Genomics Services Laboratory

Overview of Services

 

The Institute for Genomic Medicine Genomics Services Laboratory (GSL), located within the Research Institute at Nationwide Children's Hospital, is a core resource providing advanced sequencing technologies and comprehensive genomic services to support both internal and external researchers. Our expertise spans a range of high-throughput genomic assays, and we offer personalized support in experimental design, quality control for DNA/RNA starting materials, sample preparation, next-generation sequencing (NGS), and initial data processing (if needed).  

Library preparation services include a variety of sequencing applications to meet diverse research needs. These include genome and exome sequencing, bulk RNA-seq, small RNA sequencing, microbial and metagenomic whole genome and RNA-seq, as well as multiple single-cell applications using 10x Genomics Chromium (3' Gene Expression, 5' Gene Expression + V(D)J enrichment, Fixed RNA Gene Expression, and ATAC + Gene Expression multiomics).  Spatial transcriptomics is also available via 10x Genomics Visium (including Visium HD) technology. Additionally, we support epigenomic studies with ChIP-Seq and ATAC-Seq, facilitated by Hamilton Starlet automation for precise, high-throughput sample processing. 

 

Sequencing services, the GSL is equipped with multiple Illumina platforms, including two NovaSeq X Plus (full service coming in Q2 2026) four NovaSeq6000 systems, which deliver high-throughput, flexible sequencing options with various flow cell types and read lengths (50–250 base pairs). We also offer lower-throughput sequencing using the Illumina NextSeq2000, MiSeq, and iSeq systems. Short-read sequencing is further supported by the Singular Genomics G4 instrument. For long-read applications, we offer library generation and sequencing using Pacific Biosciences Revio system.

 

Data analysis services, IGM’s Computational Genomics Group offers a range of flexible data analysis services to support diverse sequencing applications, from basic data delivery to advanced downstream analyses.

• Sequencing Data Delivery (No Analysis)
  Raw sequencing data can be delivered as FASTQ or BCL files. This option is included with Sequencing Only services and does not involve downstream analysis.
• Alignment to Reference Genome
  Sequencing reads are aligned to the appropriate reference genome, with supported versions includingGRCh38, GRCm38, and GENCODE annotation. Alternative genome or annotation versions may be accommodated upon request; users are encouraged to contact us to discuss specific requirements. Deliverables include aligned reads in BAM format along with standard alignment quality metrics.
• Standard RNA-seq Analysis
  This service includes delivery of raw FASTQ files, comprehensive preprocessing quality control (including trimming, adapter removal, and contaminant metrics), alignment summaries with BAM files, and feature-level count summaries.
• RNA-seq Differential Expression Analysis
  Building on the standard RNA-seq analysis, this service provides differential expression analysis (recommended minimum of four biological replicates per group). Deliverables include spreadsheets with unfiltered expression data, comparison-specific results, and a summary report with plots and statistics.
• RNA Fusion Detection Analysis
  Fusion detection analysis is available for RNA-seq data to identify candidate gene fusions using validated computational workflows.
• Standard Whole Exome Sequencing (WES) Analysis
  Includes alignment and SNV/INDEL calling and annotation for germline and somatic variants (when applicable), along with CNV/LOH and quality control for human samples.
• Standard Whole Genome Sequencing (WGS) Analysis
  Includes alignment and SNV/INDEL calling and annotation for germline and somatic variants (when applicable), along with CNV/LOH and quality control for human samples.
• miRNA-seq Analysis
  miRNA-seq data can be analyzed using our in-house pipeline or delivered as FASTQ files for customer-side analysis (e.g., Qiagen workflows). The in-house pipeline includes adapter trimming, sequential alignments to miRNA, piRNA, tRNA databases, and final alignment to the human reference genome to support comprehensive small RNA profiling.
• PacBio Data Analysis
  Support is available for PacBio applications including Iso-Seq, HiFi, MAS-Seq, plasmid, Kinnex, and Kinnex Single-Cell Additional reporting options can be provided as needed.
• 10x Genomics Single-Cell Analysis                                                                                                                                                                                                                                                                 We provide data delivery and downstream analysis for 10x Genomics assays, including 3′ and 5′ Gene Expression (with or without On-Chip Multiplexing), Fixed RNA (Flex), Multiome ATAC + Gene Expression, and Visium Spatial Transcriptomics. Customers may choose raw data delivery (BCL or FASTQ files) or analysis services. Standard single-cell analysis (where applicable) includes quality control, dimensionality reduction, clustering, cell type annotation using established human and mouse reference datasets, differential expression analysis based on cell type annotations, and gene set enrichment analysis. Custom analysis options are available by consultation and may include alternative annotation references, advanced differential or pathway analyses, pseudotime analysis, and tailored workflows for Multiome and spatial transcriptomics projects.

 

Nucleic Acid Extractions services offered by the Institute for Genomic Medicine aim to isolate high-quality DNA and RNA to support a wide range of research applications. Co-isolation of both DNA and RNA can be performed from blood, cells, snap frozen tissue, and FFPE tissue. DNA-only isolations are available from saliva and buccal swabs, as well as from the sample types listed above. Additionally, we offer isolation for non-human snap frozen and FFPE tissues. All extracted nucleic acids undergo quality assessment, including High Sensitivity Qubit assays for quantification and quality evaluation with the Agilent Tapestation 4200. 

 

The Steve and Cindy Rasmussen Institute for Genomic Medicine (IGM) is supported by the Nationwide Foundation Pediatric Innovation Fund.  Publications resulting from data generated in IGM Genomic Services Core should cite the Nationwide Foundation Pediatric Innovation Fund. 

  

Contact Information

 Katherine Miller, PhD, Director

Amy Wetzel, PhD, Operations Manager

 

Phone: 614-722-5321 (select option 2 for GSL)

Office: 614-355-3530

Email: IGM Genomic Services <IGMGenomicServices@nationwidechildrens.org>

 

 

Location and hours of operation

 

Hours	Location
Mon - Fri 8:30 a.m. - 4:00 p.m.	The Abigail Wexner Research Institute at Nationwide Children's Hospital                            575 Children's Crossroads, 2nd Floor (Research Building 3), WB2160                             Columbus, Ohio 43215

 

How to Submit Samples

 

1. Initiate and sumit your request

1. Under Core Facilities, select Nationwide Children’s Hospital (NCH) and Genomics Services Laboratory (GSL).
2. Initiate “Next Generation Sequencing Request”.
3. Enter the project description information on NGS form.
4. The GSL will issue a quote upon completion of your request.
5. Agree to quote and provide payment information.
6. Payment information must be supplied before work on samples will begin.

2. Complete Project Intake Form (PIF) and Sample Submission Form (SSF)

• IGM PIF and SSF (IGM Genomic Services - Sample Submission Form)
• Of note, the SSF should only be completed once the iLab order has been submitted

3. Non-NCH Users

• Non-NCH users must also sign a master service agreement (MSA) or confirm with the GSL that an institutional MSA is currently in place and attach a hard copy of the purchase order (PO) to their iLab order prior to completing the SSF.

 

 4. Project or Sample Related Communication

• Email IGMGenomicServices@nationwidechildrens.org for questions regarding service offerings and delivery of samples.

 

 5. Ship or Delivery of your Samples

• If delivering your samples in person, please contact IGM Genomic Services to schedule a specific day and time.
• If shipping samples, please ship to address below.

Institute for Genomic Medicine

Attn: IGM Research Sample Receipt and Accessioning Team

Nationwide Children’s Laboratory Services

700 Children’s Drive, Room C1955

Columbus, OH 43205 U.S.A.

• If shipping your samples, please send the FedEx tracking number and include a shipping manifest with sample information (identifiers, specimen type, etc.) to the IGM Genomic Services group email listed above to ensure efficient receipt and triaging of samples.

 

 Sample Submission Guidelines 

• Please submit samples in Eppendorf 1.5 ml LoBind tubes (Fisher Sci; Cat#13-698-791), or Eppendorf™ twin.tec™ 96 Well LoBind PCR Plates, Skirted (Fisher Sci; Cat# E0030129512). Tubes should be clearly labeled and readable with GSL order number, sample identifier, and lab name/PI.
• For RNA/DNA QC services, submit samples in 0.2mL PCR strip tubes.
• Samples may be suspended in dH2O (preferred), EB Buffer (10mM Tris-Cl, pH 8.5), or RSB buffer (10mM Tris-Cl, pH 7.4, 10mM NaCl, 3mM MgCl₂). TE buffer is NOT acceptable - EDTA in these buffers can interfere with the various enzymes that are used during library preparation. 

 

QC Services for Nucleic Acids

Service	QC Method	Input material	Required Concentration Range	Volume required
RNA QC	Tapestation HS/ RNA Screentape	RNA	0.5 - 500 ng/µL	6 µL
	Qubit BR/HS RNA	RNA	4 - 1200 ng
DNA/Library QC	Tapestation HS D1000 Screentape	Final library < 1kbp	10 - 1 ng/µL	8 µL
	Qubit HS DNA	DNA, Library	0.1 - 120 ng
Qubit	Qubit DNA HS/BR DNA	DNA	0.1 - 4000 ng	5 µL
	Qubit RNA HS/BR RNA	RNA	4 - 1200 ng
DNA/RNA Tapestation QC	Tapestation HS RNA Screentape	RNA	0.5 - 10 ng/µL	5 µL
	Tapestation RNA Screentape	RNA	25 - 500 ng/µL
	Tapestation genomic DNA Screentape	Genomic DNA	10 - 100 ng/µL
	Tapestation HS D1000 Screentape	DNA < 1 kb	10 - 1000 pg/µL
	Tapestation HS D5000 Screentape	DNA < 5 kb	10 - 1000 pg/µL
qPCR DNA Library QC	Tapestation HS D1000 Screentape	DNA < 1 kb (Library)	10 - 1000 pg/µL	5 µL
	KAPA Library Quantitative Kit	Illumina Final Library	0 - 200 nM

 

Library Preparation Services for Illumina Short-Read Sequencing

Service	Library Prep Method	Input	Recommended Conc. (Qubit- based)	Lowest Acceptable Conc.	Minimum Volume Required
Human Whole Exome Sequencing (WES)	NEB Ultra II FS IDT xGEN Exome Research Panel v2 + CNV	100 ng	>20 ng/µL	4 ng/µL	20 µL
Mouse Whole Exome Sequencing (WES)	Twist Mouse Exome Panel	50 ng	>20 ng/µL	2 ng/µL	20 µL
Whole Genome Sequencing (WGS)	NEB Ultra II FS	200 ng	>25 ng/µL	4 ng/µL	20 µL
FFPE DNA - WGS/WES	Claret SRSLY	50 ng	>25 ng/µL	4 ng/µL	30 µL
FFPE and Total Stranded RNA-seq	NEB Ultra II Directional	100 - 1000 ng	>50 ng/µL	10 ng/µL	20 µL
FFPE RNA/Total RNA-seq	Genomics Watchmaker	10 - 1000 ng	>10 ng/µL	10 ng/µL	25 µL
Stranded Total RNA-Seq	NEB Ultra II Directional	100 - 1000 ng	>50 ng/µL	10 ng/µL	20 µL

 

Library Preparation Services for PacBio Long-Read Sequencing

Service	Input Material	Concentration (ng/µL) using Qubit	Minimum Volume Required (µL)	Recommended Amount (ng)
Genome (HiFi)	Genomic DNA with 90% >30Kb	>50	50	≥2500
Plasmid	Plasmid DNA Linearized	>50	50	≥1000
IsoSeq RNA	RNA (DNAsed) with RIN >7	>50	20	≥600
Kinnex RNA	RNA (DNAsed) with RIN >7	>50	12	≥600
Kinnex scRNA	High quality cDNA from 10X	>2	15	≥30

 

Sample Submission Guidelines for Sequencing Services (Client-Submitted Libraries that do NOT require DNA Library QC)

Sequencer	Per Lane or Flow Cell Unit	Minimum Volume (µL)/Unit	Concentration (nM)
PacBio Revio SMRT Cell	SMRT cell	TBD	TBD
Illumina Sequencers
NextSeq2000	Flow Cell	80	2.0
MiSeq v3 (PE75bp, PE300bp)	Flow Cell	20	10
NovaSeq6000: SP, S1	Flow Cell	220	1.5
NovaSeq6000: SP-Xp, S1-Xp (2-lanes)	Lane	45	1.0
NovaSeq6000: S2	Flow Cell	320	1.5
NovaSeq6000: S2-Xp (2-lanes)	Lane	60	1.0
NovaSeq6000: S4	Flow Cell	640	1.5
NovaSeq6000: S4-Xp (4-lanes)	Lane	70	1.0
NovaSeq X Plus: 1.5B (2-lanes) – Currently available for 10X assays – coming soon for all other services	Lane	40	2.0
NovaSeq X Plus: 10B (8-lanes) – Currently available for 10X assays – coming soon for all other services	Lane	60	2.0

 

Sample Submission Guidelines for Nucleic Acid Extraction Services

Sample Type	Analyte	Method of Extraction	Recommended Submission Amount
Blood	DNA	Inorganic (High Volume) or Magnetic Bead-based	4ml in EDTA
	DNA/RNA Co-Extraction	Column-based
WBC/PBMC	DNA	Magnetic Bead-based	1.00E+07 Cells
	DNA/RNA Co-Extraction	Column-based
Saliva	DNA	Magnetic Bead-based	Oragene Collection Tube
Buccal Swab	DNA	Magnetic Bead-based	4 Swabs
Frozen Tissue	DNA	Column-based	30-50mg
	DNA/RNA Co-Extraction
FFPE Tissue	DNA/RNA Co-Extraction	Isotachophoresis	150-300mm2 total tissue surface area at 10-micron thickness or FFPE Block
Serum/Plasma	RNA	Column-based	2ml

 

 

Website

https://www.nationwidechildrens.org/specialties/institute-for-genomic-medicine/genomic-services