Saint John’s Cancer Institute Sequencing Center

The Saint John’s Cancer Institute Genomic Sequencing Center is an Illumina Sequencing Provider and CORE facility as part of HTG’s Preferred Academic Centers of Excellence (PACE) program. Our general sequencing services include Human and Mouse Exome, RNA-seq, Targeted Resequencing and Custom Enrichment, OMNI-ATAC-Seq, miRNA-seq, ChIP-seq, EPIC 850k Methylation array, and Sequencing for Pre-made Libraries. We utilize Illumina NextSeq 550, Illumina MiSeq, and Oxford Nanopore.

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

Next Generation Sequencing Services

The Saint John’s Cancer Institute Sequencing Center is an Illumina Sequencing provider, one of a few select laboratories in a service partnership with Illumina that has demonstrated proficiency in next generation sequencing at the highest research industry standard. We provide sequencing services to both internal and external collaborative researchers and welcome opportunities to discuss how we can meet your specific needs.

From library preparation to producing high quality sequencing data, we offer a variety of sequencing services to meet today’s fast-paced research environment. Led by Dr. Dave Hoon, our sequencing services include sample QC/processing, HTG Molecular Diagnostics, general RNA, DNA and MicroRNA Sequencing Services, methylation array, as well as Nanostring GeoMX DSP quantification. Collaborators can utilize the forms below to submit a sample to our sequencing center.

Next Generation Sequencing - Saint Johns Cancer Institute

HTG Molecular Diagnostics

HGT Sample - Saint Johns Cancer Institute
The Saint John’s Cancer Institute is partnering with HTG Molecular Diagnostics
The Saint John’s Cancer Institute Genomic Sequencing Center is now partnering with HTG Molecular Diagnostics as a preferred CORE facility as part of HTG’s Preferred Academic Centers of Excellence (PACE) program, serving the U.S. West Coast in targeted panels profiling miRNA, immunology, oncology, and more, using direct assays of diverse sample inputs ranging from cell lines, total RNA, plasma/serum, and FFPE tissues. Based in Tucson, Arizona, HTG Molecular Diagnostics’ mission is to advance precision medicine, automating highly multiplexed molecular profiling from solid and liquid samples in support of clinical discoveries.

To learn more about HTG Molecular, click here.

HTG Features and Workflow

General Sequencing Services

  • Human and Mouse Exome
    Exome enrichment focuses on the coding regions of the genome and is a cost-effective alternative to whole genome sequencing. Exome sequencing captures 50 Mbp of coding exonic regions with high specificity and coverage.
  • RNA-seq
    Analyzing the transcriptome with mRNA-focused sequencing provides researchers with information to characterize gene expression, gene fusions, alternative splicing, and novel transcripts. Standard coverage ranges from ~20-50 million reads and can be scaled to meet specific project objectives.
  • Targeted Resequencing and Custom Enrichment
    Isolating genomic regions of interest with targeted gene enrichment panels allows for cost-effective, focused detection of germline and somatic mutations. Pre-defined cancer panels cover over 300 cancer-related genes with high specificity and deep coverage. Custom gene panels can also be designed to meet specific project objectives.
  • OMNI-ATAC-Seq
    OMNI-ATAC-Seq is a new and improved assay designed to decrease background noise generated by mitochondrial DNA by ~20% from the original ATAC-Seq method for transposase-accessible chromatin region profiling. Explore chromatin accessibility and identify open/closed regions of DNA with only 10k cells. Standard coverage from ~50 million reads and can be scaled to meet project objectives.
  • HTG Edge Sequencing - Saint Johns Cancer Institute
    HTG Edge Sequencing supports limited specimens – Saint John’s Cancer Institute
  • miRNA-seq
    Extraction-free direct assay on HTG EdgeSeq of 2,083 miRNA from plasma, serum, FFPE, and cell lines. Low-input requirements make this assay ideal for limited specimens. Standard coverage is ~1 million reads per sample.
  • ChIP-seq
    Analyze interactions between genomic bound protein and DNA to identify binding-sites for transcription factors and other proteins. Standard coverage from ~20-50 million reads per cell line and can be scaled to meet project objectives.
  • EPIC 850k Methylation array
    Quantitatively interrogate DNA methylation level for >850K CpG sites from a variety of specimen sources, including FFPE tissues, cell lines, and frozen tissues.
  • Sequencing for Pre-made Libraries
    We can also sequence your pre-made Illumina-compatible libraries. The NextSeq 550 and MiSeq are priced on a per run basis.

Instruments

Our Sequencing Center is an Illumina Propel-Certified Service Provider, one of a few select laboratories in a collaborative service partnership with Illumina that have demonstrated proficiency in next generation sequencing at the highest industry standard.

    Mi Seq - Saint Johns Cancer Institute
    The sequencing team at Saint John’s Cancer Institute discuss images and findings using illumina MiSeq.

  • Illumina NextSeq 550
    High output mode can generate up to 400 million reads per run with single read sequencing and up to 800 million reads per run with paired-end sequencing and offers rapid turnaround time. Mid output mode can generate up to 130 million reads per run with single read sequencing and up to 260 million reads per run with paired-end sequencing.
  • Illumina MiSeq
    Ideal for small scale projects with rapid turnaround time. In a single run the MiSeq can generate 12-15 million reads with single read sequencing or 24-30 million reads with paired-end sequencing.
  • Oxford Nanopore
    Direct and real-time sequencing of native DNA/RNA, or sequencing amplified samples. Read length is not limited from short to ultra-long, and beneficial for methylation research without bisulfite conversion biases.

Policies and Pricing

Pricing will depend on the assay types, the number of samples to be processed, read depth, read length, and the run mode and turn-around time desired. To learn more about our sequencing services or schedule a consultation to discuss your research project and sequencing needs, please email us at Suyeon.Ryu@providence.org or Dave.Hoon@providence.org.

For Saint John’s Cancer Institute internal investigators, the study designs as well as the up-front source of funding should be discussed. Project tasks are completed in received orders and the level of work. Trello website is shared with all internal investigators for weekly updates of on-going projects.

Sample Requirements

Quality of starting material is a key factor in producing optimal sequencing data and results. The following are general sample requirement guidelines for our library preparation and sequencing services. All samples must pass our quality control requirements before they can be processed for sequencing. Please contact us for more detailed sample submission requirements specific to your project.

  • General Guidelines
    In prior to submission, all DNA/RNA samples should be extracted and de-identified. Any human specimens must be NIH IRB approved. The specimens should be suspended in water, low TE, or elution buffer and stored in low binding 1.5 ml tubes. The top and side of each tube should be clearly labeled with the sample name, date, institution and/or PI’s initials. The sample submission forms including the quality analysis results are required for sample submission.
  • DNA Sample Requirements
    Please provide sample analysis results measured by Qubit, Agilent 2100 Bioanalyzer or TapeStation in one or multiple forms. NanoDrop quantification alone is not recommended.
  • Exome Sequencing
    Purity: OD260/280 = 1.8-2.0 without degradation and RNA contamination
    Concentration: 30ng/µl or above
    DNA amount for each library: ≥400 ng high quality genomic DNA or ≥2.5 µg FFPE DNA
  • RNA Sample Requirements
    Please provide analysis results of the RNA sample using at least two of the following methods: Qubit, NanoDrop, Agilent 2100 Bioanalyzer, and Agilent 2200 TapeStation. Please purify samples, avoiding contamination by polycarbonate, protein and exonuclease. Please send samples in molecular-grade water or Buffer EB without nuclease inhibitors such as EDTA.
  • mRNA Sequencing
    Purity: OD260/280 = 1.8-2.0; OD260/230 >1.8; RIN ≥ 8 for high quality total RNA or %DV200 ≥ 30% for FFPE total RNA
    Concentration: ≥20ng/µl
    Total RNA amount for each library: ≥500 ng of high quality total RNA or ≥300 ng of FFPE total RNA

Sequencing Team - Saint Johns Cancer Institute

How can we help you?

Forms

Please utilize the forms below to engage the sequencing department at Saint John’s Cancer Institute. For additional information, please call: 310-582-7215.

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.