PureTarget · PacBio HiFi · 38 Repeat Expansion Loci

See inside the repeat. Motif, size, methylation, phase.

More than 1 in 300 people carry a repeat expansion disease allele, yet most repeat expansions are missed or only roughly sized by routine short-read sequencing and PCR assays. PureTarget captures each locus with ~2 kb of flanking sequence and sequences it with PacBio HiFi reads that span repeats up to ~35 kb.

Plan Your Project → Learn the Basics
38 loci
PureTarget 2.0
~35 kb
repeat span in single reads
Motif, size, methylation
characterisation
Cas9-based, PCR-free
capture
About the Service

Repeat Expansion Panel at Nucleome Informatics

Tandem repeat expansions cause more than 50 inherited neurological, neuromuscular and ophthalmic disorders. Expanded alleles are often too long for PCR, too repetitive for short reads and too GC-rich for standard workflows.

Huntington diseaseMyotonic dystrophy 1 & 2Friedreich ataxiaFragile X syndromeALS/FTD (C9orf72)Spinocerebellar ataxias
38repeat expansion loci (PureTarget 2.0)
~163 kbtotal target, ~2 kb flanks per locus
No PCRCas9 capture, amplification-free
HiFisequenced on PacBio Revio or Sequel IIe

What one HiFi read tells you

A single read spans the entire repeat plus its flanks, so each locus is reported directly — not inferred.

Allele sizeRepeat units and bp, with confidence
Motif & interruptionsComposition and interruption analysis
MethylationCalled at applicable loci
Co-occurring SV/CNVDetected alongside the repeat genotype

Why it matters

One assay, 38 diseasesReplaces the many separate PCR assays of conventional practice.
No PCR dead endsAlleles too large to amplify are read directly.
Interruptions change prognosisMotif interruptions (e.g. SCA8, FMR1 AGG) are visible, not inferred.

Validated analysis toolchain

TRGTRepeat genotyping with the targeted preset
ParaphaseResolves paralogous genes
SawfishCo-occurring structural variants and CNVs
Report. Clinical-style structure with methods and limitations. Research-use and clinical-reporting options are discussed at intake.
Learning Path

From first principles to expert-level analysis

New here? Start with Foundations. Planning a study or reviewing results? Jump to Practitioner or Expert. Each level builds on the one before it, so you can read this page as a short course or dip in where you need to.

Start here if you are new to this service — six ideas that explain what it is and why it matters.

LEVEL 1

What is a repeat expansion?

A stretch of DNA where a short motif (3–6 bp, sometimes longer) is repeated many times. When the repeat count grows beyond a threshold, it becomes unstable and causes disease — e.g. CAG repeats in HTT causing Huntington disease.

LEVEL 1

Why do standard tests miss these?

PCR-based tests fail when the repeat is too long to amplify; short-read sequencers cannot map reads that are mostly one repeated motif. Long reads read straight through the repeat.

LEVEL 1

What is PureTarget?

PacBio's targeted panel that captures 38 known repeat expansion loci (plus ~2 kb of flanking DNA each) using Cas9 enzymes instead of PCR, then reads them with highly accurate HiFi long reads.

LEVEL 1

Which diseases are covered?

Huntington disease; myotonic dystrophy 1 and 2; fragile X syndrome and fragile X-associated disorders; Friedreich ataxia; ALS/FTD (C9orf72); most dominant spinocerebellar ataxias (SCA1, 2, 3, 6, 7, 8, 10, 12, 17, 36, 37...); CANVAS (RFC1); Fuchs endothelial corneal dystrophy (TCF4); spinal and bulbar muscular atrophy (AR); DRPLA (ATN1); and others.

LEVEL 1

How accurate is it?

HiFi reads are ≥99.9% accurate post-consensus, and because each read spans the whole repeat, allele sizing is direct rather than inferred from fragment length.

LEVEL 1

Is this a diagnostic test?

The assay and analysis are performed to clinical-grade standards; reporting pathways (research vs clinical) are agreed at intake in line with applicable regulatory requirements.

For scientists planning a project or reading a report: how each step works and how it can mislead.

LEVEL 2

Sample requirements

High-molecular-weight DNA is essential (e.g. Nanobind extraction; typically 1–4 µg with ≥50% of fragments ≥30 kb and acceptable GQN). Blood is the standard source; other tissues may be discussed.

LEVEL 2

The Cas9 capture principle

Cas9 enzymes with locus-specific guide RNAs cut and attach adapters at the target ends — enrichment without PCR. This preserves very long molecules and avoids amplification bias against large expansions.

LEVEL 2

Sequencing and analysis

Libraries are sequenced on Revio or Sequel IIe; reads are processed with TRGT (targeted preset) for genotyping, Paraphase for paralogous loci, and Sawfish for structural variants. PacBio's PureTarget Carrier Pipeline (PTCP) WDL workflow supports carrier-screening-style reporting.

LEVEL 2

Methylation calling

Because each molecule is read natively, methylated bases are detectable directly — important at FMR1 and other CGG-rich loci where methylation status affects interpretation.

LEVEL 2

Interruption analysis

The report includes motif composition per allele — e.g. CAA interruptions in CAG tracts, AGG interruptions in FMR1 CGG repeats — which influence stability and risk.

LEVEL 2

Multiplexing and throughput

96 samples per run on Revio with SPRQ chemistry makes cohort-scale studies (e.g. ataxia or dystonia cohorts) economically practical.

For study design: the decisions that determine whether the data answers your question.

LEVEL 3

Beyond the 38 loci — custom PureTarget panels

PacBio's design pipeline supports custom panels: additional repeat loci and non-repeat regions up to ~15 kb and beyond 15 kb with adjusted design rules. Discuss custom guide-RNA design with us for research cohorts.

LEVEL 3

Phase and haplotype context

Because reads span the repeat plus flanks, expansions can be assigned to parental haplotypes — valuable in family studies and for distinguishing de novo events.

LEVEL 3

Combining with exome/genome data

PureTarget complements WES/WGS: run it reflexively when short-read data shows unexplained neurological phenotypes, or in parallel for comprehensive rare-disease workups.

LEVEL 3

Cohort and founder-allele studies

Direct repeat sizing enables founder-allele tracking and precise prevalence estimates in Indian populations — where most repeat loci have never been systematically surveyed.

LEVEL 3

Quality metrics to expect

Per-locus read depth, allele-size confidence intervals, methylation fractions, and TRGT/Paraphase QC outputs are included in every report.

LEVEL 3

Reporting standards

We document panel version (2.0), analysis tool versions, and reference thresholds per locus, following PacBio's validated workflows.

Tandem repeat
a DNA motif repeated head-to-tail.
HiFi
PacBio's highly accurate long reads (circular consensus sequencing).
TRGT
PacBio's tandem-repeat genotyping tool.
Paraphase
a tool for resolving paralogous genes from HiFi reads.
GQN
genome quality number; a HMW-DNA integrity metric.
Premutation
an intermediate-size repeat allele (e.g. FMR1 55–200 CGG) that is unstable on transmission.
The Science

How it works, in two figures

PacBio's PureTarget application notes describe the 38-locus panel, ~163 kb capture design, and TRGT-based analysis; the >1-in-300 carrier frequency estimate for repeat expansion alleles comes from population-scale short- and long-read surveys (Ibañez et al., 2024). See references below.

Figure 1 Why long reads win. schematic
PCR & short-read approaches PureTarget HiFi reads Large expansions fail to amplify Repeats too repetitive to map One locus per assay Single reads span repeats up to ~35 kb Motif interruptions visible directly 38 loci in one assay
Figure 1 | Why long reads win. (Illustrative schematic, not sample data.)
Figure 2 PureTarget workflow. schematic
HMW DNA (Nanobind) Cas9 capture of 38 loci Revio / Sequel IIe HiFi sequencing TRGT genotyping Methylation & motif analysis Per-locus clinical-style report
Figure 2 | PureTarget workflow. (Illustrative schematic, not sample data.)
Technology Highlights

Built for the questions you are asking

The platforms, pipelines and standards behind this service.

PureTarget 2.0 panel — 38 loci

Covers established repeat expansion disease genes: HTT, DMPK, CNBP, FXN, FMR1, AFF2, C9orf72, ATN1, ATXN1/2/3/7/8/10, CACNA1A, PPP2R2B, TBP, BEAN1, DAB1, FGF14, NOP56, ZFHX3, RFC1, TCF4, AR, and others.

Cas9-based, PCR-free capture

Guide-RNA-directed enrichment of ~163 kb of target sequence from high-molecular-weight DNA — no amplification bias, no PCR dropout of very large alleles.

HiFi reads span the repeat

Reads up to ~35 kb span expanded alleles end to end; normal alleles sit comfortably within standard ~4–5 kb insert sizes.

TRGT repeat genotyping

PacBio's TRGT (--preset targeted) reports allele sizes, methylation, and sequence composition per locus with per-read visualisations.

Paraphase and Sawfish

Paraphase resolves highly homologous paralogous genes; Sawfish detects co-occurring structural variants and CNVs in the same data.

Multiplexing at scale

96-plex on Revio with SPRQ chemistry (automated), 48-plex manual on Revio, 24-plex on Sequel II/IIe — efficient per-sample economics for cohorts. ---

Scope Note

What this service does and does not cover

Scope note. PureTarget 2.0 covers the 38 established repeat expansion loci in the panel; expansions at loci outside the panel are not detected unless a custom panel is designed. Repeat sizes beyond the practical read-length ceiling (~35 kb in a single read) may be reported as "beyond range" rather than exactly sized. Methylation calling applies to loci where the repeat context supports it. This page describes a sequencing service; clinical interpretation and genetic counselling are provided through the requesting clinician's framework.---
Why Nucleome

Service highlights

What you can expect from our team in Hyderabad.

South Asia's first PacBio Revio service provider

Nucleome Informatics operates PacBio Revio and Sequel IIe in Hyderabad.

38-loci panel, one assay

Replace a dozen separate PCR assays with a single comprehensive test.

Interruption and methylation analysis included

Not just size — composition and methylation, where the locus supports it.

Cohort-scale multiplexing

96-plex on Revio for population and clinical cohort studies.

Custom panel design available

Extend beyond the standard 38 loci for research programmes.

Clinician-friendly reporting

Structured per-locus reports designed for downstream clinical interpretation. ---

Questions

Frequently asked, in plain language

From the basics to the finer points of design and interpretation.

basicWhich diseases does this test cover?
38 repeat expansion loci, including Huntington disease, myotonic dystrophy 1 and 2, fragile X, Friedreich ataxia, C9orf72-ALS/FTD, most dominant SCAs, CANVAS, and others — see the panel list above.
basicWhat sample is required?
Typically 1–4 µg of high-molecular-weight DNA (usually from blood). We can advise on extraction or arrange it.
basicHow is this better than the PCR test my doctor ordered?
PCR tests usually target one locus and fail on very large repeats. PureTarget reads all 38 loci directly, including alleles too large to amplify, and adds motif, methylation, and phase information.
intermediateCan it size very large expansions, like full-mutation FMR1 or long C9orf72?
HiFi reads span repeats up to ~35 kb. Alleles beyond that range are detected but may be reported as beyond the exact-sizing range rather than precisely counted.
intermediateDoes it detect methylation?
Yes, at loci where methylation is informative (e.g. FMR1), directly from the native reads.
intermediateCan family members be tested?
Yes — the assay supports familial testing and phase assignment, which is valuable for segregation analysis.
advancedWhat analysis tools are used?
TRGT (targeted preset) for genotyping and methylation, Paraphase for paralogous genes, Sawfish for co-occurring SV/CNV, and PacBio's PureTarget Carrier Pipeline (PTCP) WDL workflow where carrier-style reporting is needed.
advancedCan you design a custom panel with additional loci?
Yes — PacBio's design pipeline supports custom repeat and non-repeat targets; guide-RNA design lead times apply. Contact us to scope a custom panel.
advancedHow does this integrate with exome or genome sequencing?
PureTarget is the reflex test for unexplained neurological phenotypes after short-read sequencing, or can run in parallel for comprehensive workups. It fills the single largest blind spot of short-read WGS.
advancedWhat are the multiplexing options?
96-plex on Revio with SPRQ chemistry (automated), 48-plex manual on Revio, 24-plex on Sequel II/IIe.
References

Key literature & resources

Selected sources behind the methods and reference values on this page. Figures labelled "schematic" or "illustrative" are generated for this page, not client data.

  1. Ibañez K, et al. Estimating the prevalence of repeat expansion disease alleles. (Population-scale survey supporting the >1 in 300 carrier estimate.) 2024.
  2. PacBio. PureTarget repeat expansion panel application note (PureTarget 2.0: 38 loci, ~163 kb, Cas9-based capture). PacBio technical documentation, 2023–2024.
  3. PacBio. TRGT: tandem repeat genotyping tool documentation. PacBio, 2023.
  4. Dolzhenko E, et al. Detection of long repeat expansions from PCR-free whole-genome sequence data. Nature Methods. 2017;14(9):865–867. (Foundation for HiFi repeat genotyping approaches.)
  5. Ebbert MTW, et al. Long-read sequencing across the C9orf72 'GGGGCC' repeat expansion: implications for clinical use. Scientific Reports. 2018;8(1):6790.
  6. PacBio. PureTarget Carrier Pipeline (PTCP) workflow documentation. PacBio technical documentation, 2024.