CAG repeat in ATXN3

[sagnikbanerjee15]

Hello,

There is a well characterized CAG repeat in the ATXN3 gene (exon 10). The latest variant catalog does not have that. Could you please tell me whether it is advisable to add the entire exon (~140 nucleotides) as a potential region to probe? If not, could you please suggest a better alternative?

I launched expansionhunter with the exon as the region and it returned a very high number of repeats in one of the alleles. Upon reducing the length of the region to about 50 nucleotides, the number of repeats also reduced. Could you please guide me to the best approach to undertake here?

Thank you.

[andreasssh]

You should specify only the repeating region. I assume the entire exon contains other sequences as well and therefore messes the analysis up. You can also specify multiple repeating regions, separated by other sequence, e.g. (CAG)ATTTAT(CAT).

[sagnikbanerjee15]

Thank you for your response. All I was able to gather from the literature is that the CAG repeat occurs in the exon 10 of ATXN3. Would you be able to help me determine the location within the exon where that repeat occurs?

Thank you.

[dnil]

Try here http://strchive.org/database/ATXN3.html, https://stripy.org/database/ATXN3, https://gnomad.broadinstitute.org/short-tandem-repeat/ATXN3?dataset=gnomad_r3 or maybe https://github.com/Clinical-Genomics/reference-files/blob/ff0e8f002605a32ce54bcb2b4cb402effc734f33/rare-disease/disease_loci/ExpansionHunter-v5.0.0/variant_catalog_grch38.json#L128.

[sagnikbanerjee15]

This is perfect. Thanks