NextGen Sequencing

Contact: Jeff Delrow
Location: Thomas Bldg DE-740
Contact phone: (206) 667-2763
Contact fax: (206) 667-2825
Contact e-mail: jdelrow@fredhutch.org

The Genomics Resource offers NextGen Sequencing (NGS) using Illumina HiSeq 2500.  Services include sample QC, library prep and QC, cluster optimization (HiSeq), and sequencing.  Support equipment includes a Covaris LE220 System used in the preparation of sequencing libraries and a PerkinElmer Sciclone NGSx Automated Library Prep Workstation, as well as two Agilent Bioanalyzer 2100, an Agilent 2200 TapeStation, a Life Technologies Qubit 2.0 fluoromter and an ABI StepOne Real-Time PCR System for use in library QC.

NextGen sequencing services are obtained through a module of HutchBASE, a highly customized version of BASE v2.6 (BioArray Software Environment).  In addition to sample annotation and tracking features, the HutchBASE LIMS also automatically triggers data analysis pipeline protocols, produces data QC reports, and provides data management capabilities.

For Technical questions contact either:

Andy Marty - jamarty@fredhutch.org; (206) 667-1393

Alyssa Dawson - adawson@fredhutch.org; (206) 667-5614

Illumina HiSeq 2500 (NextGen Sequencing)

The HiSeq 2500 platform is our highest throughput sequencing platform and offers single-read and paired-end sequencing options with a maximum read length currently at 150 nucleotides. Due to the high read numbers, the HiSeq 2500 is ideal for numerous applications, including RNA-Seq, ChIP-Seq, and exome sequencing. In most cases, sequencing libraries can be multiplexed, providing an appreciable savings per sample. The degree to which libraries can be multiplexed will depend on sample composition, experimental requirements, and technical constraints. Please contact Genomics Shared Resource staff to discuss the various options.

The HiSeq 2500 can run both in rapid mode using a smaller 2-lane flow cell, and a high-output-mode using the traditional 8-lane flow cell.

Library Prep and Quality Control:  We offer library prep services using several current reagent kits, depending on the application.  Additional services include Covaris shearing, fragment and library analysis using an Agilent Bioanalyzer, and library QC and cluster quantitation using qPCR. These services are offered as a package, or as independent services.

How To Access Services:

Whole Flow Cell and Single Lane Reservations can be placed through HutchBASE (NOTE: External customers must contact the Genomics Resource directly).  Once signed in, reservations can be made using the appropriate link under the Popular Links header.  Questions or issues with using HutchBASE should be sent to genomics_IT@fredhutch.org. Those new to using NGS technology should discuss their experimental needs with Jeff Delrow (jdelrow@fredhutch.org; (206) 667-2763). Once a sequencing strategy has been determined, please contact Andy Marty (jamarty@fredhutch.org; (206) 667-1393) to reserve a spot on the schedule and discuss any unresolved technical and logistical issues.

Library Prep and QC Services should be configured in HutchBASE after a lane(s) or whole flow cell is reserved.  Specific sample requirements and recommendations are provided in HutchBASE. Please contact Andy Marty (jamarty@fredhutch.org; (206) 667-1393) for more details.

For information on Illumina HiSeq 2500 services, contact:
Sequencing Consultation: Jeff Delrow (jdelrow@fredhutch.org; (206) 667-2763)

Illumina Technical Questions: Andy Marty (jamarty@fredhutch.org; (206) 667-1393)