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In most cases, it is expected that all samples will be collected and phenotyped before applying for the NIH CIDR Program. Possible exceptions should be discussed with CIDR and the NIH supporting institute before applying.
Next Generation Sequencing Platform
Illumina HiSeq sequencers
Agilent SureSelect Human All Exon
51 Mb plus 6.8 - 24Mb custom option
54 Mb Clinical Exome
71 Mb (includes UTRs)
- Sample pretesting with Illumina QC Array which allows us to:
- Determine SNP genotypes for sample tracking and sequencing variant call QC purposes
- Identify file and/or aliquoting errors (primarily gender and/or Mendel discrepancies)
- Identify unexpected relationships among subjects and confirm expected relationships
- Identify samples that perform poorly
- Identify unexpected duplicate samples and confirm expected duplicates
- Provide, at no additional cost, genotypes sufficient for linkage analysis
- Inclusion of study duplicates and HapMap controls.
- Data will be generated to a minimum completeness level of:
- Guaranteed coverage of 90% @ 10x
- Guaranteed coverage of 95% @ 20x
- Data will be generated to a minimum completeness level of 90% of targeted bases at least 10X. Project specific options are available at a higher cost.
- SNVs and indels called and annotated
- Data quality evaluated using a robust alignment and variant calling workflow implemented via CIDRSeqSuite in-house pipeline. Any of the files detailed in the analysis workflow will be available for distribution to the PI.
CNV detection utilizing “counting” methods are also not likely to be highly successful due to the uneven coverage inherent with enrichment chemistry.
Options for Formalin-Fixed Paraffin-Embedded (FFPE) derived DNA
CIDR offers sequencing services for specimens that have been formalin-fixed, paraffin-embedded (FFPE). DNA extracted from FFPE samples exhibit a wide variation in sample quality due to the fixation process and storage conditions. CIDR has developed a workflow optimized for FFPE samples a which includes a qPCR quantitation step, reduced DNA input and a DNA repair step.
Options for Low Input DNA
A reduced input workflow is available for samples which do not meet standard DNA requirements.
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QC chip being placed on the Instrument