Whole Genome / Exome Sequencing
Technological advancements in DNA sequencing methodologies over the past few years have brought complete interrogation of the genome into reach for today’s top-tier researchers. With many years of DNA sequencing expertise and a proven track record of delivering high value results to its clients, deCODE offers whole genome and whole exome sequencing services. When you work with deCODE to sequence your genomes, we combine a consultative experiment approach, advanced instruments, quick turn-around time, and world-class analytical assistance to help you make breakthrough discoveries.
Our whole genome sequencing service tailors a flexible sequencing approach to the ultimate goals of your experiment. We use the Illumina Genome Analyzer IIx to provide assembled sequence data from paired-end assay, mate-pair assay or a combination of the two methods. For example, a typical whole genome sequencing project could be carried out using a mixture of paired-end (small InDel detection) and mate-pair (large InDel detection) assays. Approximately 90% of the sequencing reactions would use paired-end assays and 10% of the sequencing reactions will use mate-pair assays.
When you work with deCODE to sequence your genomes, we combine a consultative experiment approach, advanced instruments, quick turn-around time, and world-class analytical assistanceAlthough genomes are routinely sequenced to an expected average 30-fold (30X) sequence coverage (the number of times and individual nucleotide is called) we can alter the redundancy to fit the needs of individual researchers. For instance, a scientist may wish to stretch a research budget by sequencing dozens or hundreds of individual genomes by reducing the depth of coverage to an average 4-fold (4X). In cases like this deCODE works with its clients to “pool” the sequence data and search for novel, rare SNPs. Alternatively, if maximum DNA coverage (the total percentage of the genome interrogated by a sequencing reaction) is desired deCODE can engineer the sequencing parameters to increase sequencing coverage and then help you find the needles in the haystack.
For our whole exome sequencing service we use the Agilent SureSelect All Exon Kit to enrich your samples for the 38,000,000 bases in exon regions. Typically, we provide greater than 80-fold (80X) sequence coverage for the exome, giving you targeted insight into your samples of interest.
These services provide image analysis and base calling with Firecrest and Bustard and SNP calling and SAM/BAM file creation with SAM (Sequence Alignment/Map) Tools. Data is delivered as raw FASTQ files and assembled sequence FASTQ files. FASTQ files and other delimited files (SAM/BAM) are standard, accepted sequence data formats and they do contain quality score information for each base sequenced. Data will be made available through secure FTP download as well as delivery on physical media (secure hard disk) to a location of client designation at the completion of the entire project.
Client samples received by deCODE genetics are checked for quality prior to service. All samples are measured by spectrophotometry to obtain A260 / A280 ratio as well as by pico green methods for concentration and quality. If any samples fail to meet deCODE’s intake QC criteria, the client will be contacted prior to service and offered the opportunity to send replacement samples.
In addition to these world class service standards, we offer analytical services including:
- Detection and annotation of small InDels
- Detection and annotation of large InDels, inversions, translocation, and other Copy Number Variants (CNVs)
- Annotation of novel SNPs and InDels by comparison with latest dbSNP build, latest HapMap build, 1000 Genomes database using deCODE proprietary software and algorithms
- Haplotype reconstruction using client genotyping data, latest HapMap build, 1000 Genomes database
- Electronic pooling of whole genome / whole exome sequence data and SNP identification
The deCODE sequencing services offer a limitless variety of approaches to interrogating and understanding the genomes of interest to you. Contact us to find out how we can help you make high-impact discoveries from your sequencing research.
