PacBio Unveils a New Method for Comprehensive, Genome-wide Tandem Repeat Analysis

Rhea-AI Summary

PacBio (NASDAQ: PACB) announced a new computational analysis method called Tandem Repeat Genotyping Tool (TRGT) for studying tandem repeats (TRs) in the human genome. This tool enables comprehensive profiling of TRs and their methylation status, aiding researchers in understanding their role in diseases like ALS and Fragile X syndrome. TRGT improves the analysis of genetic variations and can identify disease-causing TRs. The tool is available on GitHub alongside a companion visualization tool, enhancing usability for genomic research.

Positive

• Introduction of TRGT enhances the analysis of tandem repeats, potentially leading to new disease insights.
• TRGT could enable identification of pathogenic variants linked to neurological disorders.
• The availability of TRGT and TRVZ on GitHub promotes further research and collaboration.

Negative

• None.

Analysis Method Supports Research on the Genetic Causes of Common Diseases

MENLO PARK, Calif., Sept. 27, 2022 /PRNewswire/ -- PacBio (NASDAQ: PACB), a leading developer of high-quality, highly accurate sequencing solutions, today announced the availability of a new computational analysis method for profiling more than a million tandem repeats (TRs) across the human genome using PacBio's native long-read HiFi sequencing data. The Tandem Repeat Genotyping Tool (TRGT: pronounced as "target") is intended to provide scientists with the ability to obtain a full characterization of the sequence and methylation status of TRs genome-wide. We believe TRGT will enable scientists to better understand the role of known TRs in human disease and could lead to the discovery of novel disease-causing TRs.

Tandem repeats are genetic sequences that are repeated in series, and they can grow in length from parent to child. Importantly, TRs have been linked to many neurological disorders such as ALS and Huntington's disease in addition to the number one cause of inherited mental intellectual disability, Fragile X syndrome.

"We developed TRGT to characterize the genetic and epigenetic variation in one of the most difficult variant classes, tandem repeats" said Michael Eberle, Vice President of Computational Biology at PacBio. "So far, tandem repeats have been understudied due to limitations in the ability of short-read sequencing technologies to sequence these regions of the genome. By combining HiFi sequencing and TRGT, we intend to provide scientists with the ability to explore and characterize these complicated genomic regions and, ultimately, better understand their biological impact."

TRGT is intended to enable research scientists to characterize the sequence composition and structure, repeat unit length, and CpG methylation for each analyzed repeat allele and flanking sequence across the genome. The improved characterization of TR variation may aid in the tertiary analysis for disease causing loci. For example, TRGT can characterize the very long (thousands of base pairs) repeats associated with certain diseases. TRGT can also identify sequence composition changes that are potentially associated with pathogenic expansions in diseases such as cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS). Furthermore, because HiFi reads can identify CpG methylation, TRGT can identify hypermethylation signals like those observed with Myotonic Dystrophy expansions.

"The TRGT method is a major improvement on repeat expansion analysis and is helping us to discover new and potentially important variants that may be associated with disease in samples from individuals with inherited disorders," said Stephan Zuchner, MD, PhD, Professor and Chief Genomics Officer of the Miller School of Medicine, University of Miami. Dr. Zuchner and his colleague, Matt Danzi, PhD, Scientist and bioinformatician, are focused on research into the characterization of repeat expansions in healthy and rare disease cohorts.

To improve usability, TRGT also comes with a companion tool, TRVZ, for visualizing the read pileups and methylation data for each repeat allele and flanking sequence analyzed.  

TRGT and TRVZ are now available on GitHub: https://github.com/pacificBiosciences/trgt/ 

About PacBio

Pacific Biosciences of California, Inc. (NASDAQ: PACB) is a premier life science technology company that is designing, developing and manufacturing advanced sequencing solutions to help scientists and clinical researchers resolve genetically complex problems. Our products and technology under development stem from two highly differentiated core technologies focused on accuracy, quality and completeness which include our existing HiFi long read sequencing and our emerging SBB™ short read sequencing technologies. Our products address solutions across a broad set of research applications including human germline sequencing, plant and animal sciences, infectious disease and microbiology, oncology, and other emerging applications. For more information, please visit www.pacb.com and follow @PacBio.

PacBio products are provided for Research Use Only. Not for use in diagnostic procedures.

Forward-Looking Statements

This press release may contain "forward-looking statements" within the meaning of Section 21E of the Securities Exchange Act of 1934, as amended, and the U.S. Private Securities Litigation Reform Act of 1995, including statements relating to future availability, uses, accuracy, advantages, quality or performance of, or benefits or expected benefits of using, PacBio products or technologies, including the use of TRGT, HiFi and other PacBio products, technologies and computational methods to sequence, characterize and potentially identify disease causing variants and epigenetic modifications in the genome, and other forward looking statements. Readers are cautioned not to place undue reliance on these forward-looking statements and any such forward-looking statements are qualified in their entirety by reference to the following cautionary statements. All forward-looking statements speak only as of the date of this press release and are based on current expectations and involve a number of assumptions, risks and uncertainties that could cause the actual results to differ materially from such forward-looking statements. Readers are strongly encouraged to read the full cautionary statements contained in PacBio's filings with the Securities and Exchange Commission, including the risks set forth in PacBio's Forms 8-K, 10-K, and 10-Q. PacBio disclaims any obligation to update or revise any forward-looking statements.

Contacts

Investors:
Todd Friedman
650.521.8450
ir@pacb.com

Media:
Lizelda Lopez
pr@pacb.com

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SOURCE Pacific Biosciences of California, Inc.

FAQ

What is the purpose of PacBio's new Tandem Repeat Genotyping Tool (TRGT)?

TRGT is designed to enable comprehensive analysis of tandem repeats across the human genome, improving understanding of their role in various diseases.

How does TRGT enhance genomic research for diseases?

TRGT allows for the full characterization of tandem repeats and their methylation status, which is critical for identifying disease-causing genetic variations.

Where can researchers access PacBio's TRGT tool?

The TRGT tool is available on GitHub, along with a companion tool for data visualization.

What diseases are associated with tandem repeats that TRGT helps analyze?

Tandem repeats have been linked to diseases such as ALS, Huntington's disease, and Fragile X syndrome.

What is the significance of the TRGT method for scientists?

TRGT provides a significant advancement in the analysis of complex genomic regions, aiding in the discovery of new genetic variants related to inherited disorders.