QTL Mapping Prototype Data Entry Interface

Mouse Genome Informatics Prototypes

Prototype Complex Trait Data Entry Form

This form is divided into a number of sections representing the major types of data found in QTL papers. Descriptions for most of the fields are hyperlinked to the field name. As this form is not stable, do not be surprised if the fields and their descriptions are out of sync! Just check back in a day or two. If things still don't make sense, contact Carol Bult

Form 1. Author/Publication Data

J Number:
To confirm this J # is correct, click HERE

Form 2. Phenotype Data

Phenotype Class:
Phenotype Mode:
Phenotype Name:
Enter alternative Phenotype Name keywords here (separated by commas):
Enter Comments About Phenotype/Traits:

Form 3. Progeny and Mapping Cross Data

Progeny Population Information:

Only one Progeny Population can be associated with each QTL Experiment.

For Recombinant Inbred and Recombinant Congenic Sets Enter the Following Information


Select the Appropriate RI set designation(s):

Select the Appropriate RC set designation(s):

For F2 and Backcross Progeny Enter the Following Information


Progeny Generation:
Progeny Population Name:
# Animals Evaluated:

Mapping Cross Data:

(There may be more than one Mapping Cross Associated with a Progeny Population)


Female Parent Strain:
Female Strain Type:
Female Parent Phenotype:
Male Parent Strain:
Male Parent Strain Type:
Male Parent Phenotype:
Cross Type:
Other Cross Type:
Comment:
Enter Another Mapping Cross for this Progeny Population?: Yes No

Form 4. QTL Detection and Estimation

Marker Map Construction

Whole Genome Scan?: Yes No

If not a Whole Genome Scan, enter specific chromosome(s) below:

Chromosome:

Marker Map Method :

Marker Coverage

Number of Markers in Analysis:
Intermarker Distance:
Comments on Markers/Map
:

QTL Detection

QTL Detection Test (select all that apply):

Signficance Threshold Used for QTL Detection :

QTL Estimation

QTL Estimation Method (select all that apply) :

Comments on QTL Estimation Model Used

Enter Comments Below:

Software Used in QTL Detection and Estimation

QTL Mapping Software (select all that apply):

Form 5. QTL Data

Phenotype

Trait:

QTL Detection

QTL Symbol :
Marker Symbol:
% phenotypic variation accounted for:
QTL Detection Test :

Marker/QTL Association Score

QTL Effects:

Additivity :
Dominance :
Epistasis :
Comments on QTL Detection
:

QTL Location Estimation

Chromosome:

Chromosome:

QTL Location:

The specific location of a QTL that has been mapped to a chromosome is not known for certain. Thus the location is described using positional probabilities or ranges. For example, QTL locations can be described

  1. as a relatively unspecific location on a chromosome (designated above),
  2. as a range in centimorgans,
    • Between: cM and cM

  3. as an interval bounded by flanking markers (with no metric refinement for location),
    • Between: Marker symbol and Marker symbol

  4. as a peak LOD score an interval bounded by flanking markers (with metric refinement for location),
    Peak LOD Score

  5. relative to the centromere (in cM).

Comments on QTL Estimation
:

The statistical confidence interval for QTL location may or may not be provided in the publication. If it is provided, it should be reported.


Confidence Interval for QTL Location

Candidate Genes Reported in QTL Region

Candidate Gene 1 Symbol:
Candidate Gene 2 Symbol:
Candidate Gene 3 Symbol:
Candidate Gene 4 Symbol:
Candidate Gene 5 Symbol:

In the QTL data retrieval form, there will be an option to show all genes currently known to occur in the QTL region since what is reported in the QTL study will quickly become out of date.


Enter data for another marker for this QTL experiment?: Yes No
QTL Nomenclature Approved?: Yes No
Candidate Gene Symbol Nomenclature Approved?: Yes No

Form 6. Comments

Phenotype affected by:

Transgressive effects noted?: Yes No Not Reported
Modifier genes proposed/identified?: Yes No Not Reported
Confirmatory analyses performed? Yes No