Explore targeted panels on the Vega benchtop system
Uncover the full picture of your region of interest with highly accurate HiFi long-read targeted sequencing, now in-house with Vega benchtop system. The unique combination of long, highly accurate HiFi reads and deep target coverage delivers a powerful approach for resolving complex loci, revealing the full spectrum of variation, including structural variants and, with PureTarget technology, methylation changes in the same assay.
From carrier screening to characterizing gene editing outcomes and complex cancer genome rearrangements, targeted HiFi sequencing is transforming translational research and clinical testing. If repetitive regions, complex targets, unclear phasing, difficult amplification, or missing methylation data are limiting your assay performance, targeted HiFi sequencing provides the clarity, completeness, and confidence needed for reliable clinical insights.
Highlights:
Targeted HiFi methods
Struggling with repetive regions?
BERRY GENOMICS LEADS THE WAY WITH AMPLICON SEQUENCING FOR GENETIC DISEASE RESEARCH
One of China’s more prominent clinical genomics companies, Berry Genomics, is a leader in the prevention of genetic birth defects. Berry achieved the first regulatory clearance of a clinical-grade long-read sequencer when the Sequel II CNDx system received Class III Medical Device Registration approval from the National Medical Products Administration (NMPA) in China. Berry was also the first customer to receive shipment of the benchtop Vega systems, which join Berry’s fleet of HiFi platforms. Berry has sequenced more than 300,000 Thalassemia samples and helped contribute to a 3-5% increase in findings compared to traditional assays.
“With HiFi long-read sequencing, we found at least 20 novel large deletions or structural variations in the Thalassemia genes that have helped contribute to a 3–5% increase in diagnosis rate compared to traditional assays.”
– Dr. Aiping Mao, Vice Director of R&D at Berry Genomics
Need clear and accurate haplotype phasing?
Targeted hybrid capture combined with HiFi long-read sequencing panels enables clear and accurate haplotype phasing across complex genomic regions. The long range and high accuracy of HiFi reads allow variants to be resolved on the same molecule, delivering confident phase determination without ambiguity from repetitive or GC-rich sequences. The result is a more complete and clinically meaningful view of inherited and disease-associated variation.
Hybrid capture app brief Agilent CGP panel and PacBio HiFi poster
Trouble amplifying your target region?
Learn how gene editing researchers are using PureTarget to characterize engineered animal models with exceptional accuracy. With high depth of coverage of native DNA, it is possible to identify mosaicism in founder lines and track inheritance in their progeny.
Read study Customer success story Watch webinar
Capture methylation and variants in the same assay?
PureTarget uses the CRISPR-Cas9 system to generate targeted native DNA libraries. This amplification-free approach retains epigenetic signals like methylation and avoids PCR artifacts.
With streamlined workflows, scalable multiplexing, and deep coverage of difficult regions, PureTarget panels replace multiple assays and give labs the power to profile challenging loci like FMR1, FXN, F8, and SMN1 in a single assay.
Carrier panel
A curated panel of hard-to-sequence genes, built to ACMG guidance and designed to reduce the need for add-on assays.
Repeat expansion panel 2.0
A comprehensive panel of 38 neurological disease targets, including 17 ataxia genes and targets for ALS/FTD, Huntington disease, and myotonic dystrophy.
Custom control panel
A set of three control targets for designing and benchmarking custom panels. Includes X-linked UBL4A and autosomal ACTB and GAPDH.
Comprehensive genotyping of the most challenging targets
Repeat expansions in the FXN and RFC1 genes occur in high frequency across many human populations, with recent estimates that 1 in ~14 individuals carry pre–mutations at RFC1 and 1 in ~100 carry pre-mutations at FXN (Ibañez et al., 2024). Accurate repeat sizing is important to identify carriers of pathogenic alleles longer than 70 repeats for FXN and longer than 400 repeats at RFC1 (Leitão et al., 2024). Long and accurate HiFi reads make it possible to distinguish among the diverse repeat motifs at RFC1, only some of which are pathogenic (Dominik et al., 2023).
RFC1 expansions
FXN expansions
| Long allele | Short allele | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Sample | Coverage | Observed motif count | Expected motif count | Coverage | Observed motif count | Expected motif count | ||||
| HM16212 | 92 | 471 | 500 | 146 | 8 | <30 | ||||
| NA16212 | 68 | 515 | 500 | 99 | 8 | <30 | ||||
| NA16202 | 49 | 817 | 830 | 86 | 8 | <30 | ||||
| NA16237 | 49 | 699 | 700 | 134 | 8 | <30 | ||||
High on-target coverage enables accurate genotyping
The PureTarget repeat expansion panel enables deep coverage for accurate genotyping of repeat expansions associated with human disease. The table below highlights typical coverage for Coriell samples with known repeat expansions. Note that 2 µg of DNA was prepared with the PureTarget repeat expansion panel of 20 targets, sequenced on the Vega system, and analyzed with TRGT (Dolzhenko et al., 2024) in the SMRT Link PureTarget repeat expansion panel analysis workflow. Full dataset available here.
| Sample | Target with repeat expansion | Total reads per sample | Mean target coverage | Coverage of expanded allele | Epanded allele size (bp) | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| 20 gene panel | ||||||||||
| HM23709 | AR | 54,252 | 343 | 182 | 147 | |||||
| NA13716 | ATN1 | 40,700 | 234 | 88 | 216 | |||||
| NA13536 | ATXN1 | 39,845 | 267 | 132 | 124 | |||||
| NA06153 | ATXN3 | 64,164 | 258 | 114 | 207 | |||||
| ND14442 | C9orf72 | 16,821 | 51 | 4 | 4563 | |||||
| HM03756 | DMPK | 52,504 | 395 | 282 | 1305 | |||||
| NA09237 | FMR1 | 36,167 | 257 | 113 | 2683 | |||||
| NA16215 | FXN | 67,939 | 245 | 62 | 2963 | |||||
| NA13509 | HTT | 58,870 | 480 | 225 | 252 | |||||
| HM23629 | PABPN1 | 50,569 | 417 | 218 | 27 | |||||
| HG01175 | RFC1 | 53,454 | 378 | 57 | 1948 | |||||
Sample to insight workflow
Extraction
Start with HMW DNA extracted from human blood or cell lines using Nanobind extraction kits.
Library prep
Targeting and library prep can be completed in 8 hours. All reagents supplied in the kit.
Sequencing
Sequence up to 48 samples per Vega SMRT Cell with 24 hour movies and optimized run conditions for PureTarget libraries.
Data analysis
SMRT Analysis is automatically configured to generate library QC, target enrichment statistics, and tandem repeat genotypes using TRGT (Dolzhenko et al., 2024).
What can you expect from one sequencing run on the Vega system?
| Targeted panels | Samples per Vega SMRT Cell | |
|---|---|---|
| PureTarget panels | 96 | |
| Amplicon sequencing | > 1,000 | |
| Hybrid capture | ||
| 20 Mb panel | 12 | |
| 2 Mb panel | 72 | |
| 100 kb panel | 288 | |
| Manual library prep with PureTarget 24 kit (103-707-900) and assumes >100x per target. | ||
References
Dolzhenko, E., et al. (2024). Characterization and visualization of tandem repeats at genome scale. Nat Biotechnol. 2024 doi: 10.1038/s41587-023-02057-3.
Dominik, N., et al. (2023). Normal and pathogenic variation of RFC1 repeat expansions: implications for clinical diagnosis. Brain. 146(12):5060-5069. doi: 10.1093/brain/awad240.
Ibañez, K., et al. (2024) Increased frequency of repeat expansion mutations across different populations. Nature Medicine. https://doi.org/10.1038/s41591-024-03190-5
Leitão, E., et al. (2024). Identification and characterization of repeat expansions in neurological disorders: Methodologies, tools, and strategies. Rev Neurol (Paris). 180(5):383-392. doi: 10.1016/j.neurol.2024.03.005.
Explore other Vega system datasets
Now, you can
Vega makes high-accuracy sequencing accessible to labs of all sizes, because every lab deserves the power of HiFi.