MIPSTR
Targeted Capture of STR Loci by smMIPs
MIPSTR is a method for multiplex genotyping of germline and somatic short tandem repeat (STR) variation across many individuals (Carlson et al., 2015). This method is a variation of the smMIP (Hiatt et al., 2013) approach and uses a novel mapping strategy.
The method uses a smMIP with a common backbone for a PCR primer, sequencing adapters, 12 bp degenerate tag, and targeting arms with locus-specific and STR-flanking sequences. Capture across genetically diverse individuals identifies germline STR variation. The use of degenerate tags identifies technical variation, and STR variation across tag-defined read groups is considered somatic variation.
Advantages:
- Capable of distinguishing technical error from somatic STR mutations
Disadvantages:
- Requires high-quality reference genome
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Estivill X. Genetic variation and alternative splicing. Nat Biotechnol. 2015;33:357-359
References:
Carlson K. D., Sudmant P. H., Press M. O., Eichler E. E., Shendure J., et al. MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals. Genome Res. 2015;25:750-761
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History: MIPSTR
Revision by sbrumpton on 2017-06-21 07:50:21 - Show/Hide
Targeted Capture of STR Loci by smMIPs
MIPSTR is a method for multiplex genotyping of germline and somatic short tandem repeat (STR) variation across many individuals (Carlson et al., 2015). This method is a variation of the smMIP (Hiatt et al., 2013) approach and uses a novel mapping strategy.
The method uses a smMIP with a common backbone for a PCR primer, sequencing adapters, 12 bp degenerate tag, and targeting arms with locus-specific and STR-flanking sequences. Capture across genetically diverse individuals identifies germline STR variation. The use of degenerate tags identifies technical variation, and STR variation across tag-defined read groups is considered somatic variation.
Advantages:- Capable of distinguishing technical error from somatic STR mutations
Disadvantages:- Requires high-quality reference genome
Reagents:Illumina Library prep and Array Kit SelectorReviews:Estivill X. Genetic variation and alternative splicing. Nat Biotechnol. 2015;33:357-359References:Carlson K. D., Sudmant P. H., Press M. O., Eichler E. E., Shendure J., et al. MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals. Genome Res. 2015;25:750-761