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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
Indexed, 100 bp, paired end runs
Agilent SureSelect Human All Exon
51 Mb plus 6.8 - 24Mb custom option
||2.5ug of genomic DNA|
| ||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|
||3 study samples (50Mb product; please inquire for 50Mb plus custom option)
- Sample pretesting with a high density SNP array
- 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 chromosomal anomalies
- Identify ethnic composition (using PCA analysis
- Identify unexpected 1st and 2nd degree relatives among subjects, confirm expected relationships
- Identify samples that perform poorly
- Identify unexpected duplicate samples, confirm expected relationships
- Inclusion of study duplicates and HapMap controls.
- Data will be generated to a minimum completeness level of:
- Guaranteed coverage of 90% @ 8x (mean 100x coverage)
- Guaranteed coverage of 95% @ 20x (mean 150x coverage)
- 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.
Only high coverage sequencing of individual samples is 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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Lab Team Coordinator, Lindsay Aker, examines a plate