Genomics Core

Van Andel Institute’s Genomics Core provides a comprehensive suite of genomics services to investigators at the Institute and beyond.

VAI’s Genomics Core uses ThirdWave Analytics Lockbox LIMS to facilitate project creation, submit sample information and track existing projects.

Project submissions

Request Genomics, Infinium, and Single Cell Sequencing Services

Spatial Collaborative Services combines expertise and technology from VAI’s Genomics Core and Optical Imaging Core to offer investigators a seamless pipeline for spatial imaging. For questions, please email [email protected].

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  • 141 peer-reviewed papers published in 2025, 74 of which were in high-impact journals
  • 15 VAI-SU2C Epigenetics Dream Team clinical trials launched to date
  • 10 clinical trials and related projects supported by VAI through the International Linked Clinical Trials Program
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Services

The Genomics Core prides itself on conducting high-caliber science and providing exceptional customer service. For questions and pricing information, or to submit a service request, please email [email protected]. For more information on requesting services, please scroll down.

SEQUENCING

10X Chromium single cell RNA sequencing
Ideal for measuring expression levels and dissecting cell types in thousands of single cells in a cost-effective manner.

10X Chromium linked read sequencing
Provides pseudo-long read whole genome and targeted sequencing to help resolve large scale genomic architecture and scaffolding, long-range haplotyping and structural variant detection.

Whole-genome sequencing
Whole-genome sequencing gives scientists the ability to comprehensively study the genome by providing a complete look at an organism’s genetic information.

Custom targeted sequencing
Targeted sequencing allows scientists to isolate and sequence a specific set of genes or areas of the genome, reducing cost and time to results as well as providing a more precise data set.

Exome sequencing
The majority of disease-associated variants are found in the exome, the region of the genome responsible for protein-coding. A type of targeted sequencing, exome sequencing gives scientists the ability to focus on genes that are more likely to be associated with a phenotype of interest while providing a faster and more cost effective alternative when whole-genome sequencing is not required.

Methylation sequencing
Focusing on CpG and enhancer-rich regions of the genome, methylation sequencing is aimed at determining epigenetic information in a more targeted, cost effective manner, when whole genome information is not necessary

Bisulfite sequencing (RRBS/WGBS)
Bisulfite sequencing interrogates the epigenetic information contained and mediated by cytosine modifications such as methylation (5mC) and hydroxymethylation (5hmC). Both reduced-representation and whole genome bisulfite sequencing options are available.

RNA-seq
RNA-seq is a precise method for analyzing the transcriptome, and provides quantitative as well as qualitative data.

ChIP-Seq
IP sequencing allows researchers to look at the specific extrachromosomal modifications (transcription factors, histone modifications) that affect gene accessibility, transcription and translation.

RIP-seq
Sequencing of actively transcribed regions of the RNA polymerase complex allows researchers to assess actively transcribed regions under specific growth conditions.

GENOTYPING

Illumina Bead Arrays
Using the iScan platform, the Illumina bead arrays allow for cost-effective interrogation of millions of unique genomic sites. Commonly run array types include: QC array, EPIC methylation array. Projects are expedited by automation on the Tecan Freedom EVO liquid handler

Real-time PCR
A staple of biomedical research, real-time PCR amplifies and analyzes specific RNAs to aid in the study of gene expression.

Digital droplet PCR
Much like real-time PCR, the digital droplet is used to study gene expression but has the added ability to partition samples on a large scale while also requiring less sample volume.

HOW TO REQUEST SERVICES

Prior to requesting genomics services, please review the appropriate submission policies found here. All requests should be submitted via email to [email protected] along with the completed, requisite form, which may be found below. Core staff will add the service request to CrossLab.

VAI staff that need a login (or further CrossLab support) should contact Lori Moon. MSU and external users that need a CrossLab account/login should go here for account creation. After logging in, external users should click “list all cores” under the Core Facilities section in the left menu and scroll down to “Cores at Van Andel Institute.”

For more information, please email [email protected].

Equipment

The Genomics Core is home to state-of-the-art equipment and expert staff who provide a range of genomics services to internal and external users. Please email [email protected] for more information.

Illumina NextSeq 500
A flexible sequencing system appropriate for small/mid-range RNAseq, ChIPseq and other next-generation sequencing applications

Illumina NovaSeq 6000
A high-throughput system for large-scale genomic, epigenomic and transcriptomic studies.

Illumina iScan with Tecan Freedom EVO
A high-throughput genotyping system that can assay 288 individuals in a single run. Assays include:

  • Infinium EPIC methylation array
  • QC array
  • MultiEthnicGlobal array
  • Omni SNP genotyping arrays

10X Genomics Chromium
A nano droplet-based library preparation system that is useful for high-throughput single cell 3′ RNA expression analysis of single cell ATAC-seq and single cell immune profiling. Linked-read DNA analysis can provide structural and CNV information from genomics samples.

Shared equipment for walk-up use

The Genomics Core also provides a suite of shared equipment for walk-up use for well-trained, internal users. For questions or to set up training, please email [email protected].

Covaris LE220 Sonicator
Optimized for high-throughput, pre-analytical sample processing, including:

  • DNA shearing for next-gen sequencing
  • Cell lysis
  • Tissue disruption
  • Compound dissolution

BioRad CFX384 Well qPCR System
Offers a 384-well format with four-color detection optics for singleplex or multiplex reactions.

Qubit 2.0 Fluorometer
Provides accurate and sensitive DNA, RNA, and protein quantitation that is ideal for low concentration samples and samples entering next-gen sequencing library preparation.

Advanced Analytical Fragment Analyzer
Provides DNA and RNA quality and integrity analysis in a high throughput manner. Up to 288 samples can be analyzed at once.

BioRad Droplet Digital PCR
Absolute quantification of DNA or RNA PCR targets at single-copy resolution. Useful for:

  • Rare target enrichment
  • Copy number variation
  • Mutation detection
  • Gene expression analysis
  • DNA methylation detection

WEB RESOURCES

Illumina Sequencing (KAPA QPCR, hyperprep, totalRNA, mRNA protocols)

Illumina Library Preparation

Illumina iScan

10x Chromium Single Cell

10x Chromium Long Read

Quantification/Qualification

Covaris LE220 Sonicator

PacBio

BioRad QX200 and Autoloader (product information)

Acknowledgments and Authorship

All work performed by VAI’s Core Technologies and Services should be acknowledged or considered for co-authorship in scholarly reports, presentations, posters, papers and all other publications. Proper acknowledgment allows us to obtain financial and other support that enables us to provide and maintain high-quality support and services. By acknowledging shared resource facilities and instrumentation in publications, presentations and other research communications, you play a critical role in ensuring their continued availability and future development.

Example acknowledgments:

  • We thank the Van Andel Institute Genomics Core (RRID:SCR_022913), especially [staff name], for their assistance with [technique/technology].
  • This research was supported in part by the Van Andel Institute Genomics Core (Grand Rapids, MI) (RRID:SCR_022913).

Selected Publications

# Equal contributions * Co-corresponding authors

Marie Adams, M.S.

Director, Genomics Core

Tracey Avequin, B.S.

Core Associate, Genomics Core

Katelyn Becker, M.S.

Core Lab Manager, Genomics Core

Brandon Compton

Core Associate, Genomics Core

Michael Davis

Core Associate, Genomics Core

Brennan Grimes, B.S.

Core Associate, Genomics Core

Andrew Hankiewicz

Core Associate, Genomics Core

Michelle Minard, B.S.

Senior Administrative Assistant II, Core Technologies and Services

Marc Wegener, B.S.

Core Associate, Genomics Core

Project Submission

VAI’s Genomics Core uses ThirdWave Analytics Lockbox LIMS to facilitate project creation, submit sample information and track existing projects. First-time users should first request a LIMS account by emailing [email protected]. 

To create a project or view an existing project, log in to the LIMS system here:

Lims Login

After project submission, samples can be brought to VAI either in person or shipped.

  • In-person sample drop-off can be scheduled by emailing [email protected] and [email protected] with the date and time you would like to drop off your materials. Please provide at least one business day’s notice of your drop-off.
  • Samples can be shipped on dry ice using an overnight courier such as FedEx. Place all samples in a secondary structural box. Please place a paper manifest in the shipping container and email any tracking information to [email protected]. Our shipping address is:
  • Van Andel Institute Genomics Core
    333 Bostwick Ave NE, Room 1211
    Grand Rapids, MI 49503