Genotyping Application Template

February 2, 2009 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 NHLBI
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 NHLBI RS&G Service.)}*

## Resubmission or Previous Review

*{Indicate whether this request is a resubmission to the NHLBI RS&G
Service. If yes, provide a maximum of two pages addressing the
criticisms from the previous NHLBI 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 (overall)
project to which this request 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 and Marker Information

## Candidate Genes

*{For projects focusing on candidate genes, provide a list of candidate
genes to be genotyped and discuss the rationale for candidate gene
selection.}*

## SNP Selection

*{Specify the number of SNPs requested, which must be 96, 384, 768,
1536, or multiples of 1536.}*

*{Describe the rationale for SNP selection (density, frequency,
heterozygosity, level of validation, relevance for the ethnic/racial
background of the study, etc.). SNPs can be in one or multiple
chromosomal regions or within candidate genes. Provide an overview of
SNP selection.}*

*{Since not every SNP will work with the Illumina system, their design
scores will need to be combined with other criteria to select your final
set of requested SNPs. Investigators are encouraged to submit their SNPs
to the Illumina Assay Design Tool prior to application submission and to
provide the Illumina design scores with their application (in the SNP
list document) if available. To obtain the design scores, submit a list
of rs numbers, a list of gene names, a region list, or a sequence list
to Illumina technical support (techsupport-ilmn@illumina.com).
Instructions for use of the Illumina Assay Design Tool as well as
templates for submission of these lists can be found at
<http://www.illumina.com/pages.ilmn?ID=75>. A poster describing the
Genotyping Center's experience with Illumina Golden Gate chemistry SNP
selection is available at
http://snpcenter.grcf.jhmi.edu/downloads/ILMNposter.pdf. The Genotyping
Center staff is also available for advice.}*

*{If a final SNP list is not submitted with this application, or if
small changes need to be made after application submission, a final SNP
list should be completed within 1 month of approval notification. DNA
samples and other materials should be sent no later than 2 months after
approval notification. If you are unable to meet this schedule, please
contact NHLBI to request a delay and communicate a revised schedule to
the genotyping laboratory.}*

*{Submit a SNP list as a supplemental document (refer to the last
section of this template). This list will include the Illumina design
scores.}*

## Number of Samples

*{Give the number of samples to be genotyped. (Note: We strongly suggest
submitting samples in multiples of 90 as 90 experimental samples are
used in each plate.)}*

## Total Project Size

*{Total number of samples X total number of SNPs. (Show calculations.)}*

*Examples of size calculations are as follows: 384 SNPs X 630 samples
for 1.04 M genotypes or 1536 SNPS X 1260 samples for 1.94 M genotypes.
Contact the NHLBI if your project exceeds 4 M genotypes.*

## DNA Source and Extraction Method

*{Specify the source of the DNA and the extraction method.*

*Optimal results are obtained with high molecular weight genomic DNA. We
require 35 ul of DNA at a concentration of 75-150 ng/ul. We discourage
the use of whole genome amplified DNA samples but if they are used, we
recommend a higher concentration range (200-400ng/ul). }*

## Approximate Number of Parent-Parent-Child Trios

*{Include this information if relevant to your sample population. This
information is useful for internal quality control.}*

# Project Details

## Specific Aims

*{Describe in fewer than 500 words why the outcomes of this analysis may
be significant to the scientific community.}*

## Description of the Project

*{Describe the previous research that serves as the basis for this
genotyping request. Include the following in the description:*

-   *For projects following up linkage, describe the original mapping
    project, including the strength of evidence for linkage.
    Investigators are encouraged to focus on a few of the best regions.
    Include plots of the genomewide linkage analyses or, if a scan has
    not been completed, equivalent results from the chromosomes that
    have been scanned. Include a brief description of analyses used to
    derive the results.*

-   *For projects following up one or more linkage signals, state
    whether the proposed sample is the same as that used for the
    original mapping project; if not, describe and justify the proposed
    study sample.*

-   *If published reports from other investigators support the proposed
    regions(s) being fine-mapped, describe these results. If there are
    none, please indicate as such.*

-   *If appropriate, include the number typed per pedigree, number
    affected and typed per pedigree, and numbers of affected relative
    pairs that are typed.}*

## Description of the Disorder or Trait

*{Describe the disorder or trait being investigated and describe any
unique features of the disorder/trait that would single out this project
for special consideration. Include a complete outline of the phenotypic
evaluation of study subjects.}*

## Background Information

*{Provide background information about your previous research, including
the rationale for carrying out this particular study.}*

## Genetic History

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

## Project Sample

*{Describe the project sample, including sample selection criteria
(specific criteria for inclusions and exclusions). Briefly describe any
previous genotyping of the samples (e.g., genes or SNPs previously
genotyped in the sample).}*

## 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.}*

**RS&G Service Data Release Policy:** It is the policy of the NHLBI RS&G
Genotyping Service to submit summary allele frequency information to
public databases (dbSNP currently) after a minimum delay of 1 month from
the date that the data have been delivered to the investigator. Unless
otherwise instructed, the source of the data will be anonymous and will
not identify the PI's name or study details. (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 genotyping services, we ask that any
publications resulting from the genotyping data you receive contain the
following acknowledgment of the Laboratory Center that provided the
service:

"Genotyping services were provided by the Johns Hopkins University under
U.S. Federal Government contract number N01-HV-48195 from the National
Heart, Lung, and Blood Institute."

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

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

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

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

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

## Data Analysis

*{Provide power calculations. Describe analysis plans for the data.
Include approaches and any specific software to be used. If appropriate
for the study design, discuss the following:*

-   *How map errors will be assessed since genetic maps are based on
    interpolations of existing wider spaced marker maps and are likely
    to contain errors.*

-   *How genotyping errors will be detected and what will be done to
    address these errors during data analysis.*

-   *How linkage disequilibrium among the SNPs will be accounted for
    since many linkage software programs assume linkage equilibrium
    among all marker loci.}*

## Future Research Plans

*{Provide future research plans and the impact of genotyping 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/).) ***

SNP List

*Required document from section 6.2.*

Pedigree Diagrams

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

IRB or Equivalent

*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 circumstances 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*.