, data submitter, interventions, study design and other convenient groupings (Supplementary Data, Navigation and Finding Data: S1–S8). Brieﬂy, over 750 strains of mice are represented Table 1. MPD current contents Phenotype measurements (including pending) [S7] collectively 600 strains SNPs [S11] Total calls (excluding imputed) Genomic locations Number of strains with data Gene expression strain surveys [S12] Number of probesets Strains [S2, S3] Strain types Inbred Recombinant inbred strains F1 hybrids Wild-derived inbred Chromosome substitution strains Other Recombinant inbred panels AKXD AXB BXA BXD BXH CXB ILSXISS LGXSM SWXJ Chromosome substitution panels C57BL/6J-Chr#A/J/NaJ C57BL/6J-Chr#PWD/Ph/ForeJ Animal vendors and repositories Animal Resources Centre (AUS) B&K Universal (UK) Charles River Harlan Laboratories The Jackson Laboratory Nihon Clea, Tokyo (Japan) Pasteur Institute (France) RIKEN BioResource Center (Japan) National Institute of Genetics—Shigen (Japan) Taconic 3000 350 million 8+ million 450+ 8 280K 761 208 330 87 70 38 28 9 2 23 19 10 in MPD with phenotypic and/or genotypic data available. Strain names are kept updated with current nomenclature, and linkouts to other databases are provided. Table 1 provides an inventory of strains, strain panels and strain sources (also Search or Browse Strains: S1, S2, S3). Investigators associated with MPD as data contributors or as formal collaborators represent approximately 150 institutions from 14 countries supported by over 80 funding agencies and research foundations worldwide (Investigators: S4; Large-Scale Initiatives: S5). Phenotype data MPD contains approximately 3000 phenotypic strain survey measurements, collectively representing approxi- mately 600 of the 750+ strains in MPD (Find Measurements: S6, S7, S8). Most measurements (70%) include data for both sexes. On an average, 20 strains are tested per measurement, but as many as 72 strains have been tested in a single project (CGDpheno1, pending). Currently available phenotypic measurements are classiﬁed as baseline (64%), aging-related data (14%) or controlled studies of intervention effects