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Rapid Multiplexed Genotyping of Simple Tandem Repeats using Capture and High-Throughput Sequencing

2013; Wiley; Volume: 34; Issue: 9 Linguagem: Inglês

10.1002/humu.22359

1098-1004

Audrey Guilmatre, Gareth Highnam, Christelle Borel, David Mittelman, Andrew J. Sharp,

RNA and protein synthesis mechanisms

Although simple tandem repeats (STRs) comprise ∼2% of the human genome and represent an important source of polymorphism, this class of variation remains understudied. We have developed a cost-effective strategy for performing targeted enrichment of STR regions that utilizes capture probes targeting the flanking sequences of STR loci, enabling specific capture of DNA fragments containing STRs for subsequent high-throughput sequencing. Utilizing a capture design targeting 6,243 STR loci 90% success rate, whereas only 12% of STRs with ≥80% (G+C) were genotyped in our assay. Analysis of a parent-offspring trio, complete hydatidiform mole samples, repeat analyses of the same individual, and Sanger sequencing-based validation indicated genotyping error rates between 7.6% and 12.4%. The majority of such errors were a single repeat unit at mono- or dinucleotide repeats. Altogether, our STR capture assay represents a cost-effective method that enables multiplexed genotyping of thousands of STR loci suitable for large-scale population studies.