BioMart and Browser Task

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We walk you through this exercise – follow along on your browser.

Answer 6

A DELETION ON CHROMOSOME 6 ASSOCIATED WITH MENTAL RETARDATION

Human 

GOAL

In this tutorial, we will explore a deletion on the short arm of human chromosome 6 associated with mental retardation using the Ensembl browser and BioMart.

 

BACKGROUND

Krepischi et al detected a heterozygous deletion on 6p21 in a patient with mental retardation. Using array CGH, the deletion was mapped to a 812.77 kb segment on 6p21.31–21.32 (chr6:33,273,955–34,086,729); the distal breakpoint was mapped to a 14.3 kb interval (chr6:33,259,651–33,273,955); the proximal breakpoint was located on a 123 kb segment (chr6:34,086,729–34,209,880).

Note: the genomic coordinates mentioned above are relative to the GRCh37 (hg19) genome assembly.

See also: Krepischi ACV, Rosenberg C, Costa SS, Crolla JA, Huang S, Vianna-Morgante AM. 2010. A novel de novo microdeletion spanning the SYNGAP1 gene on the short arm of chromosome 6 associated with mental retardation. Am J Med Genet Part A 152A:2376–2378.

 

 

Steps

TOPICS COVERED

  1.  Viewing the deletion and its breakpoints (displaying DECIPHER in) the Ensembl web browser
  2. Retrieving a list of the genes encompassed by the deletion using BioMart

 

(1) Viewing the deletion and its breakpoints using Ensembl

Search the region 6:33259651-34209880 in the human genome and note the overview of the whole deleted region, including the breakpoints.

Go to the Ensembl v70 homepage (http://www.ensembl.org).

Click the Human icon. Search for 6:33259651-34209880 in the text box.

Click Go.

This directly leads to the Region in detail page. Note that our region of interest is indicated by the red box in the 1Mb overview panel (middle panel) and shown in more detail in the bottom panel.

Before adding new tracks, first remove any tracks added in the previous exercises.

Click Configure this page in the side menu.

Click Reset configuration.

Click on the tick.

Help

hovering over the track title and clicking the Turn track off icon in the pop-up menu can also delete individual tracks.

Add the DECIPHER (DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources) track. Note this an external data track.

Click Configure this page in the side menu.

Type decipher in the Find a track box.

Select decipher – Normal.

Click on the tick.

 

To have a closer look at the distal breakpoint, simply change the coordinates at the top of the bottom panel.

Change the coordinates in the Location box to 6:33259651-33273955, for example.

Click Go.

Similar for the proximal breakpoint: change the coordinates in the Location box to 6:34086729-34209880.

Click Go.

 

Question 1a

Do the breakpoints encompass any genes?

Yes, the distal breakpoint encompasses (parts of) three genes, i.e. PFDN6, RGL2 and TAPBP, while the proximal breakpoint also encompasses (parts of) three genes, i.e. GRM4, CYCSP55 and HMGA1. Note, the distal breakpoint region is shaded in red/orange, meaning another haplotype is available for that region (this is the MHC region in the human chromosome 6).

 

(2) Retrieving a list of the genes encompassed by the deletion using BioMart

Using BioMart it is very easy to generate an Excel spreadsheet that contains the following information for all genes that are encompassed by the deletion (including the breakpoint regions): Ensembl Gene ID, genomic coordinates, name and description. To see whether or not any of the genes has been reported to be associated with mental retardation according to the Online Mendelian Inheritance in Man (OMIM) database (http://www.omim.org). You can also include the MIM Morbid Description.

 

Step 1: Dataset

Go to the Ensembl homepage (http://www.ensembl.org).

Click the BioMart link on the toolbar. 

Start with all human Ensembl genes.

Choose the Ensembl Genes 70 database.

Choose the Homo sapiens genes (GRCh37.p10) dataset.

 

Step 2: Filters

Now filter for the genes on chromosome 6.

Click on Filters in the left panel.

Expand the REGION section by clicking on the + box.

Select Chromosome - 6.

Make sure that the box in front of the filter is checked (this should happen automatically), otherwise the filter is not turned on.

Click on Count.

This should give you 2819 / 60684 Genes.

 

Now filter further for genes that are in the region from bp 33,259,651–34,209,880.

Under base pair, select Gene Start (bp)33259651, then select Gene End (bp)34209880.

Click on Count.

This should give you 33 / 60684 Genes.

Help

Note that all the filters you choose are recorded and confirmed in the left hand side menu.

 

Step 3: Attributes

Specify the attributes to be included in the output (note that a number of attributes will already be selected by default).

Click on Attributes in the left panel.

Expand the GENE section by clicking on the + box.

Deselect Ensembl Transcript ID.

In addition to the default selected Ensembl Gene ID, select Description, Chromosome Name, Gene Start (bp), Gene End (bp) and Associated Gene Name.

Expand the EXTERNAL section by clicking on the + box.

Select MIM Morbid Description.

 

Step 4: Results

Have a look at a preview of the results (only 10 rows of the results will be shown).

Click the Results button on the toolbar.

If you are happy with how the results look in the preview, output all the results to an Excel spreadsheet.

 

Select Export all results to File – XLS.

Tick the box Unique results only.

Help

BioMart is ‘transcript-centric’, which means that it will often give a separate row of output for each transcript of a gene, even if you don’t include the Ensembl Transcript ID in your output. To get rid of these redundant rows, use the Unique results only option.

Click Go.

This should give you an Excel spreadsheet with 33 rows of results.

 

Question 2a

Are there any genes encompassed by the deletion associated with mental retardation according to the OMIM database?

Yes, according to the OMIM database the SYNGAP1 gene has been associated with autosomal dominant mental retardation (http://www.omim.org/entry/612621).