2023 ACMG Annual Clinical Genetics Meeting Digital Edition: Poster Gallery-Simultaneous Analysis of 50+ Different Repeat Expansions with Twist Target Enrichment and PacBio HiFi Sequencing

Pdf Summary

Researchers from Twist Bioscience and Pacific Biosciences have developed a method to simultaneously analyze more than 50 different repeat expansions using a combination of target enrichment and PacBio HiFi sequencing. The scientists designed gene panels that target various short tandem repeats (STRs) using a proprietary algorithm. The protocol involves fragmented genomic DNA, followed by end-repair, adapter ligation, and PCR barcoding. Multiple hybridizations can be performed overnight, with up to 8 pooled samples per hybridization. Post-capture libraries undergo SMRTbell library preparation and are sequenced on a PacBio instrument. The method allows for the comprehensive coverage of 50+ different pathogenic repeats of wild type length, and the detection of individual repeat motifs and methylation levels. Clinical validation with confirmed repeat expansion is ongoing. Short-read sequencing is limited in determining the exact length, sequence composition, and methylation status of long expansions, but the current method provides a scalable and cost-efficient solution to accurately measure STRs. The researchers used the Tandem Repeat Genotyper Tool (TRGT) to benchmark the performance of the target enrichment workflow in reference samples with known repeat expansion alleles. This tool accurately characterizes tandem repeat regions and expansions. The method enables high-resolution characterization of hundreds and thousands of gene regions, including structural variation and haplotype phasing information. The study demonstrates the potential of using Twist target enrichment panels in combination with PacBio long HiFi reads for the analysis of STRs.

Asset Subtitle

Presenting Author - Tina Han, PhD; Co-Author - Holly Corbitt, PhD; Co-Author - Egor Dolzhenko, PhD; Co-Author - Nina Gonzaludo, PhD; Co-Author - Sarah Kingan, PhD; Co-Author - Po-Yuan Tung, PhD; Co-Author - Esteban Toro, PhD; Co-Author - Chad Locklear, MS;

Meta Tag

Triplet and Other Repeats

NextGen Sequencing

Methodology

Genomic Methodologies

Genome sequencing

Genetic Testing

Bioinformatics

Co-Author Chad Locklear, MS

Co-Author Esteban Toro, PhD

Co-Author Po-Yuan Tung, PhD

Co-Author Sarah Kingan, PhD

Co-Author Nina Gonzaludo, PhD

Co-Author Egor Dolzhenko, PhD

Co-Author Holly Corbitt, PhD

Presenting Author Tina Han, PhD

Keywords

repeat expansions

target enrichment

PacBio HiFi sequencing

gene panels

short tandem repeats

SMRTbell library preparation

methylation levels

clinical validation

Tandem Repeat Genotyper Tool

structural variation