DNA Sequencing Services

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. If you do not find the DNA sequencing service you need for your project in the list below, please contact us.

Upon delivery to our facility, all DNA samples are evaluated for concentration by Qubit®. DNA submitted for PacBio sequencing will further be run on TapeStation or Fragment Analyzer to check integrity of the DNA. Before submitting samples, please review our sample submission requirements.

Choosing the correct DNA sequencing service for your samples depends on the organism, total DNA available for input, and project goals. Contact us with questions regarding experimental design or DNA service options. Most next generation sequencing projects require special consideration. We recommend contacting us before initiating a project with us.

All of the services listed below are compatible with current Illumina sequencing platforms. The adequate sequencing platform for your project will depend on sequencing depth (sequencing throughput) and read length required for your project. PacBio sequencers can also be used for amplicons sequencing and whole genome sequencing either in combination with Illumina sequencing or by itself.

Services

Whole Genome Sequencing
Whole genome sequencing 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.  500bp DNA-seq libraries are usually made and sequenced on Illumina HiSeq platforms to produced millions of reads that can be mapped to the reference genome allowing the identification of SNVs, indels.

De Novo Whole Genome SequencingFor assembly of a novel genome. The method of assembly dictates the types and construction of libraries for sequencing. We offer standard DNA-seq libraries with different insert/fragment sizes and mate pair libraries. We also offer PacBio large insert size libraries prep for sequencing on PacBio sequencers.  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.

To contruct mate pair libraries, we use Illumina's Nextera Mate Pair kit. We can generate 3-5kb, 5-7kb, or 7-10kb libraries. Mate pair libraries may be sequenced on all Illumina sequencers.

To construct standard DNA-seq libraries, we use Kapa Hyper prep kits. Insert size can be tweaked to accommodate the requirements of the assembler that will be used to assemble the data.

To construct PacBio libraries, we use the PacBio large insert library prep kit.

Whole-Exome Sequencing
Whole-exome sequencing refers to sequencing all of the protein-coding genes in a genome. The exome represents less than two percent of the human genome but contains about 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.
Whole-exome sequencing consists of preparing a genomic DNA library and selecting only the subset of the library that encodes the protein coding genes by in-solution enrichment (hybridization) of the library to biotinylated oligonucleotide capture probes and immobilization on streptavidin-coated beads. The captured DNA is then sequenced using Illumina high throughput DNA sequencing technology. We currrently provide Whole Exome capture using the IDT xGen® Exome Research Panel, which has a capture size of 39Mb.  We also offer capture using the NimbleGen SeqCap EZ Exome Library v3.0, which has a capture size of 64Mb. 

Custom Targeted Sequencing
Custom targeted sequencing is designed to isolate and deep-sequence a specific region of the genome. Targeted sequencing includes methods such as gene panels, cancer panels, or amplicon sequencing where regions or genes of interest are amplified and sequenced.

Whether you are interested in a few genes, or a few thousand genes, we can design a gene panel that assays your genes of interest with high sensitivity and specificity. Specific genes or mutations that have established relevancy to a particular cancer phenotype can be sequenced using available cancer panels. Other regions of interest such as the hypervariable regions of the microbial 16S rRNA gene, used to determine the type and relative abundance of bacterial and archaeal species in heterogeneous samples (e.g. soil, marine, or gut microbiome) can be sequenced by amplicon sequencing.

  1. For in-solution capture, we offer NimbleGen SeqCap EZ Library captures. A Custom capture panel needs to be designed and ordered directly from Roche.
  2. For amplicon-based capture, please contact us.
  3. We will also accept any amplicon that you have amplified, and we will create a sequencing library from the DNA. Sequencing libraries can be prepared for sequencing on Illumina sequencers or PacBio sequencers if amplicon size is too long for Illumina sequencing (typically 600bp).

Methyl-Seq
Methylation sequencing can be done at the whole genome lever or using a cheaper more trageted approach.  Mehyl-seq allows the detection of 5mc, 5hmc, and/or 5fc methylation across a genome.

Sequencing of ChIP/HiC/other DNA
We do not perform ChIP or 4C/5C/HiC protocols, but we will create a sequencing library from the DNA obtained from those protocols and sequence it to the requested specifications.