How To Find Repeat Expansion Using Exome/Genome Sequencing Data?

Question

[michealsmith]

Many diseases esp. neurological diseases are caused by tandem repeat expansion, for example trinucleotide/hexanucleotide repeat, though pathogenic mechanism is still not fully clear. And I think it's extremely challenging to look for such short repeat expansion from sequencing data; basically such expansion can be regarded as novel insertion. For large novel insertion, based on read alignment, we may find the breakpoint but may never figure out the exact inserted sequences (because it's too large); and another approach is to assemble sequences to find out large novel insertions.

Above is just my own thinking, what programs/algorithms would you recommend for identification of repeat expansion from sequencing data?

Answer 1

[matted]

The first page of Google hits for "short tandem repeat high throughput sequencing" gives multiple useful links:

• 'Short-read, high-throughput sequencing technology for STR genotyping'
• 'lobSTR: A short tandem repeat profiler for personal genomes'
• 'NG-STRider: A tool to infer Simple Tandem Repeat (STR) alleles from high throughput genomic sequencing data'

Answer 2

[onter]

This paper from NAR describes an NGS tool for genotyping STRs called RepeatSeq, with code available on github:

http://www.ncbi.nlm.nih.gov/pubmed/23090981 and https://github.com/adaptivegenome/repeatseq

Very recently there is also the paper http://www.ncbi.nlm.nih.gov/pubmed/23696428 on "Rapid multiplexed genotyping of simple tandem repeats using capture and high-throughput sequencing."

Answer 3

[niuyw]

Now, there are four tools dedicated for identification of repeat expansion using NGS data (WES or WGS).

See this review for details: Recent advances in the detection of repeat expansions with short-read next-generation sequencing