Genomics Resource Center - Laboratory Services
Using multiple complementary high-throughput platforms, the GRC provides a full range of genomic laboratory services. In addition to the sequencing applications listed below, the GRC performs sample preparation, quality control assessment, and library construction for each of our platforms and also provides customized applications and methods development. Each sequencing service includes data processing, quality control, and delivery. We deliver high-quality, filtered sequence data and associated quality scores via Aspera file transfer, hard media, or NCBI deposit. Our laboratory services can be combined with our analysis services to provide comprehensive data generation and analysis for your project. Services are provided on a fee-for-service basis and each project is customized to the needs of the investigator.
For more information or to discuss your research needs, please contact the GRC.
de novo Whole Genome Sequencing
In the absence of a finished or high-quality draft reference genome sequence, we utilize one or more of our platforms in combination to generate a high-quality draft genome sequence.
Comparative Genome Resequencing
Using one or more sequencing platforms, high-quality draft genome sequences are generated for comparative analysis with an available reference genome sequence.
Human Genome Sequencing
As efforts to expand personalized genomic medicine have grown, human genome sequencing has become a more common and effective tool for the identification of genome-wide SNPs, indels, structural variants (SVs), and copy-number variants (CNVs). In collaboration with the Human Genomics research group at IGS, the GRC has developed efficient and high-quality pipelines for sequencing and analyzing both individual genomes and large populations.
Human Exome and Custom Targeted Sequencing
For many projects, identification of variants within protein coding sequences is both more effective and more efficient than whole genome sequencing. Using sequence capture technologies from both Agilent and Nimblegen in combination with Illumina sequencing, the GRC generates high-quality enriched exome sequences. These capture technologies can also be used to target customized regions of the human genome or other genomes. We have successfully used this technology to capture and sequence the genomes of multiple unculturable or difficult-to-isolate pathogens.
Cancer Genome & Exome Sequencing
In order to accurately identify somatic mutations associated with cancer samples, we sequence the genome and/or exome of both the cancer and adjacent normal tissue. Because cancer samples can be highly heterogeneous, we target ultra-deep coverage to identify mutations. By comparing the normal vs. tumor exome and genome sequences, we can identify mutations unique to the cancer.
Transcriptome Analysis (RNA-Seq)
One of the fastest growing areas of genomics, this application can be used to answer questions about gene expression and regulation and to discover novel transcripts, SNPs, and splice variants. Strand-specific RNA-Seq can identify the sense strand for each transcript. Different library construction methods can be used to target mRNA only or combinations of mRNA, miRNA, ncRNA, and other families of RNA molecules. In collaboration with faculty investigators at IGS, the GRC has developed a method for simultaneous sequencing of host and pathogen transcriptomes in infected cells. The PacBio Iso-Seq method enables long-read sequencing of full-length transcripts to better identify and reconstruct isoforms.
Using multiple platforms depending on the project, we sequence DNA isolated from an organismal or ecological sample to investigate the constituent community of organisms and functional profile present in the sample. An RNA-Seq approach to a metagenomic sample can be used to generate metatranscriptomic data the describes the combined expression profile of the community.
The Illumina platform enables the investigation of DNA-protein interactions and DNA methylation through the sequencing of chromatin-immunoprecipitated (ChIP) DNA and bisulfite converted DNA respectively. Resulting data can be aligned to a reference genome to generate maps of protein binding positions and methylation sites. The PacBio SMRT sequencing technology can be used to natively detect a wide range of modified nucleotides and motifs.
High-throughput amplicon sequencing can be used to generate 16s rRNA community profiles of metagenomic samples, sequence many viral genomes in parallel, validate hundreds of variants identified in previous experiments, or sequence any combination of multiplexed amplicons. Depending on the goals and scale of the project, any of our sequencing platforms can be used for this application.
Digital Molecular Profiling
The NanoString nCounter Analysis System enables the profiling of hundreds of mRNAs, microRNAs, SNVs, CNVs, or protein on one platform with high sensitivity and precision. The nCounter’s digital counting capability provides highly reproducible data over 5 logs of dynamic range and does not require any amplification steps that might introduce bias to the results. An additional advantage of nCounter chemistry is that it is highly tolerant of difficult sample types such as FFPE and crude-cell lysates.