In July 2025’s publication roundup we’re proud to show how HiFi sequencing is playing a major role in advancing our understanding of the human brain, and autism in particular.
Several new studies used long-read data to explore regions of the genome that have been historically difficult to access, including segmental duplications, repetitive DNA, and complex structural variants. From uncovering hidden mutations in well-studied autism genes to mapping human-specific gene expansions that may have shaped brain evolution, researchers are building sharper, more complete pictures of genetic variation.
By combining phased genomes, methylation profiling, and capture-based enrichment with HiFi sequencing, these teams pushed past the limitations of short reads to identify rare variants with functional relevance to development and disease.
See how this month’s studies are helping evolve what’s possible in autism research, neurogenetics, and structural variant discovery.
Jump to topic:
Brain evolution | Pangenome discovery | Repetitive DNA | Structural and repeat variation
Brain evolution
Human-specific gene expansions contribute to brain evolution
In this study, researchers from UC Davis, WashU, NIH, UCL and the UK generated “a comprehensive resource for studying gene expansion drivers of human brain evolution.”
Key highlights:
- “Only 10% of SD98 regions [autosomal sequences sharing >98% identity with other genomic regions] are ‘‘accessible’’ to short reads, resulting in <10% sensitivity to detect variants and a depletion of GWAS hits.”
- Using the T2T-CHM13 reference, researchers identified 213 duplicated, human-specific gene families, and 1,002 paralogs as human-specific duplicated genes — a 5-fold increase compared to previous studies.
- The study included analysis of 13 priority human-specific duplicated (pHSD) gene families representing 30 paralogs, noting “none of the paralogs fully reside within short-read-accessible genomic regions due to their high identity.”
- This included 112 HGSVC & HPRC haplotypes and targeted probe-based capture PacBio sequencing of 172 individuals, which:
- “Uncovered some of this hidden variation”,
- “demonstrated the efficacy of long-read data to uncover hidden signatures of natural selection”, and
- “implicates two new genes in possibly contributing to hallmark features of the human brain.”
- This included 112 HGSVC & HPRC haplotypes and targeted probe-based capture PacBio sequencing of 172 individuals, which:
- “Variants discovered using the T2T-CHM13 genome enabled the identification of human-duplicated genes potentially contributing to traits and diseases not previously assayed in genome-wide selection screens”.
- For example: “Our analysis identified 231 SD98 genes (110 human-duplicated paralogs) co-expressed in modules enriched for autism genes, including several within disease-associated genomic hotspots.”
Conclusion:
HiFi data were essential to this study in two key ways: (1) enabling the T2T-CHM13 assembly to identify novel human duplicated genes—over 30% of which were missing from the GRCh38 reference; and (2) using capture HiFi to uncover hidden variation across SDs, revealing evolutionary selection signatures. This resource paves the way for future long-read studies of variation in human populations and disease cohorts, especially autism. According to the authors, single-cell Kinnex kits are also on their radar to better define expression and isoform profiles.
Pangeome Discovery
Pangenome discovery of missing autism variants
In this preprint, researchers from UW, China, UCSF, NYU, Baylor, TX Children’s report findings that “highlight the potential of phased genomes to discover complex more pathogenic mutations and the power of the pangenome to restrict the focus on an increasingly smaller number of SVs for clinical evaluation.”
Key highlights:
- Authors used PacBio to generate “phased and near-complete genome assemblies (average contig N50=43 Mbp, QV=56) for 189 individuals from 51 families with unsolved cases of autism.”
- They leveraged the HPRC/HGSVC pangenome to filter out common SVs, facilitating identification of potential pathogenic variants, to “essentially exclude 99% of the more common variants allowing us to focus on 202 private or de novo SV variants per child.”
- Through this approach, they “identified three pathogenic variants …, as well as nine candidate de novo and biparental homozygous SVs, most of which were missed by short-read sequencing.”
- Examples include:
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- A de novo stop-gain mutation in SYNGAP1: “not reported in three prior SRS analyses of this family.”
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- An 874 bp de novo DEL in MECP2: “previously missed in three rounds of clinical testing, including two gene panel sequencing tests through ARUP Laboratories and Quest Diagnostics, and one test of WES through Ambry Genetics.”
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Conclusion:
“Advanced sequencing techniques such as LRS will be required to reveal the full spectrum of mutations contributing to autism.”
Repetitive DNA
In this preprint, researchers from UW find that “LRS increases DNM [de novo mutation] discovery by 20-40% over previous Illumina-based studies.”
Key highlights:
- In this study, “HiFi data [was] derived from blood and cell lines for a total of 157 samples from 42 families affected with simplex autism.”
- The team “identified an average of 95.3 DNM events per child—a 20-40% increase in DNM discovery per sample when compared to earlier short-read studies of the same samples”, “and more than doubles the discoverable number of PZMs [postzygotic mutations] that emerged early in embryonic development.”
- Authors noted “Another major advantage of LRS is the ability to phase variants assigning them unambiguously to parental haplotypes. Without pedigree information, short-read data can typically be used to phase up to 20% of DNM calls, but we were able to phase 97.7% and 97.0% of autosomal SNVs and indels, respectively.”
- “The mutation rate is significantly increased for classes of repetitive DNA, where segmental duplication (SD) mutation shows a dependence on the length and percent identity of the SD.”
Conclusion:
This study reinforces the power of HiFi long-read sequencing to uncover significantly more de novo and postzygotic mutations than short reads while also enabling accurate phasing without the need for pedigree data. With near-complete resolution of variants, even in repetitive regions like SDs, HiFi sequencing provides the clarity needed to push autism genetics research forward.
Structural and repeat variation
In this preprint, researchers from UCSD and Rady’s demonstrate “how long read-whole genome sequencing (LR-WGS) can resolve complex genetic variation and its functional consequences and regulatory effects in a single assay.”
Key highlights:
- Performed LR-WGS on 243 individuals (158 HiFi, 109 ONT) from 63 ASD families, resulting in an increased detection of gene-disrupting SVs and TRs by 29% and 38%, respectively.
- Reported the “identification of novel exonic de novo germline and somatic SVs that were not detected previously with short read WGS.”
- Found that “rare SVs, TRs, and damaging SNVs together accounted for 6.2% … of the heritability of ASD” (“SVs contributed the largest proportion”).
- Emphasized that “LR-WGS offers critical advantages. These include precise resolution of fine-scale structural features, improved characterization of complex rearrangements, and the ability to jointly analyze genetic variants and DNA methylation at single-haplotype resolution.”
Conclusion:
This study highlights the power of LR-WGS—particularly HiFi—to uncover novel germline and somatic variants missed by short reads, while improving detection of SVs and TRs that contribute meaningfully to ASD heritability. With the added ability to analyze genetic variants and DNA methylation on the same haplotype, HiFi provides a more complete and functional view of complex variation in a single assay.
Ready to make long-read sequencing discoveries of your own?
The studies featured this month are strong examples of how HiFi sequencing is helping researchers uncover disease-relevant variants that were missed by short-read approaches, even in families who’ve undergone multiple rounds of testing. By accessing regions of the genome that were previously off-limits, these teams are pushing past longstanding barriers in autism research and neurodevelopmental biology.
More broadly, they show how the combination of long-read sequencing and pangenome references is making it easier to identify pathogenic variants and better understand genetic risk across populations. As one team put it: “As the human pangenome continues to grow and more complete genetic information emerges, the potential to discover variants of pathogenic significance will increase.”
HiFi sequencing is helping make that potential a reality and bringing clarity to clinical research and opening up new questions we’re now better equipped to answer.