Nature Methods Paper Leverages PacBio Sequencing Technology to Develop the Platinum Pedigree Benchmark, a New Standard for Accurate Characterization of Variation in the Human Genome that Improves Training for AI Models
PacBio
The most comprehensive, family-based variant dataset ever published will improve variant classification using AI-based tools
MENLO PARK, Calif., Aug. 04, 2025 (GLOBE NEWSWIRE) — PacBio (NASDAQ: PACB), a leading provider of high-quality, highly accurate sequencing platforms, today announced the results of a study published in NatureMethods describing a new, comprehensive truth-set of genomic variation which characterizes simple and complex variation. These improved benchmarks were used to retrain Google’s DeepVariant, a popular AI-based variant calling tool, resulting in a 34% reduction in erroneously called variants. This resource (the Platinum Pedigree) was built by scientists from PacBio in collaboration with researchers at the University of Washington, the University of Utah, and several other institutions.
Combining inheritance-based validation with long-read sequencing, this benchmark accurately characterizes variants, even in difficult, repeat rich regions of the genome, producing the most complete view of validated genetic variation to date.
“Comprehensive benchmarking datasets that include all variant types are foundational to progress in genomics methods development and the application of AI-driven tools, as well as to our understanding of genomic variation for both research and diagnostic purposes,” said Zev Kronenberg, lead author and Senior Manager at PacBio. “The Platinum Pedigree benchmark doesn’t just include simple variants in easy-to-sequence regions, it includes variants from across the entire genome, including regions that were previously excluded from benchmarks due to their complex nature.”
The Platinum Pedigree dataset was developed using deep sequencing from three sequencing platforms across a 28-member, multi-generational family (CEPH-1463). By tracking the inheritance of genetic variants from parents to multiple children, the study confidently catalogs over 37 Mb of genetic variation segregating within the family from single nucleotide variants to large structural variants.
The dataset introduces the first large pedigree-validated tandem repeat and structural variant truth sets. It also adds more than 200 million bases extending the benchmark regions to 2.77 Gb, including difficult-to-map areas such as segmental duplications and low-complexity regions.
A Benchmark Built for the Dark Genome
As a demonstration of the value of improved benchmarks to improve AI and ML methods, the researchers retrained Google’s DeepVariant – a popular software tool that employs deep learning to identify genetic variants – using the Platinum Pedigree benchmark data. This updated DeepVariant model reduced errors by up to 34% genome-wide, including even higher gains in the most challenging regions of the genome.
“This benchmark pushes accuracy where it matters most,” said Michael Eberle, senior author and Vice President of Computational Biology at PacBio. “It enables better evaluation of variant calling pipelines and accelerates the development of methods that finally reach the full genome, including some of the complex regions that are important for human health.”
A New Standard for Clinical and Population Genomics
The Platinum Pedigree benchmark is freely available and already being used by scientists to develop new sequence analysis tools and validate clinical sequencing workflows. It also provides a roadmap for future benchmarking efforts, especially those involving more complete genomes like T2T-CHM13.
The full dataset, analysis code, and pipelines are publicly available at:
About the Study
The study, “The Platinum Pedigree: A long-read benchmark for genetic variants,” was published in Nature Methods on August 4, 2025. It was led by scientists at PacBio, the University of Washington, and University of Utah, with support from the NIH and Howard Hughes Medical Institute.
About PacBio
PacBio (NASDAQ: PACB) is a premier life science technology company that designs, develops, and manufactures advanced sequencing solutions to help scientists and clinical researchers resolve genetically complex problems. Our products and technologies, which include our HiFi long-read sequencing, 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 contains “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. All statements other than statements of historical fact are forward-looking statements, including statements relating to the uses, advantages, quality or performance of, or the benefits or expected benefits of using, PacBio products or technologies, including in connection with the Platinum Pedigree dataset, its potential to enable better evaluation of variant calling pipelines and accelerate development methods that reach the full genome, and other future events. You should not place undue reliance on forward-looking statements because they are subject to assumptions, risks, and uncertainties that could cause actual outcomes and results to differ materially from currently anticipated results. These risks include, but are not limited to, rapidly changing technologies and extensive competition in genomic sequencing; unanticipated increases in costs or expenses; and other risks associated with general macroeconomic conditions and geopolitical instability. Additional factors that could materially affect actual results can be found in PacBio’s most recent filings with the Securities and Exchange Commission, including PacBio’s most recent reports on Forms 8-K, 10-K, and 10-Q, and include those listed under the caption “Risk Factors.” These forward-looking statements are based on current expectations and speak only as of the date hereof; except as required by law, PacBio disclaims any obligation to revise or update these forward-looking statements to reflect events or circumstances in the future, even if new information becomes available
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