November’s standout publications show how PacBio technology is impacting advances in human genomics research. This month’s selection includes studies on accurate variant detection in paralogous genes, a new visualization tool for navigating pangenome graphs, and repeat expansion research revealing potential disease-modifying patterns. Also featured: a low-cost, high-resolution HiFi assay for newborn screening in clinical research settings.
If your focus is on rare disease, working on targeted panel design, or resolving gene duplications, this month’s highlights show how HiFi continues to drive meaningful insights across the genome.
Jump to topic:
Human genomics | Pangenomes | Motif patterns | Targeted sequencing
Human genomics
HiFi sequencing accurately identifies clinically relevant variants in paralogous genes
In this monumental preprint, the HiFi Solves EMEA Consortium – including Radboud Netherlands, Bioscientia, U Lübeck & Kiel Germany, Med U Innsbruck Austria, and PacBio -concludes that “PacBio HiFi lrGS, particularly when integrated with Paraphase, enables comprehensive variant detection in previously difficult-to-assess genomic regions.”
Key highlights
- Researchers found that“Short-read sequencing methods … remain limited in highly homologous genomic regions, such as segmental duplications with gene-pseudogene pairs”, and “often require complex, locus-specific assays for accurate analysis.”
- The study evaluated “PacBio HiFi lrGS combined with Paraphase, a dedicated haplotype-based variant caller, in 86 individuals with 125 known clinically relevant variants across 11 paralogous loci.
- Standard HiFi variant callers detected 95 of the 125 variants, while
- The remaining 30 variants were only identified by Paraphase.
- Together, combined approach detected all known variants, including SNVs, InDels, CNVs, SVs, and gene conversions with accurate phasing and gene-pseudogene copy number detection.”
- The researchers concluded that:
- “lrGS is ready for a wider implementation, possibly as a first-tier diagnostic approach for individuals with suspected variants in these paralogous regions”,
- It also “starts enabling to move from a variant centric view in human genetics to an allelic and haplotype-resolved view”.
Conclusion:
HiFi sequencing that consistently and accurately identifies variants across genomic regions that were previously invisible to standard testing methods, getting it closer to being ready as a first-tier diagnostic test for rare inherited disease (RID).
Pangenomes
Beyond reference bias: Making pangenomes accessible with PangyPlot
In this preprint, researchers from SickKids Canada and the Canadian Cystic Fibrosis Gene Modifier Consortium introduce PnagyPlot, “a genome browser that simplifies exploration of pangenome graphs”.
Key findings
- “Linear reference genomes … remain limited by reference bias, which skews read mapping and variant discovery”, a distortion that “can hinder or misinform disease interpretation”, and “particularly for populations that are genetically distant from the reference.”
- Example: “The PRSS1–PRSS2 locus exemplifies the effect of reference bias. A common CNV in this region induces a strong reference bias effect known to produce clinical misinterpretations with short-read data.”
- To address this, researchers developed “PangyPlot, a genome browser that simplifies exploration of pangenome graphs by retaining linear-style navigation, integrating gene annotations, abstracting complex variation into interpretable structures”, and the “ability to display both base-level and large structural variation”.
- Leveraging 165 PacBio assemblies, the team fine-map two CF-relevant regions – on chromosome 7 (CFTR, PRSS1–PRSS2) and “a repeat-dense CF modifier locus on chromosome 5”-, “capturing a broad spectrum of genetic variation”, and including “rare SNVs associated with European, South Asian, Middle Eastern, and Ashkenazi Jewish ancestries”
- In the chr5 region (enriched for VNTRs and short repeats), they characterized three GWAS SNV-associated repeats with highly polymorphic length distributions—repeats that are challenging for short reads to resolve. This enabled better structural understanding and supported new disease hypothesis generation.
- Researchers found that: “these examples demonstrate PangyPlot‘s capacity to make population level variation interpretable”
Conclusion:
As we move beyond the limitations of the reference genome, human pangenomes, built from PacBio HiFi data, are becoming the new foundation for understanding genetic variation and disease. Tools like PangyPlot are essential for unlocking the full value of pangenomic data, making complex variation accessible, interpretable, and actionable for cohort-wide analysis.
Motif patterns
Novel ATXN10 Repeat Motif Patterns in Peruvian Families Modify Disease Onset
In this study, researchers investigated the genetic architecture of spinocerebellar ataxia type 10 (SCA10) in six multigenerational Peruvian families using PacBio PureTarget repeat expansion panel.
Key highlights
- Researchers identified three mixed repeat motif patterns and ratios of (ATTCT)n and (ATTCC)n, which were correlated with variation in age at disease onset and evidence of anticipation.
- These patterns highlight the complexity of repeat expansions and underscore how different motif configurations can influence disease progression.
- Findings point to the importance of long-read sequencing to resolve large repeat expansions at the nucleotide level – something not feasible with conventional approaches.
Conclusion:
HiFi-based targeted repeat analysis offers a more granular and clinically relevant view of repeat expansions, helping researchers better understand repeat expansion disorders like SCA10.
Targeted sequencing
Newborn genetic screening of congenital adrenal hyperplasia using long-read sequencing
This retrospective study evaluated a HiFi-based, cost-effective method for both first-tier carrier screening and newborn screening of congenital adrenal hyperplasia (CAH) using long-read sequencing of dried blood spots.
Key highlights
- Used full-length amplicon sequencing across five CAH-related genes in 73 retrospective cases:
- 12 confirmed CAH cases
- 18 false-positive cases flagged by biochemical screening
- 43 healthy newborns (control group)
- All 12 CAH cases were accurately identified, with detection of 11 pathogenic variants in CYP21A2, including:
- 8 SNVs/indels
- 3 large deletions
- The method enabled direct resolution of cis vs. trans variant phasing and distinguished functional genes from pseudogenes, a known challenge for CAH diagnosis.
- Designed as a one-reaction system using HiFi reads, the assay increased throughput and reduced cost to ~$20 per sample, supporting its scalability.
Conclusion:
This HiFi-based newborn screening method offers high accuracy, variant-level clarity, and affordability—demonstrating strong potential for integration into public health programs for early CAH detection.
Ready to make discoveries of your own?
We are encouraged by just how far researchers can go when they have access to complete, high‑resolution genomic data. Across human genomics, pangenomes, repeat disorders, and targeted newborn screening, HiFi sequencing continues to reveal variation that standard methods overlook.
As the field leans further into allelic, haplotype‑resolved, and multiomic views of the genome, PacBio tools are helping teams work with data that more accurately reflects biological reality.
Stay tuned for next month’s round-up of recent publications using PacBio technology.
Ready to explore what HiFi can do in your lab? Let’s get started.