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Custom Targeted

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.

NIH CIDR Program Application Details

Next Generation Sequencing Platform

Illumina HiSeq sequencers

Run Parameters

Indexed, 100 bp, paired end runs

Enrichment Method

Agilent SureSelect Target Enrichment

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 Requirements

	Total:	2.25ug of genomic DNA
	Concentration:	30ng/ul (75ul)
	Diluent:	DNA should be sent in 1XTE, pH 8.0 (10mMTris, 1mM EDTA). Do not use water
	Sources:	Blood, cell line or saliva
		Please inquire about other DNA sources

Services Include

Sample pretesting with 96 SNP barcode panel for all samples, 10% of samples will also have a high density SNP array run to better assess sequencing variant calling quality
This 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 1st degree relatives among subjects, confirm expected relationships
Identify samples that perform poorly
Identify unexpected duplicate samples, confirm expected duplicates

Inclusion of study duplicates and HapMap controls.
Data will be generated to a minimum completeness level of > 95% coverage at 8X.
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

Only high coverage sequencing of individual samples are supported. We cannot accommodate the analysis of pooled samples or low coverage study designs at this time.

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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