VAI’s Pathology and Biorepository Core (PBC) integrates anatomic pathology expertise with biorepository and biospecimen science for investigator- and project-driven research. The Core builds upon strengths in standard histology, microscopy, molecular processing, and biobanking, along with novel technologies to test and apply best practices in biospecimen science. The Core’s focus on pathology and molecular quality metrics provide complementary emphasis on high-quality biospecimens and interpretable results with which to validate experimental models and extend them to clinical samples, thereby advancing the Institute’s mission to improve the health and enhance the lives of current and future generations.

The Pathology and Biorepository Core is led by Dan Rohrer, Core Director, and Dr. Galen Hostetter, Director of Pathology, a board-certified pathologist with NIH fellowship training in medical genetics. The PBC has been accredited by the College of American Pathologists (CAP) since 2012.

Core provides iPSC cell culture laboratory with access to curated and validated iPSC lines for neurodegeneration research. Provides robotic and fully automated high-content imaging system to perform high-throughput screening on living brain cells (iPSC derived through reprogramming) to understand the mechanisms behind neurodegeneration at the molecular level.

Van Andel Institute (VAI) is committed to conducting high-quality animal research in an ethical and responsible manner to advance science and improve human health. The VAI Vivarium provides state-of-the-art housing, care, and support for mouse, rat, and zebrafish models, serving VAI investigators, collaborators, and the broader research community.

The facility maintains the highest level of biosecurity for rodent barrier housing and is designed to support rigorous, reproducible research. All animal procedures are performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals. The Institute’s program is fully accredited by the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) International, reflecting the highest standards of animal care and welfare.

The VAI Flow Cytometry Core provides cell analysis and sorting services. We have a Cytek Aurora, Beckman Coulter CytoFLEX S, Attune CytPix, SONY MA900, and a BD FACSSymphony S6

Full service Next Generation Sequencing, Single Cell Genomics, and Spatial Transcriptomics facility. Provides the services in:
- experimental design support
- NGS library generation
- Illumina, Element and Nanopore Sequencing
- single cell preparation and library generation
- spatial slide preparation and imaging
- spatial transcriptomic and epigenomic profiling

The VAI Mass Spectrometry Core (MSC) is committed to developing scientific partnerships with research labs to develop and deploy LC/MS and GC/MS methods specifically tailored to meet the needs of every project. The MSC houses a comprehensive suite of technologies and staff expertise to deliver high quality metabolomics, lipidomics, and proteomics capabilities to VARI scientists and collaborators. The process begins with experimental design support to ensure samples are handled properly, necessary controls are included, and the study is sufficiently powered. Analytical capabilities are combined with custom informatics and statistics solutions to enable faster analysis and more approachable data interpretation. Specific capabilities in the MSC include:

Metabolomics and Lipidomics – Three liquid chromatography-mass spectrometry (LC/MS) systems (Thermo Orbitrap ID-X, Thermo Orbitrap Exploris 240, and Agilent 6470 QQQ) and three gas chromatography (GC)/MS systems (Agilent 5977b (2), Thermo 7610 ISQ) are dedicated to small molecule analysis. These instruments deploy an array of standard methods, annotated with a chemical library of over 1000 compounds, to maximize compound coverage in every sample. For metabolomics these methods routinely detect 200+ compounds including TCA cycle intermediates, glycolysis, nucleotides, amino acids, urea cycle, vitamins, cofactors tryptophan/kynurenine metabolism, acyl-CoA’s, acyl-carnitines, polyamines, and others. For lipidomics, 500+ lipid species are routinely annotated including phospholipids, ceramides, triacylglycerides, cardiolipins, cholesterol esters, and more. These methods can be operated in an untargeted manner, allowing for screening for biomarkers and novel metabolites/lipids, and in the context of stable isotope tracing, which allows for assessment of metabolic movement. Further, in line with the scientific partnership mission of the MSC, custom methods are routinely developed to quantitate project-specific compounds of interest.

Proteomics – Two nano LC/MS systems (Orbitrap Eclipse and Orbitrap Exploris 480) are dedicated to protein analysis. The expertise and instrumentation will readily make available many proteomics applications including bottom-up quantitative proteomics, tandem mass-tag proteomics, post-translational modification analysis (including phosphoproteomics and histone PTM characterization), protein-protein interactions, intact protein structural elucidation, and more..

Bioinformatics – The MSC has a staff bioinformatician who is dedicated to developing and maintaining informatics pipelines for mass spectrometry data analysis and visualization. This custom data visualization platform transforms daunting excel documents into communicative and interactive figures. Additional layers of data and analysis available through an intuitive user interface, researchers can dive as deep into metabolic pathways and quantitative analyses as demanded by their research questions. Flexible and comprehensive data reporting allows clients to download processed data in excel as well as figures for publication and presentation. The bioinformatician further enables project specific informatics and statistics solutions to ensure robust and informative results for every research question.

Major equipment in the facility includes:
• Thermo Scientific Orbitrap ID-X LC/MS
• Thermo Scientific Orbitrap Exploris 240 LC/MS
• Thermo Scientific Orbitrap Eclipse nanoLC/MS
• Thermo Scientific Orbitrap Exploris 480 nanoLC/MS
• Agilent 6470 Triple Quadrupole LC/MS
• Agilent Infinity 1290II UPLC
• Agilent 5977B GC/MS (2)
• Thermo Scientific ISQ7610 EI/CI enabled GC/MS

The VAI Bioinformatics and Biostatistics Core provides comprehensive, high-quality bioinformatics and statistics expertise for the Van Andel Institute and external organizations.

The Core develops and maintains automated and customizable workflows for processing and analyzing many types of genomic data; supports the design of rational, robust and reproducible experiments and proposals; assists in the preparation of manuscripts, grants and presentations; and provides education and training in the use of cutting-edge software and analysis methods. The Core can contribute to many types of bioinformatics or statistical projects.

The mission of the VAI Transgenic Core is to provide genetically modified animal models for our collaborators in support of their research.

When these models are preexisting this provision can take the form of rederivation or reconstitution for the purpose of importing animals into our Vivarium’s barrier.

In the absence of preexisting models our Core works closely with partnering labs to generate their ideal mutation de novo, often using CRISPR technology. Usually beginning with a brief consultation, this process involves discussing factors such as ideal background strain, molecular methods for optimizing the intended genetic change, mutation induction strategies, screening approaches and eventual QC of the new mutant line with the overall goal of giving our collaborators a fully informed, realistic picture of their projects timeframe, pitfalls and workflow.

Additionally, our Core provides mouse sperm and embryo cryopreservation services for the purpose of archiving and distributing valuable lines.

The Van Andel Institute is an AAALAC-accredited facility. All procedures are conducted according to the NIH Guide for the Care and Use of Laboratory Animals. We understand how important excellence in animal care is for producing quality research and are committed to the highest quality standards in pursuit of this principle.

VAI cryo-EM core facility encompasses state-of-the-art cryo-electron microscopes (Krios, Arctica), which are supported by expert staff and a robust high-performance computing cluster with extensive cloud capabilities. The VAI cryo-EM core also provides a wide range of cost-effective and efficient biological EM services.

The Optical Imaging Core within Van Andel Institute is located in Grand Rapids, Michigan and offers an array of brightfield and fluorescence imaging techniques to help investigators tackle a wide range of research questions. The Optical Imaging Core is committed to providing top-notch services to assist customers with experimental design and optimization, instrument training, image acquisition, and data analysis