Saint John’s Cancer Institute Sequencing Center

The Genomic Sequencing Center at Saint John’s Cancer Institute provides cutting-edge Next-Generation Sequencing services, accelerating advanced multiomic research and enabling comprehensive insights into translational applications.

State-of-the-Art Sequencing Services - Saint John's Cancer Institute

Next Generation Sequencing Services

The Saint John’s Cancer Institute Genomic Sequencing Center is an Illumina Propel-Certified sequencing provider and among a few select laboratories recognized for proficiency in Next-Generation Sequencing at the highest research industry standard.

Under the leadership of Dr. Dave S. B. Hoon, the Genomic Sequencing Center has upheld a rigorous standard of excellence in collaboration with global partners for over a decade. From direct customized consultation to high quality sequencing data generation, the Genomic Sequencing Center delivers tailored sequencing services to both internal and external research collaborators, meeting the demands of today’s rapidly evolving research landscape.

We welcome opportunities to discuss how we can meet your specific research needs.

Sequencing - Research Specialist - Saint John's Cancer Institute

General Sequencing Services

The Saint John’s Cancer Institute Genomic Sequencing Center is a CORE facility offering advanced Next-Generation Sequencing (NGS) services and proudly serving as an Illumina Propel-Certified Service Provider. Recognized among a few select laboratories, The Genomic Sequencing Center demonstrates proficiency in Next-Generation Sequencing at the highest standard. Our sequencing capabilities support a wide range of modern applications, including mRNA-focused sequencing, miRNA-Seq, DNA-Seq, spatial profiling, and sequencing pre-made libraries, accelerating multiomic research and enabling comprehensive insights into translational application.

Transcriptomics and Spatial Profiling

mRNA-Seq (Poly-A Capture)

Accurate measurement of gene and transcript abundance, detecting both known and novel features in coding and multiple forms of noncoding RNA. Comprehensive analysis and discovery of alternative transcripts, gene fusions, and allele-specific expression.

  • Acceptable Sample Format:FFPE, frozen tissue, cell lines, lower integrity/quality samples.
  • Minimum Input Requirement:1-1000 ng purified RNA.

Total RNA-Seq (rDNA Depletion)

Analysis of the transcriptome with mRNA-focused sequencing enables characterization of gene expression, gene fusions, alternative splicing, and novel transcripts through the enrichment of polyadenylated mRNA.

  • Acceptable Sample Format:Frozen tissue, cell lines, cell pellet.
  • Minimum Input Requirement:25-1000 ng high-quality total RNA.

Single Cell RNA-Seq

mRNA array offers 10X resolution at the cellular level for high-resolution analysis of gene expression at the cellular level.

  • Acceptable Sample Format:Cells or nuclei.
  • Minimum Input Requirement:2k-20k cells.

NanoString GeoMx Digital Spatial Profiling

Flexible and scalable spatial analysis of microenvironments using the only automated, scalable technology capable of non-destructive profiling expression of RNA and protein across distinct tissue compartments and cell populations. Transcriptome quantification, custom markers, 18,000+ genes expression in spatial context.

  • Acceptable Sample Format:Antibody protein, FFPE tissue sections. AOI and ROI Ab imaging based.

Genomics and Epigenomics

Whole Exome-Seq

Targeted analysis of coding regions in the genome, providing a cost-effective alternative to whole genome sequencing. Exome sequencing captures 50 Mbp of coding exonic regions with high specificity and coverage for both human and mouse genomes..

  • Acceptable Sample Format:FFPE, cell pellet, frozen tissue.
  • Minimum Input Requirement:1000 ng gDNA.

CUT&RUN

A groundbreaking strategy for ultra-sensitive genomic mapping of chromatin targets, offering a more robust approach for chromatin mapping compared to ChIP-Seq with lower cell requirements, enhanced signal-to-noise, and a streamlined workflow.

  • Acceptable Sample Format:CUT&RUN enriched DNA: cell lines, blood, PBL.
  • Minimum Input Requirement:0.5-5 ng CUT&RUN enriched DNA (5 ng recommended).

CUT&Tag

Based on ChIP principles while addressing ChIP limitations, CUT&Tag investigates genomic localization of histone modifications and transcription factors to identify protein-DNA interactions or DNA binding sites for proteins of interest. Unlike ChIP-Seq, live permeabilized cells or isolated nuclei serve as starting material.

  • Acceptable Sample Format:Freshly isolated, unfixed (i.e. native) nuclei.
  • Minimum Input Requirement:100k nuclei per reaction recommended.

Duet Multiomics Solution (5mC/5hmC, Methylation)

Simultaneous investigation of genetic sequence and modified cytosines in a single workflow, providing comprehensive genetic and epigenetic methylation data from low input DNA samples.

  • Acceptable Sample Format:Fresh/cryopreserved cells, fresh/flash frozen tissue.
  • Minimum Input Requirement:3-50 ng cfDNA, 10-80 ng fragmented double-stranded gDNA.

ATAC-Seq

Simple and scalable assessment of chromatin accessibility across the genome and how it may be altered by perturbation or disease, requiring a relatively small number of cells.

  • Acceptable Sample Format:cfDNA/plasma, FFPE/frozen tissue.
  • Minimum Input Requirement:500-2500 viable cells.

miRNA-Seq

Efficient, instrument-free gene expression technology for targeted measurement of miRNA expression across various sample types, without the need for extraction. Highly reproducible results ensure precise, reliable data.

  • Acceptable Sample Format:FFPE, cell lines, plasma.
  • Minimum Input Requirement:5 μm FFPE sections, 1k-4k cells, 13-30 μL plasma.

Instruments

Sequencing Platforms

Illumina NovaSeq X Plus

NovaSeq X Plus offers ultra-high-throughput sequencing, generating between 650 million-20 billion reads per run. XLEAP-SBS chemistry and onboard DRAGEN pipelines offer the highest level of data accuracy and performance.

Illumina NextSeq 2000

NextSeq 2000 systems simplify workflows while boasting superior performance and expanded applications for benchtop sequencing. Equipped with XLEAP-SBS chemistry and onboard informatics, NextSeq 2000 generates between 100 million-1.8 billion single reads per run.

Illumina MiSeq

Ideal for small scale projects with rapid turnaround time, a single run using MiSeq can generate 1-25 million single reads in a matter of hours.

Quality Control

Qubit 4 Fluorometer

Accurate and quick measurement of the concentration of DNA, RNA, or protein in a single sample.

Agilent 2100 BioAnalyzer

An established electrophoresis solution integrating an instrument, data processing software, reagents, and a microfluidic chip specific for DNA, RNA, or protein quality control.

Agilent TapeStation 4200

A high-throughput automated electrophoresis platform for fully automated, easy, and reliable quality analysis of DNA and RNA samples.

Sample Requirements

In genomic and transgenomic sequencing, maintaining high standards for sample requirements is critical to ensure the accuracy, reliability, and reproducibility of sequencing data. Samples submitted for processing must meet stringent quality control (QC) criteria—such as minimum DNA/RNA concentration, purity ratios (e.g., A260/A280), and integrity (e.g., RIN scores for RNA)—to prevent contamination, degradation, or amplification biases that could compromise downstream analyses. Poor-quality samples can lead to sequencing failures, misinterpretation of genetic variants, or the need for costly reprocessing.

2025 SJCI Assays

Assays

Sample Formats and Input

Recommended read/sample

A. Genomics
Whole Exome Sequencing (WES) FFPE sections, cell pellet, frozen tissue (?1000ng gDNA), PBMC 30M Paired-End
Whole Genome Sequencing (WGS); 30x human genome coverage Cell line, frozen tissue, PBMC 30X/90G
B. Epigenomics
Infinium MethylationEPIC v2.0 - No Restoration*** >950K genes (Non-coding inclusive) Frozen tissue, FFPE, cell line (250ng DNA), PBMC ***
CUT&RUN**; DNA Cell line, blood, PBMC, require spike-in controls (0.5-5ng DNA) Histone: 8M\nTranscription Factors: 25M
CUT&TAG** Cell line, tissue (100k nuclei), PBMC 8M
CUT&Tag-IT R-loop Fresh or cryopreserved cells (38k-500k cells), PBMC 25M
ATAC-Seq Viable cells (500-5k cells), PBMC 30M Paired-End
WGS Bisulfite Sequencing; 30x coverage Frozen tissue, cell line, PBMC 30X/90G
C. Transcriptomics
Illumina mRNA-Seq Frozen Tissue/Cell Line/PBMC (25-1000ng high-quality total RNA?) 25M Paired-End
Illumina Total Transcriptomic RNA-Seq Ribosomal depletion FFPE tissue section (1-1000ng purified RNA) 30M Paired-End
SMART-Seq V2 (FFPE) (Deep Seq) FFPE tissue section 10-20M
SMART-Seq V4 (Deep Seq) FFPE tissue section 5-10M
Targeted Gene-fusion RNA-Seq; profiling 507 fusion-tumor-associated genes FFPE/Frozen Tissues, PBMC, and Cell line (10ng total RNA, 20–100ng FFPE RNA) ~5M
Single cell/nuclei 10x genomics 5' RNA kits Cells/nuclei, >80% viable, cryopreserved 20,000+ reads per input cell
Bruker Nanostring GeoMX | Cancer Transcriptomic Atlas (CTA), 1800 genes**** Ab protein, RNA from FFPE tissue sections Recommended 30 reads per ?m^2
Bruker GeoMX | Whole Transcriptomic Atlas (WTA), 18k genes**** Ab protein, RNA from FFPE tissue sections Recommended 100 reads per ?m^2
** CUT&RUN and CUT&TAG are offered as replacements for ChIP-Seq
****GeoMX CTA / WTA costs includes GeoMX morphology marker set kits
(Tumor TME Morphology Kit ; PanCK, CD45, nucleiar stain or Melanoma TME Morphology Kit; S100B/PMEL17, CD45, and a nuclear stain)
Customizable depending on study design, Bioinformatics may be discussed
General standard cost, deviations will be adjusted accordingly: 48 AOI on one slide
*** Additional cost for poor quality FFPE tissue sections nucleic acids as restoration may be required
Preliminary bioinformatic analysis will be provided through discussion
All sequencing data will be returned through BaseSpace and will be stored temporarily
QC : All costs cover quantification and quality check RNA or DNA of specimen and QC of NGS

Submission Details

Quality of starting material is a key factor in producing informative sequencing data and results. Samples must pass specific quality control requirements before they may be processed for sequencing. Pricing will depend on the assay type, number of samples to be processed, sequencing read depth, read length, run mode, and desired turn-around time.

To request sequencing services, consultation, or sample requirements and pricing specific to your project, please submit an inquiry form. Please allow a short time for your inquiry to be processed.

Getting Started

If you have questions about sequencing services, pricing or sample requirements, please or use our form to receive a call back or email.

Sequencing preparation - Saint John's Cancer Institute
Your samples for sequencing must meet specific quality control requirements. Contact us today to learn more.

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Use the form below for all submission questions. We will respond with an answer as soon as possible.

Partnership & Collaboration

Academic Collaborators

Industry Collaborators

Saint Johns Cancer Institute Genomic Sequencing Center - Industry Collaborators

Academic and Industry Collaborators of Saint John’s Cancer Institute.

Publications

  1. Bustos, M. A., Gross, R., Rahimzadeh, N., Cole, H., Tran, L. T., Tran, K. D., Takeshima, L., Stern, S. L., O’Day, S., & Hoon, D. S. B. A Pilot Study Comparing the Efficacy of Lactate Dehydrogenase Levels Versus Circulating Cell-Free microRNAs in Monitoring Responses to Checkpoint Inhibitor Immunotherapy in Metastatic Melanoma Patients. Cancers vol. 12,11 3361. 13 Nov. 2020.
  2. Hinestrosa, J. P., Searson, D. J., Lewis, J. M., Kinana, A., Perrera, O., Dobrovolskaia, I., Tran, K., Turner, R., Balcer, H. I., Clark, I., Bodkin, D., Hoon, D. S. B., & Krishnan, R. Simultaneous Isolation of Circulating Nucleic Acids and EV-Associated Protein Biomarkers From Unprocessed Plasma Using an AC Electrokinetics-Based Platform. Front. Bioeng. Biotechnol. vol. 8 1232. 05 Nov. 2020.
  3. Bustos, M. A., Tran, K. D., Rahimzadeh, N., Gross, R., Lin, S. Y., Shoji, Y., Murakami, T., Boley, C. L., Tran, L. T., Cole, H., Kelly, D. F., O’Day, S., & Hoon, D. S.B. Integrated Assessment of Circulating Cell-Free MicroRNA Signatures in Plasma of Patients with Melanoma Brain Metastasis. Cancers. vol. 12,6 1692. 25 Jun. 2020.
  4. Wang, X., Bustos, M. A., Zhang, X., Ramos, R. I., Tan, C., Iida, Y., Chang, S-C., Salomon, M. P., Tran, K., Gentry, R., Kravtsova-Ivantsiv, Y., Kelly, D. F., Mills, G. B., Ciechanover, A., Mao, Y., & Hoon, D. S.B. Downregulation of the Ubiquitin-E3 Ligase RNF123 Promotes Upregulation of the NF-κB1 Target SerpinE1 in Aggressive Glioblastoma Tumors. Cancers. vol. 12,5 1081. 27 Apr. 2020.
  5. Lin, S. Y., Chang, S-C., Lam, S., Ramos, R. I., Tran, K., Ohe, S., Salomon, M. P., Bhagat, A. A. S., Lim, C. T., Fischer, T. D., Foshag, L. J., Boley, C. L., O’Day, S. J., & Hoon, D. S.B. Prospective Molecular Profiling of Circulating Tumor Cells from Patients with Melanoma Receiving Combinatorial Immunotherapy. Clinical Chemistry. vol. 66,1 169-177. 01 Jan. 2021.
  6. Hooda, J., Novak, M., Salomon, M. P., Matsuba, C., Ramos, R. I., MacDuffie, E., Song, M., Hirsch, M. S., Lester, J., Parkash, V., Karlan, B. Y., Oren, M., Hoon, D. S., & Drapkin, R. Early Loss of Histone H2B Monoubiquitylation Alters Chromatin Accessibility and Activates Key Immune Pathways That Facilitate Progression of Ovarian Cancer. Cancer Res. vol. 79,4 760-772. 15 Feb. 2019.
  7. Iida, Y., Salomon, M. P., Hata, K., Tran, K., Ohe, S., Griffiths, C. F., Hsu, S. C., Nelson N., & Hoon, D. S. B. Predominance of triple wild-type and IGF2R mutations in mucosal melanomas. BMC Cancer. vol. 18,1 1054. 30 Oct. 2018.
  8. Salomon, M. P., Wang, X., Marzese, D. M., Hsu, S. C., Nelson, N., Zhang, X., Matsuba, C., Takasumi, Y., Ballesteros-Merino, C., Fox, B. A., Barkhoudarian, G., Kelly, D. F., & Hoon, D. S.B. (2018). The Epigenomic Landscape of Pituitary Adenomas Reveals Specific Alterations and Differentiates Among Acromegaly, Cushing’s Disease and Endocrine-Inactive Subtypes. Clin Cancer Res. vol. 24,17 4126-4136. 1 Sep. 2018.
  9. Lin, S. Y., Huang, S. K., Huynh, K. T., Salomon, M. P., Chang S-C., Marzese, D. M., Lanman, R. B., Talasaz, AA., & Hoon, D. S.B. (2018). Multiplex Gene Profiling of Cell-Free DNA in Patients With Metastatic Melanoma for Monitoring Disease. JCO Precision Oncology. vol. 2. 17 May. 2018.
  10. Al Emran, A., Marzese, D. M., Menon, D. R., Stark, M. S., Torrano, J., Hammerlindl, H., Zhang, G., Brafford, P., Salomon, M. P., Nelson, N., Hammerlindl, S., Gupta, D., Mills, G. B., Lu, Y., Sturm, R. A., Flaherty, K., Hoon, D. S. B., Gabrielli, B., Herlyn, M., & Schaider, H. (2018). Distinct histone modifications denote early stress-induced drug tolerance in cancer. Oncotarget. vol. 9,9 8206-8222. 24 Dec. 2017.
  11. Bustos, M. A., Ono, S., Marzese, D. M., Oyama, T., Iida, Y., Cheung, G., Nelson, N., Hsu, S. C., Yu, Q., & Hoon, D. S.B. (2017). MiR-200a Regulates CDK4/6 Inhibitor Effect by Targeting CDK6 in Metastatic Melanoma. The Journal of Investigative Dermatology. vol. 137,9 1955-1964. Sep. 2017.
  12. Iida, Y., Ciechanover, A., Marzese, D. M., Hata, K., Bustos, M., Ono, S., Wang, J., Salomon, M. P., Tran, K., Lam, S., Hsu, S., Nelson, N., Kravtsova-Ivantsiv, Y., Mills, G. B., Davies, M. A., & Hoon, D. S.B. (2017). Epigenetic Regulation of KPC1 Ubiquitin Ligase Affects the NF-κB Pathway in Melanoma. Clin Cancer Res. vol. 23,16 4831-4842. 15 Aug. 2017.