Exome Sequencing

In conjunction with the Center For Inherited Disease Research, we have developed an extensive, fully automated, production-scale pipeline for processing of both whole exome and custom capture samples. We currently use Agilent’s SureSelect Target Enrichment platform.

Lower cost subsidized whole exome and custom targeted sequencing services are available through the NIH CIDR Program.

Pricing:

$1350/exome (1-8 samples)

$970/exome (9-72 samples)

$650/exome (batches of 72)

Pricing is for 90% targeted at 20x.  If project needs require a different depth metric, please inquire.

Please inquire about custom capture, as pricing changes depending on capture size and sample volume.  Capture sizes can range from 500Kb and up.

Sample Requirements:

  • 2.5μg of high molecular weight DNA at 50ng/μl
  • DNA should be sent in 1xTE, pH8.0(1mM Tris, 1mM EDTA).  Please avoid using water.
  • DNA source:  blood, cell line, or saliva.  Other sources can be used with caveats.

Service Overview:

  • DNA QC
  • Sample pre-testing using a high density SNP array
  • Automated Library Prep
  • Automated Capture
  • Sequencing to a minimum completeness level of 90% coverage at 20X or greater
  • Target enrichment report, including capture specificity and completeness
  • Quality metrics, including mapping statistics, library fragment size, hybridization and selection metrics, mapping stats, GC bias, and basecall quality distributions
  • Sensitivity/Specificity to SNP array data
  • Concordance with array data
  • Annotated SNP/indel list for targeted regions (dbsnp, snp type, refseq genes, etc.)

Data Quality

We are committed to providing the highest quality exome and custom capture data available. A team of dedicated scientists review every exome produced. Our current analysis team consists of at least 4 scientists, 3 laboratory managers, 3 statisticians, and 3 bioinformaticians.

We sequence to a completeness metric rather than mean depth as the former gives you a much better idea of how many positions are ‘callable’. Depth is a poor metric for assessing the quality of exome data. Capture efficiency, library duplication levels, and library complexity are a few examples of factors that can determine how well your exome is covered.

Data quality is monitored and evaluated using a robust alignment and variant calling workflow implemented via CIDRSeqSuite, our in-house pipeline.

Our pipeline is based on open source tools including bwa, Picard, and the GATK2. We can provide detailed information upon request.

Data Delivery:

Data will be returned via our high speed aspera server.  Our typical release includes the following:

  • Annotated variant lists
  • SNPS/indels in VCF format
  • BAM alignment files
  • QC report
  • BED files for regions targeted
  • Genotyping files
  • Analysis Pipeline details
Place Your Order