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2018 Scientific Report

  • Text
  • Institute
  • Biology
  • Methylation
  • Molecular
  • Mechanisms
  • Epigenetic
  • Michigan
  • Vari
  • Scientific

Genomics Core MARIE

Genomics Core MARIE ADAMS, M.S. Ms. Adams earned an M.S. in genetics from Iowa State University and is an expert in the latest next-generation sequencing techniques. She joined VARI in September 2016 from the University of Wisconsin Biotechnology Center, where she managed the next-generation sequencing core. SERVICES The Genomics Core provides a comprehensive catalog of sequencing, genotyping, and cytogenetic services to support research into the genomic, transcriptomic, and epigenomic bases of diseases such as cancer and neurodegenerative disorders. Core staff collaborate with over 45 VARI and external investigators to design and implement robust protocols and experimental design. STAFF Julie Koeman, B.S., C.G.(ASCP) CM Lori Moon, E.M.B.A. Mary Rhodes, B.S. STUDENT Sarah Harrie Sequencing services offered include whole-genome, exome, and targeted DNA sequencing; mRNA expression, total RNA transcriptome, translatome, and targeted RNA sequencing; and ChIP-seq, methyl-seq, whole-genome bisulfite sequencing, and targeted bisulfite sequencing, all using Illumina sequencing platforms. Additionally, single-cell and long-read sequencing are facilitated through the 10X Genomics Chromium system. We constantly evaluate new assays to provide the most up-to-date service in this evolving field. High-throughput genotyping services are performed using the Illumina iScan system and include the MethylationEPIC Array, Omni-series genome and exome arrays, Neuro Consortium array, and QC array. Other arrays are easily accommodated on request. We are also available for qPCR and SNP assays. Cytogenetic capabilities include FISH probe creation, validation, and analysis; chromosome breakage studies; transgene localization; and trisomy 8 and 11 mouse embryonic stem cell screens. 50 | VAN ANDEL RESEARCH INSTITUTE SCIENTIFIC REPORT

Bioinformatics and Biostatistics Core MEGAN BOWMAN, Ph.D. Dr. Bowman earned her Ph.D. from the University of Wisconsin – Madison. She completed postdoctoral research in genomics and bioinformatics with the United States Department of Agriculture and Michigan State University prior to joining VARI in 2016. SERVICES Established in April 2013, the Bioinformatics and Biostatistics Core serves the analytical needs of VARI by providing high-quality computational and statistical support to the research laboratories. The broader mission of the BBC is to strengthen and advance bioinformatics and biostatistics at VARI through collaboration, education, and methods development. STAFF Benjamin Johnson, Ph.D. Zachary Madaj, M.S. Lori Moon, E.M.B.A. * Mary E. Winn, Ph.D. Emily Wolfrum, M.P.H. * Formerly manager of the BBC, now Program Manager in the Office of the Cores. The BBC provides statistical consulting and experimental design, including sample size determination and randomization procedures, and we analyze a wide variety of data related to next-generation sequencing, such as genomic variant detection and annotation, differential expression, DNA copy number determination, and differential methylation analyses. We offer expertise in systems-level analysis, including gene-set and network-based analyses, time-series data, tumor growth, drug response, and other small or large data sets using appropriate statistical and computational methods. We also assist in the preparation of research grants, manuscripts, and data deposition. The Core focuses on reproducibility and rigor via robust statistical design, analysis, and the maintenance of version-controlled source code. We support the greater educational mission of the Institute, helping students and staff develop an analytic approach and skills in experimental design through seminars, lectures, and workshops. VAN ANDEL RESEARCH INSTITUTE SCIENTIFIC REPORT | 51

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