Loss of heterozygosity (regions of homozygosity in microarrays)

Click here for a more detailed version as a PDF.

The Regions of Homozygosity reported from a microarray test can be used to get a list of genes in those regions. The regions are typically reported as a BED file (Browser Extensible Data), with many lines in one of the following 2 types of format:

chr2  27300000  27330000

or

chr2:27,300,000-27,330,000

You can use either of the 2 formats above to get a list of genes using the UCSC Table Browser using the following steps:

  1. Go to https://genome.ucsc.edu/cgi-bin/hgTables.  If you’ve used this page before, your browser will save your settings in cookies and these will persist even if you refresh the page.
  2. In “assembly” choose the desired assembly, typically Dec. 2013 (GRCh38/hg38) or Feb. 2009 (GRCh37/hg19).
  3. In “track” choose “NCBI RefSeq”
  4. In “region“: 
    • On the first run click the “define regions” button and on the resulting screen, paste many lines of regions such as “chr2:27,300,000-27,330,000” into the text area.
    • On subsequent runs, “defined regions” will be remembered by the browser and already selected; choose “change” or “clear” if you want to change the regions.
  5. Click the “submit” button
  6. In “output format“, choose “selected fields from primary and related tables“
  7. Click the “get output” button
  8. Check the “name2” checkbox
  9. Click the “get output” button

For the single BED file line above and the HG38 assembly, we got the following output consisting of a header line and several lines with HGNC gene symbols, including many repeated symbols:#name2
TRIM54
TRIM54
TRIM54
TRIM54
TRIM54
UCN
MPV17
MPV17
MPV17
MPV17
MPV17
MPV17
MPV17
GTF3C2
GTF3C2
GTF3C2
GTF3C2

Paste the full output from the UCSC tool into the text area at the top of Regions of Homozygosity accessed via the Double Helix on the top black navigation bar.  Don’t bother to remove the header or the repeated HGNC symbols; the Regions of Homozygosity analysis automatically removes these.

When the parents are first cousins, thousands of lines of HGNC gene symbols are obtained, with many repeated symbols but typically ~2,000 unique genes, of which only hundreds will have known human biallelic phenotypes.  From the tiny gene list above, the last time we checked, only the MPV17 gene has a known human phenotype.

When you click the Next button above, you will see the “Genotype” tab of the Dx screen.  If you’ve already entered a robust set of findings for the patient, the genes with highest pertinence for the differential diagnosis for the patient will be high in the list of pertinent genes.  You can enter additional positive or negative findings to help distinguish among the most pertinent genes and choose which to sequence.  The useful findings suggested on the “Add findings” and “Add tests” tabs of the Dx screens can help choose findings on which to comment or other types of testing that can be helpful.