RESEQUENCING Application Template

November 1, 2006, Application Submission

**Please note that your application may not exceed 10 pages.
Supplementary documents, listed in the last section of this template,
are NOT included in this page limit. Instructions and explanatory text
provided in italics and included within brackets in this template, for
example, *{Limit to 250 characters.}*, should be removed or replaced
with your actual text when completing your application. Please note that
your completed application must be submitted as a clearly labeled,
separate electronic Portable Document Format (PDF) file. Instructions
for creating PDF files are available at
[http://rsng.nhlbi.nih.gov](http://rsng.nhlbi.nih.gov/).**

# Project Title

## Project Title

*{Limit to 250 characters.}*

# Principal Investigator Information

  ------------------------------- ------------- ---------- ------------- ------------- --------------------
  **Name:**                                                                            

  **Title:**                                                                           

  **Affiliation                                                                        
  (Organization/Institution):**                                                        

  **Address:**                                                                         

  **City, State, ZIP Code:**                                                           

  **Telephone:**                                **Fax:**                 **E-mail:**   
  ------------------------------- ------------- ---------- ------------- ------------- --------------------

# Alternate Contact Information

  ------------------------- ------------------- --------------------------
  **Name:**                 **Telephone:**      **E-mail:**

                                                
  ------------------------- ------------------- --------------------------

# Key Personnel Information

*{In the table below, list key personnel on the project.}*

  -----------------------------------------------------------------------
  **Name:**               **Affiliation:**        **Role on Project:**
  ----------------------- ----------------------- -----------------------
                                                  

                                                  

                                                  

                                                  

                                                  

                                                  

                                                  

                                                  

                                                  

                                                  
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# General Project Information

## Summary Description of Request

*{Provide a concise summary description of your request to the RS&G
Service. Limit to 500 words. (Note: This is not the same as an abstract
of the grant or overall research project to which this request is
related, but rather a summary description of the specific request you
are making to the RS&G Service.)}*

## Resubmission or Previous Review

*{Indicate whether this request is a resubmission to the RS&G Service.
If yes, provide a maximum of two pages addressing the criticisms from
the previous RS&G Service review of this project*. (Note: Two
resubmissions are permitted ensuing original submission.)}

  -------- --------------------------- -------- ---------------------------
           **Yes**                              **No**

  -------- --------------------------- -------- ---------------------------

## Project Funding

*{Provide the following funding information for the larger project to
which this project is related.}*

  ----------------- ----------------- ----------------- -----------------
  **Grant Name:**                                       

  **Source:**                                           

  **Grant Number:**                   **Funding         
                                      Amount:**         

  **Funding Start                     **Funding End     
  Date:**                             Date:**           
  ----------------- ----------------- ----------------- -----------------

## Potential Overlap

*{Discuss any scientific and/or budgetary overlap of this application
with your current and future funding.}*

# Sample Information

*{If multiple panels are planned to be assayed against different sets of
genomic regions, please include separate subsections for each DNA
Panel‑Genomic Regions combination (subsection 6.1 \<Set#\>, 6.2
\<Set#\>, 6.3 \<Set#\>, etc.). For example, to specify two DNA panels
each with a different list of genomic regions, describe the first DNA
panel in subsection 6.1.1, describe the second DNA panel in subsection
6.1.2, describe the desired genomic regions for the first DNA panel in
6.2.1, describe the desired genomic regions for the second DNA panel in
6.2.2, describe the total project size in section 6.3, describe the
project size for the first panel in subsection 6.3.1, and describe the
project size for the second panel in subsection 6.3.2.}*

## Description of the DNA Sample Information

*{Depending on the total number of amplicons required for the study and
the plate layout used for high‑throughput processing, the resequencing
laboratories may recommend modification to sample panel sizes and
genomic regions in order to reduce the number of empty wells on
processing plates. Sample panel sizes as multiples of 47 and/or 94 are
strongly encouraged.*

-   ***Standardized DNA Panel:** Coriell Cell Repository DNA panels from
    the major ethnic groups (African, African American, European, or
    Asian) that can be used for development of an SNP map. For projects
    using a standard DNA panel, indicate which panel, the number of
    samples requested, and the rationale for the selection.*

-   ***Investigator-Supplied DNA Panel:** The investigator must supply
    high-quality DNA samples. Pending approval, these samples will be
    used for the resequencing project. The amount of DNA required is 120
    ng per 1 kb of baseline sequence to be processed. The investigator
    is required to calculate the amount of DNA available, given the
    amount of baseline sequence to be generated per sample (determined
    by the investigator in section 6.2 below) using:*

    -   *0.120 X total baseline sequence in kb = ug DNA required per
        sample*

    -   *Therefore, if an investigator determines that he or she would
        like to obtain (after completing the Genomic Region Description
        Table in Section 6.2 below) 10 kb of baseline sequence per DNA
        donor, then the investigator would need to have on hand 10 x 120
        ng DNA = 1.2 ug DNA to provide to the resequencing laboratories.
        For projects using an investigator-supplied DNA panel(s),
        indicate the number of samples requested for resequencing and
        the rationale for their selection. In addition, provide a
        justification for using these panels rather than Coriell Cell
        Repository DNA panels.}*

## Genomic Regions

  ------------------- ----------- ---------------- -------------- ------------
  **Gene Name (HUGO   **Entrez\   **Gene           **Coverage     **Number of
  or ENSEMBL_ID) or   Gene ID**   Reference**      Preference**   bp From Gene
  RefSeq ID or                                                    Identifier
  Region**                                                        and Sizing
                                                                  Table**

                                                                  

                                                                  

                                                                  

                                                                  

  **Total bp**                                                    
  ------------------- ----------- ---------------- -------------- ------------

*{Complete the table above to describe the regions you are requesting
for resequencing. Refer to the Gene Identifier and Sizing Table
spreadsheet found at <http://rsng.nhlbi.nih.gov/scripts/resources.cfm>
to determine the size of the region in base pairs. Enter this value,
selecting from either "Standard" or "Full" coverage values. A
description of each cell within the table above follows below:*

-   ***Gene Name (HUGO) or RefSeq ID or Region***---*List the accepted
    gene name or investigator-assigned region name. For HUGO genes, list
    the resource used to reference this gene (ENSEMBL, UCSC).*

-   ***Entrez Gene ID***---*Each HUGO gene should have a corresponding
    Entrez Gene ID found at
    <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene>.*

-   ***Gene Reference***---*Enter* *resource used to identify the gene
    or region and gene collection. The most common resources will be
    either ENSEMBL or UCSC, and the most common gene collections will be
    RefSeq or Ensembl*.

-   ***Coverage Preference***---*For each genomic region, select one of
    the available options below:*

1.  ***Standard Resequencing Coverage** (exon and conserved noncoding
    sampled)**:** This option covers approximately 5 to 10 percent of
    the genomic region and includes*

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a.  *2 kb upstream of the 5' most exon*

b.  *Full exon coverage (intron/exon boundaries)*

c.  *Conserved (mouse and rat) noncoding regions (criteria to be
    determined based on UCSC data)*

d.  *2 kb downstream of the 3' most exon*

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```
2.  ***Full Resequencing Coverage** (complete coverage)**:** This option
    covers approximately 85 to 95 percent of the genomic region and
    includes*

```{=html}
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```
a.  *2 kb upstream of the 5' most exon*

b.  *Full exon coverage*

c.  *Full intron coverage*

d.  *2 kb downstream of the 3' most exon*

> ***Only regions refractory to PCR amplification or sequencing (e.g.,
> low-complexity repeats) are excluded.***

3.  ***Custom Resequencing Coverage:** Provide specific genomic
    coordinates (chromosome, begin, end) on the most current version of
    the human NCBI build (currently 36) for each proposed region. Note:
    If you specify multiple genes at a given locus, indicate if you
    would like intergenic regions to be scanned and the level of
    coverage (e.g., sampled every 10 kb, resequencing of conserved
    noncoding regions, etc.).*

-   ***Number of bp from Gene Identifier and Sizing Table completed in
    table above***---*Enter* *total baseline sequence for the desired
    region to be sequenced. For genes found in the Gene Identifier and
    Sizing Table spreadsheet (located at
    <http://rsng.nhlbi.nih.gov/scripts/resources.cfm>), include this
    value, selecting from either "Standard" or "Full" coverage values.
    For genomic region, define the length between the 5' most to the 3'
    most position*.*}*

## Total Project Size

*{"Total bp" X "Total number of samples" = "Total Project Size" (Show
calculations.)}*

# Project Details

## Description of the Disorder or Trait 

*{Describe the disorder or trait to be mapped. Include a complete
outline of the phenotypic evaluation of study subjects and justify the
use of the service for this effort, if applicable. Where appropriate, be
sure to include specific criteria for inclusions and exclusions.}*

## Background Information

*{Describe any unique features of the disorder/trait that would single
out this project for special consideration. Provide background
information about your previous research, including the rationale for
carrying out this particular study.}*

## Genetic History 

*{Give the genetic history/ancestry of the sample population(s) and
indicate if the study populations are thought to be relatively isolated
genetically.}*

## Evidence of the Trait's Heritability

*{Provide evidence of the trait's heritability.}*

## Brief Description of Studies Identifying This Region as a Target for Resequencing 

*{Give a brief description of studies identifying this region as a
target for resequencing.}*

## Availability of Information Regarding This Region

*{If available in dbSNP (<http://www.ncbi.nlm.nih.gov/SNP/index.html>)
or HapMap
([http://www.hapmap.org/](http://www.hapmap.org/cgi-perl/gbrowse/gbrowse/hapmap)),
specify here:*

-   *The number of SNPs identified in the targeted region and their
    dbSNP identifier (e.g., rs number).*

-   *The average allele frequencies of each SNP in the targeted region.*

-   *Identification of the SNPs with genotype data in the targeted
    region.*

-   *The version of dbSNP you used and date viewed (e.g., Build 124,
    February 9, 2005).}*

## Data Analysis

*{Describe analysis plans for the data, including the methodology and
any specific software to be used. For example:*

-   *How would you use the genotype data generated by sequencing?*

-   *How would you determine the potential functional impact of variant
    information, whether it has been previously described (in public
    database) or novel?*

-   *Describe any analyses of statistical association that you may
    perform with such variant information.}*

## Data Use and Dissemination 

*{Describe the plan to use the data generated by this project and any
plans to share the data with other investigators or programs (e.g., with
coordinating centers or curators for projects such as the Framingham
Heart Study or the Pharmacogenetics and Pharmacogenomics Knowledge
Base).}*

**RS&G Service Data Release Policy**: It is the policy of the NHLBI RS&G
Service to submit variation data to public databases (dbSNP currently)
after a minimum delay of 1 month from the date that the variation data
have been delivered to the investigator. (For complete policies, refer
to the Application Guidelines page at
<http://rsng.nhlbi.nih.gov/scripts/appCriteria.cfm>.)

  -- --------------------------------------------------------------------
     **Yes, I will adhere to the NHLBI RS&G Service data release
     policies.**

  -- --------------------------------------------------------------------

  -- --------------------------------------------------------------------
     **No, I cannot adhere to the NHLBI RS&G Service data release
     policies**

  -- --------------------------------------------------------------------

> (**Provide reason for declination below.** If a longer minimum delay
> is necessary, you must submit a request specifying the revised
> timeframe and providing complete details to justify the extension
> beyond 1 month, for example, if the DNA samples to be used have been
> obtained from another project that has conflicting formal written
> guidelines.)

**RS&G Service Acknowledgment Statement**: If your application is
approved and you receive resequencing services, we ask that any
publications resulting from the resequencing data you receive contain an
acknowledgment of the Laboratory Center that provided the service:

"Resequencing services were provided by the University of Washington,
Department of Genome Sciences, under U.S. Federal Government contract
number N01-HV-48194 from the National Heart, Lung, and Blood Institute."

Or

"Resequencing services were provided by J. Craig Venter Institute under
U.S. Federal Government contract number N01-HV-48196 from the National
Heart, Lung, and Blood Institute."

  -- --------------------------------------------------------------------
     **Yes, I will acknowledge receipt of resequencing services in all
     publications.**

  -- --------------------------------------------------------------------

  -- --------------------------------------------------------------------
     **No, I cannot acknowledge receipt of resequencing services in all
     publications.**

  -- --------------------------------------------------------------------

**(Provide reason for declination below.)**

## Future Research Plans

*{Provide future research plans and the impact of resequencing on future
research plans.}*

## Applicant with Previously Approved Project

*{Please provide a brief description of the outcome of use of data from
previous service request (if applicable). An assessment of this
information will be a factor in evaluating the current request to use
the NHLBI RS&G Service.}*

Supplementary Documents

*{The following supplementary documents should be submitted with your
completed application when appropriate. These documents are NOT included
in the 10-page limit for your application. Submit each as a clearly
labeled, separate electronic Portable Document Format (PDF) file to
accompany this application. **Please note that all files must be in PDF
format. (Instructions for creating PDF files are available at
[http://rsng.nhlbi.nih.gov](http://rsng.nhlbi.nih.gov/).) ***

Pedigree Diagrams

*If appropriate, pedigree diagrams may be included along with a key for
all symbols and data.*

IRB or Equivalent

*For non-Coriell DNA, provide documentation indicating IRB approval to
genotype the DNA samples. Accompanying documentation (supporting letter
or Material Transfer Agreement) should also indicate that samples will
be anonymous, and under no circumstance will any existing link between a
unique identifier and an individual be provided.*

Biographical Sketches of Key Personnel

*Use NIH format*.

Support Letters from Collaborators

Literature Cited

Reprints or Preprints

*If appropriate, include a maximum of two supporting manuscripts that
you consider essential for the review of this application.}*