PacBio helps researchers usher in a new era of genomics with cost-effective tools to accurately identify tandem repeat changes causing human disease and detailed sequences of specific genes At scale.
After the completion of the first draft of the human genome in the early 2000s, the research and clinical community was overflowing with excitement that this milestone had marked the dawn of the genomic era. The first project held the promise of new technologies and medical breakthroughs.
Although this tremendous achievement opened up new possibilities, there were still discoveries to be made. In the 2010s, the scientific community realized that even the best human genome assemblies of the time contained many gaps to be filled and errors to be corrected. In 2021, researchers addressed these challenges by using HiFi reads to assemble the first human reference genome without gaps, including centromeric regions and entire short arms of five human chromosomes.
At PacBio, we are inspired by these advances in genomic discovery and excited to continue creating new technologies to inspire innovation. Recently we announced Exam, That’s itand MAS-Seqthree new products to provide the most accurate long-, short-, and single-cell RNA sequencing data possible.
In addition to these press releases, we are also pleased to present to you TRGT with TRVZ Companion Tool and HiFi Targeted Enrichment Panelstwo solutions (software and chemistry) that further extend the groundbreaking capabilities of PacBio sequencing, fueling the ability to confidently unravel even the most challenging genome complexities.
Analyze and visualize tandem repeats with TRGT
A new tandem repeat analysis and visualization tool to achieve comprehensive detection of single nucleotide variants, structural variants and indels with haplotype resolution.
What are tandem reps?
A tandem repeat is a length of DNA of two or more nucleotides that is repeated back-to-back (called a repeat motif), from two to more than one hundred times on a chromosome.
Due to their repetitive nature, genomic regions containing long tandem repeats have been notoriously difficult to analyze accurately. This is due to mathematical uncertainties in trying to piece together and align short readings that cannot cover the full length of the repeat.
Why tandem reps are important
Although they are non-coding sections in genes, tandem repeats make up nearly 4% of the entire human genome and are highly influential in biology, accounting for most structural variants longer than 50 bp. Because tandem repeats are rarely translated into proteins, these highly repetitive regions are also extremely variable with significant influence on phenotypic variation and a host of genetic diseases in humans.
Table: Adam English, Baylor College of Medicine
To date, tandem repeats have been linked to changes in gene expression in cancers and are associated with over 50 nervous system diseases including ALS, FXS, ataxias, autism spectrum disorders and schizophrenia. Understanding tandem repeats and accurately capturing and cataloging their sequences is the first step to understanding how they drive disease, which could one day lead to the discovery of biomarkers, drug targets and the development of therapies.
How TRGT + TRVZ Can Revolutionize Your Tandem Repeat Analysis
PacBio HiFi sequencing combined with the all-new TRGT+TRVZ software solution eliminates the challenges of tandem repeat analysis with conventional approaches by providing researchers with extended reads (>10,000 bp), highly accurate (99.9% ) and a suite of analysis tools dedicated to listening to the specifics of this unique and powerful data.
TRGT + TRVZ capabilities include:
- Size genotyping and mosaicism estimation
- Sequence composition analysis (including breaks and multi-repeat regions)
- CpG methylation call 5mC
- Visual display of haplotype-resolved read stacking and methylation status
Together, HiFi sequencing and TRGT help break down complex mathematical hurdles of the past, allowing researchers to answer critical questions about the role these important genomic regions play in everything from trait evolution to disease biology. .
Explore TRGT in more detail in this on-demand presentation by PacBio scientist and co-developer Egor Dolzhenko. If you’re ready to try out this exciting new analytics tool, TRGT is now available on GitHub.
Get HiFi readings of only the genes you care about At scale
Rapidly increase the throughput and cost-effectiveness of variant detection with HiFi reads using new HiFi target enrichment panels developed in collaboration with Twist Bioscience.
What is target enrichment?
Target enrichment is a general term for a variety of pre-sequencing DNA preparation methods that are used to focus exclusively on a specific gene or region of interest in the genome, dramatically improving the scale, cost and resource efficiency of a sequencing study.
How target enrichment works
To exclude all superfluous information from the genome and drill down into specific areas of interest, researchers typically use one of two approaches: target amplification using the polymerase chain reaction (PCR) or physical capture of the target via DNA- DNA hybridization between the sample and a probe.
PCR-based methods (also called targeted amplicon sequencing) involve designing primers for the area(s) of interest and performing PCR that replicates the target sequence to such an extent that it drowns out completely any unwanted DNA from a sample. These amplified molecules or “amplicons” can then be subjected to additional downstream manipulations prior to sequencing, including barcoding and multiplexing. The advantages of amplicon enrichment include a relatively simple workflow and the ability to study samples with very low DNA input. Disadvantages include difficulty with large genomic regions and the introduction of data biases inherent in PCR chemistry.
The alternative approach, commonly referred to as hybrid capture, circumvents the problems associated with PCR bias and size limitations by allowing the researcher to physically select and remove sequences of interest from a sample. This is accomplished by first binding a short piece of DNA, commonly referred to as a probe, to the desired piece of sample DNA. Unlike the primers used in PCR, the probes used in hybrid capture are not used to initiate the synthesis of a complementary strand of DNA. Instead, the probe is attached to a magnetic bead that helps hold the target molecule in place, which washes away the rest of the sample. This remaining set of molecules is then moved along the preparatory and sequenced workflow.
The benefits of HiFi target enhancement with Twist tiles
PacBio has partnered with Twist Bioscience to offer target enrichment options that beautifully integrate the strengths of HiFi sequencing and Twist’s proprietary chemistry to get the most information with the least sequencing. Using a hybrid capture approach, the Twist HiFi enhancement offers these key benefits:
- Fully customizable panel design
- High capture efficiency using dsDNA probes
- Data with excellent specificity and uniformity
- Increase sequencing depth per sample or number of samples per sequencing cycle
- Haplotype phase
Together, these capabilities enable researchers to engage in information-rich exploratory genotyping experiments with the added throughput and cost savings of a targeted methodology. By focusing on the locus of interest to the exclusion of other genomic regions, a single HiFi sequencing sequence can achieve significantly greater depth or accommodate more samples than would be possible with a single HiFi sequencing approach. whole genome. For research programs aiming to study unknown areas of the genome, Twist dsDNA probes can be used as a hook to attach to as little as 60 bp of a known sequence allowing HiFi sequencing to read in the unknown region .
Watch the webinar on demand
Your partner in the pursuit of discovery
At PacBio, we are committed to being a reliable partner that supports and inspires your scientific success. With TRGT and HiFi Enrichment Panels you can focus on the right solutions for your research goals. If you have any further questions, contact us to discuss how PacBio can help you turn your research vision into a concrete reality.
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