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Resequencing Estimation Table

All applicants requesting Resequencing services must use the information in the following spreadsheet to complete their applications. The information in the Table will provide an accurate estimate of the number of bases to be Resequenced for the proposed project.

The spreadsheet contains resequencing coverage estimations for all genes in the Ensembl version 39 annotation of the NCBI version 36 human genome.
This estimation was made for:

  • (i) Protein coding exons only
  • (ii) All exons (UTR and coding) only
  • (iii) NHLBI Standard (2 kb upstream, all exons, introns conserved with both mouse and rat - calculation methods are outlined below, 2 kb downstream)
  • (iv) NHLBI Full (2 kb upstream, all exons and introns, 2 kb downstream)

For (i), (ii) and (iii), all target regions were flanked by 50 bp. If the target region is sufficiently large overlapping amplicons (of size 575 nts) will be required to cover the region however, the number of bases estimate reports the non-redundant value. Note that estimates are not anchored by primer design constraints which will determine the actual amount of sequencing.

Calculations method for conserved intronic regions: Conserved introns are calculated by using all human-mouse, human-rat pairwise alignments greater than 100 bp and greater than 80% identity. These co-ordinate spans can be found at the ECR browser (ecrbrowser.dcode.org). The genome versions used for the analysis were mm8 (mouse) and rn4 (rat). The final set of human conserved intronic regions was then calculated by using the intersection of the sets of human-mouse and human-rat in human genomic co-ordinates.

Alternatives to Excel

Users who do not have Microsoft Excel can download one of these free alternatives:

PDF Converters

The application process only accepts files in Portable Document Format (PDF). Several products and services are available to create PDF files, some of which are included in this Resources for PDF Products list.

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