HLA Pedigree Analysis Tool PURPOSE This tool is to identify haplotypes from unphased genotypes of related individuals. This can be performed for any number of families, provided the appropriate format is used. The next two sections describe the proper format of the data and operation of the pedigree analysis tool. The subsequent sections provide more information on the tool itself. NOTE: the families currently in the field are examples and not real individuals. Any resemblance to HLA genotypes living or dead is coincidental. FORMAT The input field requires an individual identifier (ID), relation to the reference person (Relationship), and the typings for HLA‐A, ‐B, ‐C, ‐DRB1, and –DQB1, in that order. The first person in each family must have a relationship of “patient”, “donor”, “self”, or “target”. The tool looks for this relationship to determine where the data is divided between one family and other. The pedigree analysis tool computes the probability of sharing exactly one haplotype by inheritance with respect to this individual. And example family of a patient and a sibling: ID Rel Alpha Self Beta Sib A1 A2 B1 02EZMM 02EHST 35EGSP
24:02 02:FDUC 39:06
B2
40HHUN
40:HPNT
C1
C2
DRB11
04FKSU
08:02
DRB12 DQB11
04FKST 04:FAZU DQB12
Note that the pedigree analysis tool is able to handle either version 2 or version 3 nomenclature or a mixture of the two. The proper format for entering this into the pedigree analysis tool is comma‐delimited lines. The above family would be: Alpha,Self,02EZMM,02EHST,35EGSP,40HHUN,,,04FKSU,04FKST,,
Beta,sib,24:02,02:FDUC,39:06,40:HPNT,,,08:02,04:FAZU,,
Note that the untyped loci (in this case, HLA‐C and DQB1) require comma separation as placeholders. At present, the pedigree analysis tool assumes the locus by position. For users of Microsoft Excel or other spreadsheet software, individual datasheets can be exported as comma‐delimited files, indicated with a .CSV extension. To do this: 1. Click on the sheet you wish to export 2. Find the “Save As” command (it may be necessary to select “Other Type” under the “Save As” menu) 3. Near the bottom, there should be a field with a label similar to “Save as type” 4. Scroll through the options to find either CSV or comma delimited 5. Name the file and save OPERATION The current tool requires cut‐and‐paste on the part of the user. Figure 1 shows the initial state of the pedigree analysis tool with sample data included. Use is fairly straightforward. 1. Select and delete sample data from the input window 2. Copy and paste data to be analyzed to the input window 3. Click on the “Analyze Typings” button below the input window 4. Results appear below the input window (Figure 2) Figure 1. Initial appearance of the HLA Pedigree Analysis Tool with sample data. This should be how the
page appears when the user first opens the link.
The output is separated by family (Figure 2) with the ID of the first person (designated as either “donor”, “patient”, “self”, or “target”) is used as the family identifier. Notes for each locus follow the haplotype pair for each person. These notes represent comments or explanations of the results. These notes are in the order of the data input: HLA‐A, ‐B, ‐C, ‐
DRB1, and ‐DQB1. The current version has reported issues with these return notes (see below). Results may be downloaded using the link in the bottom section just below the heading “CSV output.” The results are in a comma delimited format that is readily imported into spreadsheet software or parsed for further analysis. Figure 2. Output from the sample data shows the identification of haplotypes. Each family is presented
separately. The two haplotypes of each individual are followed by notes on the loci. The notes follow the
order of loci as presented in the haplotypes. At the bottom is a link to download the results and a comma
delimited form the output that can be copied and pasted.
ALLOWED RELATIONS The current tool is limited in the number of types of familial relations allowed and focuses on the immediate family (parents, siblings, children). Relations are converted into a standard format used to calculate the probability of sharing exactly one haplotype by inheritance. Any unrecognized relation is given the “other” designation. Any relation with designation of “other” is still included in haplotype resolution, but is given lower relevance. Although limited, the pedigree analysis tool is still capable of resolving relations even if all relations, except the initial “self”, have the “other” designation. The results will not be as robust compared to the other familial designation. NOTE: A quirk of the current tool is it allows an individual to have any number of parents. This is discussed below. These are the allowed relations: Relation Designation Relation Designation Self Sibling Target Sib Self Patient Sib1 Donor Sib2 Mother Sib3 Father Parent Sib4 Sibling Parent Sib5 Child Sister Kid Brother Child Son Half‐Sib Daughter 1/2 Sib QUIRKS AND KNOWN PROBLEMS Family Relations  An individual may have an unlimited number of parents. Equal weight will be given to the haplotypes resolved for the reference person, siblings, and the children of the reference person.  Grandparents, grandchildren, nieces, nephews, aunts, and uncles will receive the designation of “other.”  Resolving haplotypes is focused on the reference person. The more distantly related to the reference person, the less rigorous the results. Allele Codes  Alleles corresponding to the allele codes are read from a flat file. As more allele codes are generated, this file will become more out of date. Return Notes  The return notes have not been well implemented. The code reflects whether the situation occurred with any of the relations. It is intended to reflect issues that occur when no call can be made for a locus.  Inaccurate return notes have been reported. The matter is being addressed. Reported Errors PLANNED IMPROVEMENTS Several improvements are under development.  Extended families  Inference of alleles based on shared haplotypes  Routine updating of allele codes  No requirement to designate a self/target/patient/donor SUGGESTIONS? We are always eager for suggestions on how to improve this tool! Whether it is user interface, performance, or any other improvements, we’re happy to consider any way to make this tool easier and more useful. Feel free to email the developers at: [email protected]