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Genetic Marker Maps Overview

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4.1 Genetic Marker Maps Overview

Genetic marker maps contain chromosome and distance data for individual SNP or CN markers relative to some origin, as well as other data relative to the genetic markers.

Although it is possible, normally SVS is not used to analyze genetic marker map data in its own right. Rather, genetic marker map data is associated with one or more data files containing genetic marker data that are actually being studied. Frequently, a team of analysts will have one master genetic marker map which it will use for all analysis relating to a specific study or project.

Genetic marker map files must either be downloaded from the Golden Helix, Inc. data server, Affymetrix NetAffx service, or may be imported from a text file with the values separated by commas, spaces, tabs, or another character.

At a bare minimum, there must be three columns in the genetic marker map. These columns must include:

  1. Identifiers for the genetic markers
  2. Chromosome information
  3. Distance or position information (absolute within the current chromosome)

Optionally, the genetic marker map can contain additional columns in any combination. These columns can contain any of the other fields in an Affymetrix Annotation file, or other fields listed in a text marker map. A marker map can be applied to a spreadsheet containing genetic SNP or CNV data. This will create a resulting spreadsheet whose columns are sorted according to first, chromosome, and second distance. In addition, marker map information will be stored as meta data associated with either the columns or the rows of the resulting spreadsheet, depending on if the marker names are column headers or row labels.

A marker mapped spreadsheet will have a green node icon.

Genetic marker maps need to be applied to spreadsheets for various analyses and for the plotting data in a Genome Browser. In the spreadsheet, the marker map data can be viewed by clicking on the green Map button in the upper left hand corner of the spreadsheet. Marker map fields can be hidden so that only the desired fields are shown. This is done by right-clicking on the Map button and un-checking the undesired fields by clicking on the field name. To re-show the field, click on the name again. There must be at least one field checked at all times, but this one field can be any of the fields in the marker map. To hide all fields, left-click on the Map button again.

NOTE:

  1. Versions of SVS on or after release 7.0 allow for more than six fields to be in the marker map.
  2. The current marker map sort order (for versions of SVS on or after release 4.4.2) is, as stated above, chromosome and distance.
  3. Versions of SVS between releases 4.3.0 and 4.4.2 sorted marker maps and their mapped spreadsheet columns according to chromosome, region name, gene name, and finally distance.
  4. Versions of SVS before release 4.3.0 sorted marker maps according to chromosome, region name, and distance.
  5. Versions of SVS on or before release 3.1.0 left the columns of the resulting spreadsheet in the same order as the original spreadsheet. Their maps, however, were still considered to be sorted (by chromosome, region name, and distance).

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