TANDEM REPEAT ANALYSIS
Unprecedented detection and discovery of repeat expansions
Tandem repeats play a key role in human healthand disease

Pathogenic repeat expansions are often longer than the read
lengths of short-read platforms, and their repetitive nature
makes them difficult or impossible to map. HiFi reads arehighly accurate, over 100 times longer than short reads, andoffer simultaneous 5-Methylcytosine (5mC) detection.

Tandem repeats (TR) are repeating sequences of twoor more base pairs that are adjacent to one another andare abundant thoughout the genome. Because of theirrepetitive nature, they are hypermutable, and they play a keyrole in human health and disease.1 Expansions in repeat
length in certain ranges — typically longer repeats — canbecome pathogenic. More than 50 diseases are known tobe caused by TR expansions,1 and further study could reveal
associations with more rare diseases that are currentlyunexplained.

HiFi reads can span most repeats, making it possible tocomprehensively profile variation in repeat regions and tomeasure any changes in methylation. PacBio has developedthe Tandem repeat genotyping tool (TRGT) and Tandem
repeat visualizer (TRVZ) as bioinformatics tools to accurately
profile short tandem repeats, variable number tandem
repeats, and macrosatellites.

Together with HiFi sequencing, TRGT enables
researchers to use a single library prep to:

Most abundant class of variation in thehuman genome1• >1M tandem repeats in the human genome

Accurately quantify repeat count• >10 higher mutation rate than any other variant class
Identify interrupting sequences

Known to cause disease• >50 repeat expansion disorders caused by STRs1

Determine allele phasing• Several VNTRs linked to diseases like Alzheimer’s,autism, epilepsy, and ALS2, 3Determine 5mC profile

MICROSATELLITE
Motif size: 1–9 bp

FLANK

TANDEM REPEAT
CAG

CAG

FLANK
CAG

CAG

CAG

CAG

CAG

Short tandem repeats (STRs)

REPEAT MOTIFMINISATELLITE
Motif size: 10–60 bp
MACROSATELLITE
Motif size: >100 bp

C4GC4GCG

C4GC4GCG

C4GC4GCG

C4GC4GCG

C4GC4GCG

Variable number tandem repeats (VNTRs)

Macrosatellites

TRGT is comprehensive, powerful, and practical
PCR and Southern blot assays, which are often used for
repeat expansion detection, are limited to analyzing one ora few loci at a time. Short-read whole genome sequencing(WGS) is more comprehensive but offers limited repeatexpansion resolution due to read-length limitation.

WGS with HiFi sequencing offers researchers unmatched
information density from their samples, by enabling
interrogation of genome-wide TRs, structural variants, and5mC modifications from a single library prep.

DEFINE THE REPEAT

chr3

129172576

FIND FLANKS AND TR SEQUENCE

CAGG

CAGA

ID=CNBP;STRUC=(CAGG)n(CAGA)n(CA)n129172732

ASSIGN READS TO HAPLOTYPES

05100051015 05SEGMENT THE REPEAT SEQUENCE

05055101015152020CAFigure 1: TRGT includes multiple TR catalogues to enable and simplify analysis. As an example, the definition (location and structure)of the CNBP repeat is included within the catalog of pathogenic repeats. TRGT locates reads that span the region, assigns themto haplotypes, and determines the structure of the resulting repeat alleles, which can be visualized using TRVZ.

KEY REFERENCES
1. Madsen, B. E., Villesen, P., & Wiuf, C. (2008). Short tandem repeats in human exons: a target for disease mutations. BMC genomics, 9, 410.
2. Ryan, C. P. (2019). Tandem repeat disorders. Evolution, medicine, and public health. (1), 17.
3. Paulson, H. (2018). Repeat expansion diseases. Handbook of clinical neurology, 147, 105–123.
4. Dolzhenko, E., et al. (2023). Resolving the unsolved: Comprehensive assessment of tandem repeats at scale. bioRxiv 2023.05.12.540470.
Research use only. Not for use in diagnostic procedures. © 2023 Pacific Biosciences of California, Inc. (“PacBio”). All rights reserved. Information in this document is subject to change without notice. PacBio
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102-326-546 REV03 26MAY2023