Analyzing large amounts of data can be a daunting task in any research field; this also includes applying appropriate statistical analyses to ensure the most robust conclusions can be drawn. With many areas of research now generating massive data sets, there is a growing need for accessible and freely available statistical tools. One tool recently developed by Kurbatova et al., PhenStat, is a software statistical software package designed specifically for phenotyping data. The software uses the freely available R package to provide a variety of statistical methods for the identification of phenotypic associations. R is a widely available platform commonly used in bioinformatics.
The PhenStat software itself is specifically designed for the type of high throughput data generated by large research programs, but is also suitable for small and large scale users. The software package has been tested and implemented by the KOMP2 program as part of the International Mouse Phenotyping Consortium (IMPC), which aims to produce knockout mice and carry out high-throughput phenotyping of each line in order to determine the function of every gene in the mouse genome. The consortium and its researchers are increasingly focused on reproducibility, studying both sexes, and using appropriate statistical tools and methodologies. This software aims to provide the best tools to assist in these important efforts by helping researchers produce the most robust analysis. With appropriate and well documented analysis, an increase in reproducibility of results by other parties can be enhanced, which is important for all research, but particularly for in-vivo studies where limiting expensive, redundant, and unnecessary experimentation is essential.
PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data. Kurbatova, N., Mason, J. C., Morgan, H., Meehan, T. F., & Karp, N. A. PloS one. 2014 Jul 6;.10(7), e0131274-e0131274.
NIH-Funded KOMP2 Program Leads the Way in Efforts to Ensure Reproducibility and Enhance Transparency in Research
Researchers funded by the National Institutes of Health’s Common Fund Knockout Mouse Phenotyping Program (KOMP2) are making efforts to improve methods of data collection and reporting in animal research, with the goals of making these processes more accessible and research findings more reproducible. The KOMP2 program, a part of the International Mouse Phenotyping Consortium (IMPC), aims to extensively test and generate data about mice with disrupted, or “knocked out,” genes to help better understand human biology and disease. KOMP2 researchers are examining the clinical and physical characteristics – phenotypes – of mice carrying mutations in approximately 20,000 specific genes across the genome. They hope to systematically describe each gene and its biological function.
In 2010, the United Kingdom National Centre for the Replacement, Refinement, and Reduction of Animals in Research (3R) introduced the ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines . These guidelines were designed to address an emerging problem in biomedical animal studies -- a lack of reproducibility of research results -- and improve the overall communication of research findings. The ARRIVE guidelines consist of a checklist to be used when submitting manuscripts that include animal research. They lay out reporting requirements to ensure all the information is available to allow fully reproducible research.
To enhance and embrace reproducibility in the IMPC large-scale research data collection and analyses efforts, KOMP2-funded investigators modified the ARRIVE guidelines to apply them to the large international database housing all the program data . The investigators described the process and challenges of applying the guidelines to the IMPC database May 20, 2015, in PLoS Biology. Their efforts assessed and documented how each of the IMPC centers carried out experimental procedures; details on how the data were obtained are available for download from the IMPC web portal. Investigators also developed a new and standardized language for the IMPC consortium, allowing all phenotypic data to be described in the same way and compared across research sites.
Applying the ARRIVE Guidelines to an In Vivo Database. Karp N, Meehan T, Morgan H, Mason J, Blake A, Kurbatova N, Smedley D, Jacobsen J, Mott R, Iyer V, Matthews P, Melvin D, Wells S, Flenniken A, Masuya H, Wakana S, White J, Lloyd KC, Reynolds C, Paylor R, West D, Svenson K, Chesler E, de Angelis M, Tocchini-Valentini G, Sorg T, Herault Y, Parkinson H, Mallon A, Brown S. PLOS Biology. 2015 May 20.
Researchers from the International Mouse Phenotyping Consortium (IPMC), an international effort that includes NIH funded researchers from the Common Fund Knockout Mouse Phenotyping Program (KOMP2) have developed an atlas detailing gene expression patterns in 313 different mutant mouse lines. The Consortium as a whole is currently on track to develop 8,500 mutant mice and this manuscript represents one of the first comprehensive glimpses at early expression data coming from this group of investigators. Researchers generated the mutant mouse lines using embryonic stem cells (ESCs) in which the gene of interested is replaced with a so called “reporter gene” in such a way that the reporter mimics the normal expression of the gene of interest. A simple chemical reaction on the samples results in a blue stain where the gene is expressed. This well-known LacZ reporter system can then be used to compare various staining patterns in the mice. These staining strategies were carried out in both whole mount and on frozen sections of male and female mice and embryos. The robustness and repeatability of the lacZ staining in both 3D and in sections confirmed the feasibility of using this reporter to reveal the expression of many poorly annotated genes. The generated atlas includes information on the location and possible function of many genes that currently have unknown functions.
In this study, many large organs, such as the brain, were described in remarkable detail providing new and highly specialized information on the localization patterns of gene expression for many genes. Many organs also had complex and unique staining patterns, for example, not only was a large percentage of all reporter gene expression found in the testis, but 8% of all reporter expression was found restricted exclusively in the testis. One gene with unique expression in the testis was Jazf, which has been previously implicated in endometrial cancer, but has yet to have any known role in testicular function. Overall, the atlas provides an exceptional and comprehensive resource describing the anatomical location of gene expression in mice and provides insight into unique and unknown functions that can be targeted for further study. The full resource, to be completed by the IMPC, will provide even deeper levels of detail and data for the 8,500 knockout mouse lines that will complement this effort and give insight into the roles of thousands of genes in embryonic development, adult physiology, aging, and disease.
A lacZ reporter gene expression atlas for 313 adult KOMP mutant mouse lines. West, D. B., R. K. Pasumarthi, B. Baridon, E. Djan, A. Trainor, S. M. Griffey, E. K. Engelhard, J. Rapp, B. Li, P. J. Jong and K. C. Lloyd. Genome Res. 2015;25(4): 598-607. PMID: 25591789.
Research supported by the Common Fund’s Knockout Mouse Phenotyping Program (KOMP2) has applied a new way to generate conditional knockout mice, which are mice with a gene that can be selectively eliminated in specific cells or tissues at a specific point in time. Led by Dr. K.C. Kent Lloyd, researchers at the University of California Davis modified a technology known as CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeat, that uses components of a bacterial immune system to precisely target genes for deletion (for more information on CRISPR, see this New York Times article) . In this new study, scientists modified the CRISPR system to enhance the specificity of gene targeting while also introducing genetic changes that allow the target gene to be conditionally deleted (or “knocked out”), rather than knocked out in all cells from the beginning of development. Researchers used the new technique to generate a conditional knockout of the Isoprenoid synthase containing domain (Ispd) gene. Mutations in the human ISPD gene are associated with the neurodevelopmental disorder Walker-Warburg syndrome , a severe form of congenital muscular dystrophy affecting the muscles, brain, and eyes, that typically results in death by 3 years of age. Ispd knockout mice die at birth, limiting their effectiveness in scientific research. The conditional Ispd knockout mice may allow scientists to distinguish the effects of Ispd deletion in disease-relevant tissues at different stages of development. Beyond this important gene, however, the new technique may allow easier, faster, and more efficient generation of conditional knockout mice for many genes, both within the KOMP2 project and in labs across the world.
Conditional targeting of Ispd using paired Cas9 nickase and a single DNA template in mice. FEBS Open Biology. Lee, AY and Lloyd, KC. July 2014; 4: 637-42. PMID: 25161872.
Investigators at The Jackson Laboratory have developed a novel approach that enables highly efficient generation of mouse strains from Embryonic Stem (ES) cells. This advance overcomes a major limitation in mutant mouse production; namely, the uncertainty of whether the desired mutation created in ES cells is incorporated into the mouse’s reproductive cells so that it is passed along to offspring. This process has been slow, laborious, and expensive. The Perfect Host technology ensures that chimeras made by injecting ES cells into host embryos have gametes derived only from the ES cells carrying the desired mutation. Thus all offspring are paternally derived from the ES cells and will carry the mutation. This research was made possible through support from The Jackson Laboratory, the Maine Technology Institute, in addition to several NIH Institutes and Centers, including KOMP and the use of KOMP-generated ESC cell lines. This new technology will be extremely useful for the KOMP2 program, by reducing the number of mice needed for each experiment, and greatly increasing the speed and efficiency of mouse production.
Read an interview with KOMP2 awardee Dr. Monica Justice from Baylor College of Medicine, in which she discusses her career path, current work in hematopoietic cancers and genetic syndromes, and future goals for the KOMP2 project. Find out how her early years on the farm inspired a love of biology, what experiences sparked her interest in pediatric medicine, and how she enjoys spending time outside of the lab.
Funding Opportunity Announcement to phenotype embryonic lethal knockout mice from the International Mouse Phenotyping Consortium (IMPC)!
The IMPC, a worldwide consortium that includes KOMP2 as a member, is generating an estimated 20,000 knockout mouse strains, up to 30% of which are expected to be embryonic or perinatal lethal. This funding opportunity announcement invites applications to phenotype embryonic lethal mouse strains with a long term goal of revealing important insights into normal development in addition to a variety of diseases. This funding opportunity is supported by several NIH Institutes and Centers, and is related to, but separate from, the Common Fund’s KOMP2 program.
Read the Funding Opportunity here.
See what KOMP2 has been doing lately! Download slides about KOMP2 history, current status, and future directions here.
Seven new projects receive NIH Common Fund support in fiscal year 2011 via the KOMP2 program. The program is creating a valuable genetic resource for revealing mammalian gene function, providing insight into genes that affect human health and disease.
International Mouse Phenotyping Consortium (IMPC) Policies