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Meeting Report of the 26Th International Mammalian Genome Conference Mamm Genome (2013) 24:179–189 DOI 10.1007/s00335-013-9455-1 Meeting report of the 26th International Mammalian Genome Conference Melissa A. Musser • Steven C. Munger • Teresa M. Gunn Received: 26 February 2013 / Accepted: 23 April 2013 / Published online: 15 May 2013 Ó Springer Science+Business Media New York 2013 Introduction enable us to expand the scope of our research questions and the mammalian systems we use to answer them. At the A diverse group of geneticists, clinicians, and bioinfor- same time, the Verne Chapman Lecture provided valuable maticians converged on sunny St. Pete Beach, Florida, historical perspective on the role of mammalian models October 21–24, 2012, for the 26th International Mamma- over the last half-century, and predicted the future oppor- lian Genome Conference (IMGC). Organized by Michelle tunities and challenges facing geneticists in the next 50 Southard-Smith (Vanderbilt University) and Teresa Gunn years. Abstracts from the meeting are available at (McLaughlin Research Institute) with help from the IMGS www.imgs.org, and online databases and resources pre- Secretariat, the conference attracted 148 participants from sented at the meeting are listed in Table 1. 14 countries. Investigators, postdoctoral fellows, and graduate students returned to the site of the popular 11th IMGC (1997) to share exciting advances in mammalian The power of genetics genetics and genomics research, findings that underscored the continued and future importance of mammalian genetic The power of High Throughput Sequencing (HTS) was on models to human genetics and disease research. Multiple full display at this year’s conference. Multiple groups presenters highlighted how powerful large-scale mapping successfully applied exome or whole-genome sequencing and phenotyping resources, disease models, and strain to identify spontaneous and ENU-induced mutations, while resequencing projects are fundamentally altering our others utilized deep RNA sequencing in genetically diverse understanding of gene regulation and the genetic factors mice to add new insights to transcriptional control. In an underlying complex disease. The plenary presentations intriguing plenary presentation, Greg Barsh (O-8, Hud- especially provided insight on how these new technologies sonAlpha Institute for Biotechnology and Stanford Uni- versity) illustrated how HTS technologies were opening up new opportunities to study classic genetic questions such as M. A. Musser and S. C. Munger contributed equally to this report. coat color patterning in nonmodel organisms like zebra and cheetahs. Along the same vein in a later plenary presen- M. A. Musser Division of Genetic Medicine and Center for Human Genetics tation, Vadim Gladyshev showed how HTS technologies Research, Vanderbilt University, Nashville, TN, USA enabled his group to identify a set of unique genome fea- e-mail: [email protected] tures and molecular adaptations that likely underlie the extremely long life span of the strange-looking but scien- S. C. Munger The Jackson Laboratory, Bar Harbor, ME, USA tifically adorable naked mole rat. Indeed, it was evident e-mail: [email protected] throughout the conference that HTS is pervading all areas of mammalian genetics research, and as costs continue to & T. M. Gunn ( ) fall, deep sequencing data will likely become the norm McLaughlin Research Institute, 1520 23rd St. South, Great Falls, MT 59405, USA rather than exception. With this wealth of information e-mail: [email protected] comes complexity and potential analytical traps, and 123 180 M. A. Musser et al.: 26th International Mammalian Genome Conference Table 1 Internet resources and databases presented at the 26th IMGC Resource Web address Brief description (associated abstract numbers) Mouse genome sequence, functional annotation data Genome reference consortium http://genomereference.org Mouse genome reference assembly (O-2, P-3) Mouse genomes project http://sanger.ac.uk/resources/mouse/genomes/ Full genome sequences for 17 inbred strains (O-1) Mouse genome informatics (MGI) http://informatics.jax.org Curated mouse gene and phenotype database (P-19, P-36) Fantom5 project http://fantom.gsc.riken.jp/zenbu Catalog of transcription start sites (TSS) for several model organisms (O-4) CrePortal http://creportal.org Expression and activity data for Cre transgenes and knock-in alleles (O-15) Mouse tumor biology (MTB) database http://tumor.informatics.jax.org Information on tumors, susceptibility, pathology in mice; includes patient derived xenograft (PDX) data; interactive QTL viewer (P-9, P-10) Mutant mouse resources and data International mouse http://mousephenotype.org Systematic phenotype data available for phenotyping consortium (IMPC) hundreds of mutant mouse lines (O-31, P-5, P-6, P-19, P-46) Sanger mouse genetics project http://sanger.ac.uk/mouseportal/ Portal to Sanger resources, including vectors, targeted and gene-trap cell and mouse lines, phenotype data (O-29, P-55, P-56, SO-9) Mouse mutant resource (MMR) http://mousemutant.jax.org Spontaneous mouse mutants available for study (O-5, O-6, O-7) Knockout mouse http://komp.org/ Resources for generation and distribution project (KOMP and KOMP2) of knockout mice, ESC lines, and vectors (P-40) International mouse strain resource (IMSR) http://findmice.org Searchable online database of mouse strains, stocks, and mutant ES cell lines available worldwide (P-52) European mouse mutant http://emmanet.org Mutant mouse repository and free mutant archive (EMMA) line archiving services (P-25, P-51) International mouse knockout consortium (IMKC) http://knockoutmouse.org Development of knockout mice that cover protein-coding genes and microRNA (P-46) Rare and orphan disease center http://research.jax.org/rodc Collaborative effort to make mouse models of disease commercially available (P-8) Collaborative cross and diversity outbred mouse resources Collaborative cross (CC): http://csbio.unc.edu/CCstatus/ Development status of CC strains; UNC compgen tool suite computational tools for analysis of CC and inbred strains (SO-8, SO-10, P-39, P-14, P-37) Diversity outbred (DO) stock: http://do.jax.org Repository for DO datasets and analytical data and analytical tools tools (O-3, O-10, O-32, O-46) attendees were cautioned against taking a ‘‘one reference association studies (GWAS) expand, it is clear that vali- aligns all’’ strategy when applying HTS methodologies to dation studies in nonhuman animal models, most likely the genetically heterogeneous mouse and human populations. laboratory mouse, will be a critical component of gene As HTS technologies mature and human genome-wide discovery and drug validation pipelines. While new large- 123 M. A. Musser et al.: 26th International Mammalian Genome Conference 181 scale resources and genomic technologies now make in- reconstructions and inbreeding coefficients for mice from depth genetic studies possible for almost any species, the the Collaborative Cross (CC). Several other talks reported mouse arguably remains the most powerful mammalian on studies incorporating CC mice, including Wenqi Pan’s model system. work on evaluating sperm quality across founder strains (SO-13) and Aysar Nashef’s study on susceptibility to alveolar bone loss during infection (SO-19). Chen-Ping Fu Bioinformatics Workshop (SO-8) discussed the development of an online genetic quality control resource for determining the strain com- Large-scale phenotype and genotype resources continue to position of mutant mouse strains. Morag Lewis (SO-9) increase in size and complexity, and it is clear that the described her work using array competitive genomic successful integration of high-dimensional data will be hybridization (array CGH) and whole-exome sequencing to essential to understanding disease susceptibility, mecha- identify spontaneous mutations in the Sanger Institute’s nism, and prognosis. Therefore, the next generation of Mouse Genetics Project (MGP). Although the MGP focu- geneticists will need a new set of quantitative and com- ses on creating knockout allele mice, some mice have putational competencies. An opportunity to gain these pathological phenotypes that do not segregate with the skills was provided by the optional Bioinformatics Work- knockout allele. These phenotypes are caused by sponta- shop that once again preceded the main conference. Since neous mutations that arose in the embryonic stem (ES) cell 2003, instructors have trained attendees on how to navigate lines used for gene targeting, and the mutant mice represent established and new genomic databases to find data perti- novel disease models. nent to one’s research. The conference organizers wish to Other students and postdoctoral fellows have utilized the extend their gratitude to Deanna Church, who steps down mouse as a human disease model. Christine Rubinshteyn after 10 years serving as coinstructor with Carol Bult. Dr. (S-O3) presented work identifying the Oprd1 (opioid- Church has passed the torch to Laurens Wilming, who will receptor, delta 1) as a gene influencing alcohol metabolism. work with Dr. Bult to ensure that next year’s workshop in Apcmin/? mice serve as a model for colon cancer and Salamanca will be as informative as the past 10. Heather Mentrup (SO-2) examined how differential ITCH expression in these and other mouse models affects gut epithelium lineage proportions and proliferation. Min-Hy- Training geneticists for the post-genomic age ung Lee (SO-11) presented computational and molecular work identifying CDCA7L as a male-specific genetic As
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