Genomics - DNA Analysis (La Jolla)

Overview

The Genomics DNA Analysis Facility at Sanford-Burnham in La Jolla provides next-generation sequencing services, from experimental design to data analysis. The facility has two next-generation sequencers, the Life Technologies Ion Torrent PGM and Ion Proton sequencers. Both platforms offer rapid turnaround, with sequencing run times ranging from 2-7 hours. The Ion Torrent can provide up to 1 Gb of sequencing data, with reads up to 400 bases in length. The Ion Torrent is ideal for sequencing of small genomes and targeted sequencing of predefined gene sets, such as mutations in genes associated with cancer. The Ion Proton currently produces up to 10 Gb of sequence data with read lengths up to 200 bases and will support several applications including, whole transcriptome, and whole exome sequencing. The P II chip for the Ion Proton, scheduled for release in the last half of 2013, has an advertised output of 30 Gb, sufficient for whole genome sequencing. 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 sequencing services to investigators outside of Sanford-Burnham.

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.
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Services

The Genomics DNA Analysis Core at La Jolla provides complete next-generation sequencing service, from user submitted DNA or RNA to analyzed data.
  • Next generation sequencing of DNA or RNA on the Ion Proton, or Ion Personal Genome Machine. Some of the services provided include targeted resequencing of DNA samples to identify single nucleotide variants, small insertion and deletions, and ChIP-Seq. RNA-seq options include, poly-A selected expression analysis, whole transcriptome expression analysis and small-RNA sequencing.
  • We work with DNA and RNA provided by investigators, and do all library preparation on site. There are several options for DNA target enrichment, from small custom and pre-made human disease panels, to entire human exomes (TargetSeq and AmpliSeq kits from Life Technologies). For RNA sequencing, we require that RNA be Poly-A selected, or Ribo-depleted, but can offer this service for an additional fee. Contact core for sample requirements.
  • Sample QC: Depending on the library type, incoming RNA and DNA samples are analyzed for quality and concentration by qRT-PCR, the Qubit fluorometer, or BioRad Experion.
  • Advanced data analysis. The core can provide additional support for custom workflows, and pathway analysis.

Equipment and Resources

  • The Ion Proton Sequencer can produce up to 10 Gb of sequence data in a single day with 200 bp read lengths, and a very low per base cost. The current 10 Gb capacity is enough for two full human exomes, or two whole transcriptomes per run (day).


  • The Ion Torrent Personal Genome Machine (PGM) is a smaller scale sequencer. The PGM is well suited for sequencing small genomes and targeted DNA samples, for example the cancer hotspot panel and the human disease panels from Life Technologies. The PGM has longer read lengths than the Ion Proton (400 vs. 200), and is less expensive per run.


  • 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.


  • 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).







  • 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.



  • The Nanodrop Spectrophotometer requires only 1 ul of sample to
    measure DNA and RNA concentrations.

Contact

Brian James

Brian James runs the Ion Proton, and Ion Torrent PGM sequencers in the Genomics-DNA Analysis core and provides downstream bioinformatic analysis. Dr. James started with Sanford Burnham 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.

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

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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