Rare Disease Diagnostics by HiFi Sequencing

Category

Unlocking the Genetic Code: How HiFi Sequencing Revolutionizes Rare Disease Diagnostics – Insights from Global Case Studies and Nucleome’s Expertise in India

At Nucleome Informatics, we are at the forefront of genomic innovation in India, harnessing cutting-edge technologies like PacBio HiFi long-read sequencing to solve complex genetic puzzles that traditional short-read sequencing (SRS) often misses. HiFi sequencing, known for its high accuracy and long reads, excels in detecting structural variants (SVs), repeat expansions, and variants in challenging genomic regions—leading to higher diagnostic yields for rare diseases. Drawing from recent global case studies, this article explores how HiFi has transformed undiagnosed cases worldwide and how Nucleome’s state-of-the-art services can deliver similar breakthroughs for patients and researchers in India.

The Power of HiFi Sequencing: Overcoming Limitations of Short-Read Methods

Traditional SRS, while cost-effective for basic variant detection, struggles with repetitive sequences, large SVs, and homologous regions, often leaving 10-20% of the genome unresolved. This results in “diagnostic odysseys” for patients with rare genetic disorders, where initial tests fail to identify causative variants. HiFi sequencing addresses these gaps by generating reads up to 20-30 kb with >99.9% accuracy, enabling de novo assembly, precise phasing, and methylation analysis in a single workflow.

Global studies demonstrate HiFi’s impact: In a 2025 evaluation of 100 samples with 145 known challenging germline pathogenic variants from rare disease patients, HiFi at ~30× coverage detected 93% of variants—far surpassing SRS’s 41% automated detection rate. This included SVs, short tandem repeat (STR) expansions, and imprinting defects that required multiple complementary tests under SRS. Similarly, programs like Solve-RD and Genomic Answers for Kids have boosted solve rates by 10-20% through HiFi, uncovering pathogenic aberrations invisible to short reads.

Case Study 1: Resolving Structural Variants in Neurodevelopmental Disorders (NDDs)

In a 2023 study of eight family trios with children affected by unsolved NDDs (e.g., intellectual disability and autism spectrum disorders), prior SRS exome sequencing identified no clear causes. HiFi sequencing at ~30× coverage revealed de novo germline mutations, including 24 SVs missed by SRS. Key examples include:

• A 123-bp duplication in an intron of the NXPE3 gene, validated as de novo and linked to neurodevelopmental processes.
• A 303-bp insertion in a TAOK3 intron, associated with intellectual disability.
• Multiple de novo repeat expansions in repetitive elements, potentially disrupting gene regulation.

These findings provided molecular diagnoses, guiding targeted therapies and family counseling. At Nucleome, our PacBio Sequel II platform offers similar HiFi whole-genome sequencing (WGS) for NDDs, integrated with AI-driven variant prioritization. For Indian families facing undiagnosed NDDs—prevalent in consanguineous populations—our services can detect these elusive SVs, reducing turnaround times and costs compared to overseas testing.

Case Study 2: Detecting Repeat Expansions and Insertions in Neurodegenerative and Neuromuscular Diseases

A 2023 analysis of 96 probands with suspected neurodegenerative diseases (e.g., ataxia, dementia) unsolved by SRS trio sequencing found explanations in 16 cases using HiFi at ~26× coverage. Over 40% involved long-read-exclusive variants like copy number variants (CNVs), inversions, mobile element insertions, and low-complexity repeat expansions. Notable instances:

• An FXN (GAA)n expansion in Friedreich ataxia, rescued by including low-quality reads for enhanced calling.
• A CNBP STR expansion in myotonic dystrophy type 2, confirmed via visual inspection.
• An NF1 mobile element insertion in neurofibromatosis type 1.

These variants, often in repetitive or GC-rich regions, were undetectable by SRS. Nucleome’s HiFi services, including ISO-Seq for full-length transcript analysis, are tailored for such cases. In India, where neurodegenerative disorders like spinocerebellar ataxias are underdiagnosed, our DrSeq Lab provides clinical-grade WGS and epigenome profiling to identify these hidden culprits, supporting precision medicine initiatives.

Case Study 3: Uncovering Complex Rearrangements in Sensory Disorders

HiFi has excelled in sensory loss cases, such as a 2023 study of 19 pediatric patients with unsolved sensorineural hearing loss. At 24-32× coverage, HiFi identified causes in 21%, including:

• A hemizygous deletion in OTOA.
• Loss-of-function SNVs in STRC combined with CNVs, resolved despite pseudogene homology.
• A copy-neutral inversion in MITF.

In inherited retinal dystrophies, HiFi solved all three unsolved cases with deep intronic variants, exon deletions, and complex SVs. Another example from color vision defects involved clarifying OPN1LW/OPN1MW gene cluster variants through assembly and visualization.

For Indian patients, where consanguinity increases autosomal recessive sensory disorders, Nucleome’s targeted HiFi panels and metagenomics applications (e.g., full-length 16S for infection-related hearing loss) offer comprehensive solutions. Our accredited labs ensure ACMG-compliant reporting, empowering clinicians with actionable insights.

Case Study 4: Large-Scale Cohorts and Imprinting Disorders

In 34 families with suspected autosomal recessive diseases negative after SRS exomes, HiFi at ~10× coverage identified candidates in 38%, including novel large insertions and SVs. Broader efforts, like the 100,000 Genomes Project, resolved MECP2 inversions causing haploinsufficiency in Rett syndrome-like cases. An imprinting defect (maternal uniparental heterodisomy on chromosome 14) in Temple syndrome was detected via methylation tools.

Nucleome replicates this through our rare disease diagnostics pipeline, using ML for variant annotation and high-coverage HiFi for imprinting analysis. We’ve successfully diagnosed cases like a novel SCN1A mutation in pediatric epilepsy, demonstrating our capability to end diagnostic odysseys in India.

Why Choose Nucleome Informatics for HiFi Sequencing in India?

As India’s leading genomics provider, Nucleome combines PacBio HiFi with Illumina and Bionano platforms for hybrid assemblies, ensuring >99% genome coverage. Our services include:

• Clinical Applications: WES/WGS for rare diseases, pharmacogenomics, and prenatal screening.
• Research Support: De novo assembly for non-model organisms, pan-genome studies, and biodiversity genomics.
• AI-Enhanced Analysis: Custom pipelines for SV detection, phasing, and epigenetic insights.
• Accessibility: Fast, cost-effective testing with end-to-end support, from sample collection to genetic counseling.

By bringing global HiFi advancements home, we reduce reliance on international labs, accelerate diagnoses, and foster precision medicine. Whether you’re a clinician tackling undiagnosed cases or a researcher exploring genetic diversity, Nucleome’s expertise ensures reliable, impactful results.

Contact us today at info@nucleomeinfo.com or visit our website to learn how we can solve your genomic challenges. Together, let’s decode the future of health in India.

Reference: PacBio