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1.
Figure 4

Figure 4. From: GeneLink: a database to facilitate genetic studies of complex traits.

Liability classes Within GeneLink liability classes can be defined using any combination of age, sex, and affection status.

Elizabeth M Gillanders, et al. BMC Genomics. 2004;5:81-81.
2.
Figure 1

Figure 1. From: GeneLink: a database to facilitate genetic studies of complex traits.

Main menu GeneLink's main menu available following login. GeneLink is a platform-independent, Web-accessible database. Access to GeneLink is password-protected. Here the user (lgilland) has been given import, export, view, and admin, permissions.

Elizabeth M Gillanders, et al. BMC Genomics. 2004;5:81-81.
3.
Figure 5

Figure 5. From: GeneLink: a database to facilitate genetic studies of complex traits.

Export by chromosome The Export Genotype Data screen prompts users to specify 1) which chromosome to export, 2) which trait(s) to export (Status Field), 3) how to define liability classes, 4) what file format is desired and 5) which families to include in the export.

Elizabeth M Gillanders, et al. BMC Genomics. 2004;5:81-81.
4.
Figure 7

Figure 7. From: GeneLink: a database to facilitate genetic studies of complex traits.

A, and B. Import process Outline of Import process illustrates GeneLink's ability to be used in laboratories that include duplicated samples and double scoring for quality control purposes. Import process includes within table duplicate check and across table differences check. Using the Single table import allows the differences step to be skipped.

Elizabeth M Gillanders, et al. BMC Genomics. 2004;5:81-81.
5.
Figure 6

Figure 6. From: GeneLink: a database to facilitate genetic studies of complex traits.

Export report GeneLink's Export Report provides a summary of all pertinent information relating to an export. This includes the file name (which incorporates the project ID, chromosome exported, user ID, and a random number), date the file was created and by whom. The Export Report also records which chromosome, phenotypes (status field) and families, were exported and in what file format. Finally, the Export Report also provides the distance between markers being exported.

Elizabeth M Gillanders, et al. BMC Genomics. 2004;5:81-81.
6.
Figure 3

Figure 3. From: GeneLink: a database to facilitate genetic studies of complex traits.

Allele translation The Allele Translations table provides a key linking the "translated" allele (Translation) to the original size in base-pairs score (Allele). All LINKAGE or RelCheck exports will use identical "allele translation codes." In this example, 15 alleles have been identified for marker D1S206. New alleles identified after the first export (in this example alleles 10 to 15) will be added to the end of a marker's allele translation ensuring consistent recoding of alleles across families.

Elizabeth M Gillanders, et al. BMC Genomics. 2004;5:81-81.
7.
Figure 9

Figure 9. From: GeneLink: a database to facilitate genetic studies of complex traits.

Status report GeneLink's status reports allow collaborators to easily tract the project's progress by site. Reports show markers by chromosome (in map order) and the status of each marker for each site. By site, markers can be Not started, In Lab, Genotypes Imported, Single Table Imported, Waiting for Comparison, Compared and Ready, Ready to Finalize and Ready to Export. Data can be exported only after all markers on a given chromosome for a given site are Ready to Export. In this example we are looking at markers D21S1256, D21S1914, D21S1909, D21S1252, D21S2055, D21S266, and D21S1446 on chromosome 21 for sites JHU, AAHPC, AAHPC2, Sweden, Finland and Michigan. Here data is ready to export for family sites AAHPC2 and Sweden.

Elizabeth M Gillanders, et al. BMC Genomics. 2004;5:81-81.
8.
Figure 2

Figure 2. From: GeneLink: a database to facilitate genetic studies of complex traits.

Relational design Relational design of GeneLink's 11 primary tables. Primary keys are indicated in red and foreign keys in blue. GeneLink enables pedigree information stored in the Families and Pedigrees tables to be easily merged with genotypic data stored in the Genotypes table. In the Pedigrees, Liability Classes, Trait Score, and Trait Translation tables GeneLink also manages extensive phenotypic data. The Markers and Primer tables store information regarding polymorphisms being genotyped and the Maps table stores genetic or physical map information, which determines the order in which data is exported. GeneLink's Primer and DNA tables provide labs with an easily implemented inventory system.

Elizabeth M Gillanders, et al. BMC Genomics. 2004;5:81-81.
9.
Figure 10

Figure 10. From: GeneLink: a database to facilitate genetic studies of complex traits.

A, and B. Marker (A) and individual (B) summaries GeneLink's Marker Summary provides success rates and heterozygosity for individual markers typed in the study. The Marker Summary also provides information regarding when the genotype records for this marker were imported (Import Dates). Marker quality can also be evaluated using the Flags column. Genotypes can be flagged with a T to temporarily blank scores from analyses. This is used for un-resolvable Mendelian inconsistencies. The R flag can be used for replaced DNA samples until the new DNA sample is evaluated. Neither T nor R flagged genotypes are exported. Individual summaries also provide global quality assurance information such as success or flag rates.

Elizabeth M Gillanders, et al. BMC Genomics. 2004;5:81-81.
10.
Figure 8

Figure 8. From: GeneLink: a database to facilitate genetic studies of complex traits.

A, B, and C. Example of import (A), duplicates (B), and differences (C) reports Import report stores all information regarding genotypes imported into GeneLink. This information includes number of records imported (how many unique individuals, how many markers) as well as the name of the file in which records are stored. The duplicates process checks for duplicate genotypes within a table. A duplicate is defined as records with the same FamInd ID and marker. All duplicate records are reported. If duplicate records have the same two alleles then one record is deleted. If the two duplicate records do not have matching alleles than the user is prompted to select which record to delete. The differences process looks for differences in genotypes compared across tables (independently scored by two researchers). All differences are reported and the user is prompted to resolve each appropriately. The user is given the option to save either record or if either score isn't acceptable then new genotype can be indicated.

Elizabeth M Gillanders, et al. BMC Genomics. 2004;5:81-81.

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