Population genetics programs leverage economies of scale to create large, diverse and comprehensive data sets that will be researched to fuel precision health programs for years to come. This data infrastructure should ideally contain the highest degree of high-quality genomic information and context while remaining cost-effective, in order to provide long-term benefits to clinical and scientific research communities.
PacBio technology offers trusted solutions for:
- Delivering phased genomes with high accuracy, completeness, and resolution of all variant classes
- Robust coverage across challenging and repeat-rich regions
- Genome-wide methylation status for multiomic studies
HiFi sequencing is ideal for creating differentiated population sequencing data sets that span well beyond the limitations of short-read systems.
Discover here how HiFi sequencing offers flexible genome coverage options and targeted solutions, enabling you to maximize the output of your research budget, while implementing the optimal HiFi coverage for population-wide to individual-level insights.
What is population genetics?
Population genetics is a fascinating field of biology that explores the distribution and changes of genetic traits within populations. It aims to understand the processes that shape the genetic makeup of populations and allows examining the impact of genetic variation on the health of individuals, as well as the role of genetics in the development of complex traits, such as susceptibility to certain diseases.
Precision medicine helps clinicians use information about a person’s unique genetics, environment, and lifestyle to offer that person more accurate and effective disease treatment and prevention.
GENETIC DISCOVERY AT POPULATION SCALE
Long-read sequencing with Revio provides accurate and contiguous DNA sequences for population genetics studies, including structural variations and epigenetic insights. HiFi reads offer researchers access to valuable genetic data through highly accurate and phased assemblies.
Get the most out of your population genetic data with:
Maximum data quality
The Revio system provides reliable answers through exceptional accuracy, with 90% of bases ≥Q30.
Complement your data with HiFi
Add long reads to pre-existing short-read datasets to enhance them with haplotype phasing, robust structural variant detection, pseudogene resolution, methylation profiling, tandem repeats, and segmental duplications
Cost-effective and robust solutions
Leading global precision health programs are utilizing cost-effective HiFi long reads to improve their datasets
Automated and scalable workflows
From sample prep to flexible Revio sequencing to specialized computational tools, PacBio has you covered
Building a population-specific reference genome is a cost-effective way to help your program better represent the genetic diversity in your populations of interest and to enable accurate variant calling for non-European ancestries. HiFi sequencing can easily be used to create reference genomes with high completeness, correctness, and contiguity.
Small variants (SNVs and indels) are the most abundant class of variation. However, structural variants (because they are larger in size than small variants) account for more genomic variation between two individuals than SNVs and indels combined.
HiFi sequencing accurately detects small and structural variants, allowing for a more comprehensive analysis of all variation types and the potential to improve the relatively static solve rates of short-read whole genome sequencing (WGS) and whole exome sequencing (WES).
With fuller resolution of these variant types, researchers have a better chance of truly understanding human genetic diversity and disease association.
“HiFi reads allow the accurate and simultaneous detection of all variant classes, and provide a rich genetic context of the regions of interest, paving the way for advancements in human genetics and greatly expanding the utility of SMRT sequencing.”— Fritz Sedlazeck, PhD, Associate Professor, Human Genome Sequencing Center at Baylor College of Medicine
HiFi sequencing provides accurate DNA base calls and simultaneous 5mC detection in CpG context without any additional library preparation or costs.
This feature enables the resolution of methylation profiles with phased haplotyping. Human genome researchers can also use this capability to interrogate imprinting disorders and methylation abnormalities associated with tandem repeats.
Population genetics initiatives are gaining traction around the world, allowing researchers to build diverse population health databases, and learn how biology, environment, and lifestyle affect our health, and bring us closer to a future where precision medicine is the standard.
Amplicon-based HiFi sequencing
Learn how accurate HiFi sequencing of long amplicons provides more insights by spanning entire genes, allowing for advanced haplotype construction, and discovering both rare and common variants of various types. A scalable and cost-effective solution with fewer amplicons per gene.
Learn more about:
HiFi target enrichment with Twist probes
Understand how you can get all the benefits of long and accurate HiFi reads at scale with capture probes from Twist. For challenging/particular regions of interest, the optimized Twist capture approach is the way to go.
Straightforward epigenome analysis with HiFi
Gain a more complete view of the methylation status as an additional fifth base signal in your sequencing experiment without requiring special library preparation like bisulfite treatment. Detect distinct regional epigenetic patterns, access methylation in the full genome, and identify allele-specific methylation.
Tunable HiFi Genomes
HiFi offers you genome coverage options — from 10× to 30× — with published detection performance across variant classes and methods, enabling you to maximize the yield of your research budget. Whether you are generating population-wide or individual-level insights, the coverage options of HiFi sequencing can help you achieve long-term and broad utility of the data.
What is carrier screening?
Carrier screening is a medical test that determines whether a person carries a gene associated with a genetic disorder that could potentially be passed on to their offspring.
Carrier screening is especially important in populations where the prevalence of certain genetic disorders is higher. For example, genetic disorders such as cystic fibrosis, sickle cell anemia, and Tay-Sachs disease are more common in certain ethnic and racial groups. Carrier screening can inform decisions about prenatal testing and health management.
How does HiFi sequencing advance research in single and multi-gene disorders?
Many of the target genes involved in recessive disorders such as spinal muscular atrophy, thalassemia, and congenital adrenal hyperplasia have been historically challenging to sequence. Without the right sequencing tools, they require a combinatorial approach to fully uncover their genetic makeup and context.
However, PacBio whole-genome and targeted long-read sequencing solutions, in combination with specialized variant callers, enable a robust and cost-effective solution for those challenging regions, drive consolidation of conventional molecular methods, and enable more scientific insights.
Targeted sequencing for complex genes
With targeted sequencing, you only sequence the genomic regions you care about. HiFi targeted sequencing offers cost-effective and scalable sequencing of specific genomic regions, with hybrid capture and amplicon workflows available for your customized needs.
HiFi reads provide accurate haplotype resolution and comprehensive detection of all variant types, while also providing acces to difficult-to-sequence regions like those with high homology, GC-rich and repetitive regions. It can also resolve complex genes and pharmacogenes such as SMN1/2, FMR1, GBA, HBA, LPA, PMS2, and CYP2D6.
Introducing Paraphase by PacBio — an informatics method for uncovering secrets of spinal muscular atrophy
For the first time, PacBio is enabling high-throughput, comprehensive profiling of SMN1 and SMN2 with Paraphase by PacBio. A new paper highlights how this tool can fundamentally change the way we study SMA and what we can learn.
New tools to support population and disease genetics research
Characterization of complex tandem repeat regions
With over a million tandem repeats in the human genome, they play a key role in human health and disease, and have been linked to gene expression changes, genome instability in cancer and over 50 diseases of the nervous system including ALS, FXS, ataxias, autism spectrum disorders, and schizophrenia.
Here is a suggested toolkit of solutions for characterizing complex tandem repeat regions:
Tandem repeat genotyping tool (TRGT)
- Size genotyping and mosaicism estimation
- Sequence composition analysis (interruptions, regions with multiple repeats)
- CpG methylation analysis
Tandem repeat visualizer (TRVZ)
- Haplotype-resolved read pileup and methylation state display
Genome-wide TR catalog
- Annotations of TRs with population distributions of sizes and methylation
Resolving segmental duplications in disease-related genes
Segmental duplications comprise 7% of the human genome, affecting many clinically relevant genes.
Segmental duplications are hotspots for structural variations, including deletions, duplications, and gene conversions.
Our new tool, Paraphase, enables:
- Identification of standard carriers (1+0)
- Haplotype-based screening of silent carriers (2+0) — haplogroup analysis
- Pathogenic variant detection — phased
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