Genomics - DNA Analysis (La Jolla)


The Genomics DNA Analysis Facility at SBP in La Jolla provides next-generation sequencing services, from experimental design to data analysis. The facility provides high throughput sequencing on the Illumina NextSeq 500, the Thermo Fisher Ion Torrent PGM and Ion Proton sequencers. As a core facility, the sequencing facility provides state-of-the-art equipment and expertise, which would be impractical for individual labs to maintain. The core also provides amplification-free analysis of RNA expression using the NanoString nCounter, and additionally provides sequencing and analysis services to investigators outside of SBP.

Included in the cost of sequencing is basic bioinformatic analysis (SNP/InDel calling, transcript abundance). The core also provides advice on experimental design, and guidance on the capabilities of next-generation sequencing. Advanced bioinformatic and systems biology analysis is available through the Bioinformatics & Data Management core in La Jolla.

Tech-Shared Resources Four Tabs


Next Gen Sequencing
The facility provides high throughput sequencing on the Illumina NextSeq 500, the Thermo Fisher Ion Torrent PGM and Ion Proton sequencers. All three platforms offer rapid turnaround, with sequencing run times ranging from 2-29 hours. The NextSeq 500 can sequence 20 RNA-seq, or ChIP-seq libraries per day. The Ion Torrent is ideal for sequencing of small genomes and targeted sequencing of predefined gene sets. The NextSeq500 and the Ion Proton support several applications including, whole transcriptome, and whole exome sequencing.

Human cell line authentication and mycoplasma testing services
are available through the Genomics core. We use the GenePrint 10 System from Promega to preform short tandem repeat (STR) analysis on genomic DNA submitted to the core. STR data is processed by the core in GeneMarker HID, and allele calls are returned to the customer. For commercially available cell lines, the core will search STR profiles against databases of know STR profiles (ATCC, RIKEN, JCRB, and DSMZ) and return the best match.

Microarray based global analysis of human gene expression
is available on the Illumina BeadStation platform. Illumina has discontinued mouse and rat arrays, so for such gene expression analysis, contact Brian James to discuss RNA-seq options. For human RNA samples, the facility confirms RNA quality, and then performs microarray analysis as well as initial data analysis. Array data are returned to the investigator, and if desired, also passed on to the Bioinformatics Core for more detailed analysis.

Quantitative real-time PCR (Q-PCR) service
is predominantly SYBR green-based analysis, but hybridization probe (e.g. TaqMan) approaches are supported. Starting with RNA, the facility will utilize primers from investigators, or design custom primers and perform Q-PCR. The facility provides control primers and assists with experimental design, as well as providing basic relative quantitation analysis. Q-PCR analysis in the facility can also provide gene, RNA, or viral copy number data.

Capillary DNA sequencing
is being outsourced, with three vendors picking up samples at SBP and typically returning results within 24 hr.

Equipment and Resources

NetSeq 500

The NextSeq 500 Sequencing System from Illumina provides the widest range of sequencing applications. The flexible, scalable system offers tunable read lengths and output options to support research needs. It can sequence 20 RNA-seq, or ChIP-seq libraries per day and supports Whole-Genome Sequencing and Exome Sequencing.

Ion Proton Sequencer

The Ion Proton sequencer from Life Technologies offers up to 10 Gb of sequence data with the PI chip, and as much as 30 Gb with the PII chip available mid 2013. The Ion Proton has read lengths up to 200 bases, and the capacity for whole transcriptome or whole exam sequencing.

Nanostring nCounter-Amplification-free RNA Analysis

The nCounter is an excellent instrument for analyzing the expression of a substantial number (e.g., 100) of genes and micro RNAs in a large number of samples, such as validation of putative biomarkers in clinical samples, including FFPE samples.

Agilent 2100 Bioanalyzer

The Agilent 2100 Bioanalyzer system provides sizing, quantitation and quality control of DNA and RNA. The 2100 Bioanalyzer is especially useful for assessing the integrity of submitted RNA samples.

Qubit Fluorometer

The Qubit Fluorometer gives an extremely accurate measurement of DNA, RNA or protein. Depending on the probes used, the Quibit will only measure the targeted molecule, and will not quantify non-targeted contaminating nucleic acids (primers, or RNA in a DNA prep).



Brian James

(858)646-3100 ext. 4084
Email Brian James

Brian James runs the Genomics core and provides downstream bioinformatic analysis. Dr. James started with SBP in 2013 after leaving the MD Anderson Cancer Center, where he ran the sequencing bioinformatic support service for the Department of Experimental Therapeutics Next-generation sequencing core. Dr. James received his Ph.D. in Molecular and Cellular Biology from the University of Arizona, where he studied development and integrin signaling in Drosophila melanogaster. Please contact Dr. James for advice on next-generation sequencing projects or experimental design for core services.

Price List

Because of complex prices due to multiplexing and reagent packaging, contact the Facility Director for pricing on specific projects

Ion Proton AmpliSeq™ Exome (2 samples per PI chip, Low input requirement, as little as 50ng DNA)each, set of 2$1,086.75$2,117.15
Ion Proton Whole Transcriptome 200 bp fragment (three samples per P1 chip, 20-26 million reads)each, set of 3$600.75$1,170.35
Ion Proton Whole Transcriptome 200 bp fragment (two samples per P1 chip, 30-40 million reads)each, set of 2$803.25$1,564.85
NanoString Sample Processing microRNA (per sample)each$67.50$131.50
NanoString Sample Processing mRNA (per sample)each$47.25$92.05
PGM Ion AmpliSeq™ Cancer Hotspot Panel v2 (40 genes, 8 barcoded samples on 316 chip)each, set of 8$336.15$654.87
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