The Sequencing and Genomic Technology shared resource provides a large array of DNA sequencing services, such as Whole Genome Sequencing, Whole Exome Sequencing or Targeted Sequencing.
Whole genome sequencing can be used for interrogating single-nucleotide variants (SNVs), insertions and deletions (indels), structural variants (SVs), and copy number variants (CNVs) in coding and non-coding regions of the genome. We construct and sequence DNA-seq libraries on Illumina platforms to produce millions of reads that can be mapped to a reference genome for variant calling. We also perform long-read sequencing on long read Oxford Nanopore GridION. This technology is particularly useful if you are looking for regions of the genome inaccessible to short read sequencing.
De Novo Whole Genome Sequencing is used for assemblies of novel genomes. We offer standard DNA-seq libraries preparation with different insert/fragment sizes and Illumina mate pair libraries to sequence on our Illumina sequencers. We also offer large insert size libraries preparation to sequence on our long read sequencer the ONT GridION.
The method of assembly dictates the types and construction of libraries for sequencing. Please verify the library construction requirements for the assembler of choice before submitting samples, as many assemblers have specific requirements for the construction of the libraries providing sequence.
Whole-exome sequencing targets only the protein-coding regions of the genome, which make ups <2% of the human genome while containing ~85% of known disease-causing variants. Whole-exome sequencing allows for the identification of genetic variation that is responsible for both mendelian and common diseases without the high costs associated with whole-genome sequencing.
We prepare a genomic DNA library and select only the subset of the library that encodes the protein through hybrid capture-based target enrichment. We sequence the captured DNA libraries on Illumina platforms. We provide Whole Exome capture for human samples using the IDT xGen® Exome Research Panel, which has a capture size of ~40Mb, as well as whole exome services for mouse, rat, zebrafish using Agilent SureSelect kits or other vendors.
To ascertain the patterns of methylation at a genome-wide level, we prepare and sequence bisulfate-treated genomic libraries. We also provide methylation sequencing using a cheaper more targeted approach with Twist Methylome, which targets 3.98 M cpG through 123 Mb of genomic content to target biologically relevant methylation markers.
Custom targeted sequencing is designed to isolate and deep-sequence specific regions of the genome. Targeted sequencing includes genomic panel capture or amplicon sequencing, where regions of interest are amplified and sequenced.
For capture methods, both available and custom panels can be used. Specific genes or mutations that have established relevancy to a particular cancer phenotype can be sequenced using available cancer panels. For custom capture, we offer Twist, Agilent SureSelect, and Roche SeqCap captures. With a list of your regions of interest, we facilitate the design and ordering of custom panels from these companies. For 16S rRNA gene, please contact the Microbiome Core Facility.
We also accept any amplicon that you have amplified to create a sequencing library from the amplified DNA for sequencing on Illumina short-read sequencers or GridION sequencers for reads >600 bp.
We do not perform ChIP or 4C/5C/HiC protocols, but we will create a sequencing library from the sheered DNA obtained from those protocols and sequence it to the requested specifications.