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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 or Nimblegen SeqCap
Enrichment Size Options
1.0 - 499 Kb
0.5 - 2.9 Mb
3.0 - 5.9 Mb
6.0 - 11.9 Mb
12 - 24 Mb
- 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 > 95% of targeted bases covered at least 10X. Project specific options are available at a higher cost.
- Data will be generated to a minimum high density SNP array concordance of >99% within targeted regions.
- 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. Image and intensity level data is not retained.
- Analysis Workflow
- Variant filtering will be based on study design (modified VQSR or hard filtering)
CNV detection utilizing “counting” methods are also not likely to be highly successful due to the uneven coverage inherent with enrichment chemistry.
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Lab Team Coordinator Nina DiFabion examines a flowcell