Next Generation Sequencing
The John Wayne Cancer Institute 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. We provide sequencing services to both internal and external researchers and welcome opportunities to discuss with you how we can meet your specific research needs.
The John Wayne Cancer Institute Genomic Sequencing Center is now partnering with HTG Molecular as a preferred CORE facility serving the U.S. West Coast in targeted panels profiling miRNA, immunology, oncology, and more from diverse sample inputs ranging from total RNA, plasma/serum, and FFPE.
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.
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 is a new and improved assay designed to decrease background noise generated by mitochondrial DNA by ~20% from the original ATAC-Seq method. Explore chromatin accessibility and identify open/closed regions of DNA with only 50k cells. Standard coverage from ~50 million reads and can be scaled to meet project objectives.
Extraction-free direct assay of 2,083 miRNA from plasma, serum, FFPE, and cell lines. Low-input requirements make this assay ideal for precious specimens. Standard coverage is ~1 million reads per sample.
Analyze interactions between 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.
We can also sequence your pre-made Illumina-compatible libraries. The NextSeq 550 and MiSeq are priced on a per run basis.
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.
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.
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.
The John Wayne Cancer Institute Sequencing Center is equipped with an Illumina NextSeq 550 with two run modes allowing for flexibility and scalability to support a broad range of project sizes and designs. Ideal for whole genome or exome with larger sample sizes, the High Output Mode on the NextSeq 550 can process up 120 Gb of high quality sequence. For smaller scale projects or targeted sequencing applications, the Mid Output Mode on the NextSeq 550 can produce up to 39 Gb of high quality sequencing in as little as 26 hours.
The Sequencing Center is also equipped with an Illumina MiSeq to offer flexibility and fast turnaround time for sequencing small projects, small genomes, or targeted sequencing panels. The MiSeq also offers longer reads lengths (300 bp) and is fully compatible with all libraries that can be sequenced on the Illumina NextSeq.
Pricing for next generation sequencing will depend on the number of samples to be processed, read depth, read length, and the run mode desired. To learn more about our sequencing services or schedule a consultation to discuss your research project and sequencing needs please email us at hoonD@jwci.org.
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.
DNA and/or RNA specimens should be suspended in water, low TE, or Qiagen 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 form along with the appropriate quality analysis results as detailed below are required for sample submission.
DNA Sample Requirements
Please provide sample analysis results measured by Qubit, Agilent 2100 Bioanalyzer, or Agilent 2200 TapeStation in one or multiple forms. NanoDrop quantification alone is not recommended. For genomic DNA please submit a photograph of the sample separated by agarose gel electrophoresis (1-2%) to confirm the integrity and quality of the sample. Quality genomic DNA should appear as a dark, tight, high molecular weight band with no smearing below 20 kb.
Whole Exome Sequencing
Purity: OD260/280 = 1.8-2.0 without degradation and RNA contamination
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.
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
Total RNA amount for each library: ≥500 ng of high quality total RNA or ≥300 ng of FFPE total RNA
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.