Genomics Core Lab
Core Summary:
The OGI Genomics Core facility was established in April of 2013 by the Massachusetts Eye and Ear Department of Ophthalmology and with support of an NEI P30 grant (EY014104), with the goal of offering advanced genomics analysis methods and techniques to MEE investigators and affiliates.
Personnel
Associate Director: Hilary Scott, PhD.
Sr Research Technologist: Evelyn Harper
Contact:
243 Charles St.
Room 8xx
Boston, MA 02114
Services Offered:
As a CLIA-certified laboratory offering diagnostic testing to MEEI clinicians, we are able to provide the same quality services to researchers from specimen collection and accessioning through various NGS assays and bioinformatics analysis in collaboration with the MEEI Bioinformatics Center.
· The OGI offers sample processing services which include nucleic acid extraction, plasma and serum isolation and buffy coat collection. The core accepts samples Monday through Friday, from 9 AM to 4:30 PM. Please notify staff if you are dropping off plasma, serum or buffy coat samples to ensure immediate processing and storage in one of -80C freezers if requested. We provide secure storage and retrieval services for samples that were extracted by our core, these will continue to be monitoring by our LIMS until ready for downstream processing by the OGI Genomics Core. Freezers are monitored 24/7, and staff are on-call to address any issues.
· The Genomics core provides a wide range of sequencing services including both Sanger sequencing and next generation sequencing (NGS). Sanger sequencing is available every Monday/Wednesday/Friday with sample drop-offs the night before at 4pm and results returned the next business day. High-throughput Sanger sequencing (96-well plate) is accepted daily at 4pm for the next day’s run.
We offer library preparation for amplicon sequencing, plasmid sequencing, whole exome sequencing, selective exon capture and next generation sequencing (NGS) for ocular disease genes (RetNeT, glaucoma, optic neuropathy, mitochondrial DNA), whole genome sequencing. Generating high-quality data on the Illumina sequencing platform requires high-quality libraries which begin with your samples. Please follow submission guidelines carefully to ensure best results.
We can also load your prepared libraries or pools to your specifications on our Illumina Miseq or Novaseq. Illumina sequencing through the OGI is available by flow cell only and not on a per read basis. If you wish to share flow cells, this may affect your wait time as samples will be combined based on read-length, index compatibility and desired coverage however the wait is usually within 2-3 weeks.
We are happy to assist you with your custom sequencing project, please feel free to contact us for a consultation.
· We provide instrumentation for use by investigators after training by our staff. These same services are available to be performed by core members by request. We have a bank of thermocyclers available on a first come first use basis. Instruments available for use is indicated with an “I” in the equipment section.
Equipment:
· Biorepository: QiaSymphony for nucleic acid extraction and Thermofisher Varioskan Luxi for quantification, a -80C freezer for RNA and serum/plasma samples and two -20C freezers for DNA samples, Progeny LIMs for sample tracking.
· Nucleic Acid Analysis: Qubit Flurometeri, Thermo Scientific™ NanoDrop™ Eight UV-Vis spectrophotometeri, Agilent TapeStation 4200i.
· Molecular Biology: an Agilent SureCycler 8800, one C1000 Touchi and six T100 Biorad Thermocyclersi for Sanger sequencing reactions and NGS library preps, a Covaris LE-220plus acoustic sonicatori, Sage Science PippinHTi, and an Agilent Bravo NGS Workstationi is an automated liquid handling robot.
· Sequencing: Applied Biosystems SeqStudio Flex24 DNA analyzer for Sanger sequencing. Illumina MiSeq and Novaseq 6000 instruments for NGS. Illumina Dragen server for genomic sequence analysis.
Getting Started:
Service Request Instructions:
· All users must be trained by core staff to use any instruments. Please contact core staff for training before requesting or scheduling these instruments.
· Please read sample submission guidelines carefully to ensure your project gets processed in a timely manner and you receive the best possible results.
· Sequencing Samples: Sample ID must be no longer than 5 characters and not contain any special characters, spaces or dashes, only underscores if necessary. Each sample ID must be unique across all submissions for all samples. Example: HS_001. The sample ID must match the label on the top of the tube.
· Drop off Instructions for Sample Processing: Place whole blood samples in EDTA tubes (purple top) in the marked bin in the refrigerator in the hallway directly outside of the Genomics core in room 566A. Please fill out the sample drop-off sheet with all requested information. Samples are collected hourly by core staff.
· Drop off Instructions for Sequencing: Place samples in the approrpriate bin in the freezer located in the hallway directly outside of the Genomics core in room 566A. Please fill out the sample drop-off sheet with all requested information.
Please include the following statement in all publications and presentations from work provided by the OGI Genomics Core to assist us with NEI reporting and ensure our continued support while acknowledging the valuable work provided by our core:
Sequencing and analysis were provided by the Ocular Genomics Institute (OGI) Genomics Core and was funded by the NIH National Eye Institute Core Grant P30EY014104.NIH National Eye Institute Core Grant P30EY014104.
