Small variant benchmark from a complete assembly of X and Y chromosomes

Justin Wagner, Nathan D. Olson, Jennifer McDaniel, Lindsay Harris, Brendan J. Pinto, David Jáspez, Adrián Muñoz-Barrera, Luis A. Rubio-Rodríguez, José M. Lorenzo-Salazar, Carlos Flores, Sayed Mohammad Ebrahim Sahraeian, Giuseppe Narzisi, Marta Byrska-Bishop, Uday S. Evani, Chunlin Xiao, Juniper A. Lake, Peter Fontana, Craig Greenberg, Donald Freed, Mohammed Faizal Eeman Mootor, Paul C. Boutros, Lisa Murray, Kishwar Shafin, Andrew Carroll, Fritz J. Sedlazeck, Melissa Wilson and Justin M. Zook ()
Additional contact information
Justin Wagner: 100 Bureau Dr.
Nathan D. Olson: 100 Bureau Dr.
Jennifer McDaniel: 100 Bureau Dr.
Lindsay Harris: 100 Bureau Dr.
Brendan J. Pinto: Milwaukee Public Museum
David Jáspez: Instituto Tecnológico y de Energías Renovables (ITER)
Adrián Muñoz-Barrera: Instituto Tecnológico y de Energías Renovables (ITER)
Luis A. Rubio-Rodríguez: Instituto Tecnológico y de Energías Renovables (ITER)
José M. Lorenzo-Salazar: Instituto Tecnológico y de Energías Renovables (ITER)
Carlos Flores: Instituto Tecnológico y de Energías Renovables (ITER)
Sayed Mohammad Ebrahim Sahraeian: Roche Sequencing Solutions
Giuseppe Narzisi: New York Genome Center
Marta Byrska-Bishop: New York Genome Center
Uday S. Evani: New York Genome Center
Chunlin Xiao: National Institutes of Health
Juniper A. Lake: Pacific Biosciences
Peter Fontana: 100 Bureau Dr. Mailstop 8940
Craig Greenberg: 100 Bureau Dr. Mailstop 8940
Donald Freed: Sentieon Inc.
Mohammed Faizal Eeman Mootor: University of California Los Angeles
Paul C. Boutros: University of California Los Angeles
Lisa Murray: Illumina
Kishwar Shafin: 1600 Amphitheatre Pkwy
Andrew Carroll: 1600 Amphitheatre Pkwy
Fritz J. Sedlazeck: Baylor College of Medicine Human Genome Sequencing Center
Melissa Wilson: Arizona State University
Justin M. Zook: 100 Bureau Dr.

Nature Communications, 2025, vol. 16, issue 1, 1-7

Abstract: Abstract The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To enable technology developers along with research and clinical laboratories to evaluate variant detection on male sex chromosomes X and Y, we create a small variant benchmark set with 111,725 variants for the Genome in a Bottle HG002 reference material. We develop an active evaluation approach to demonstrate the benchmark set reliably identifies errors in challenging genomic regions and across short and long read callsets. We show how complete assemblies can expand benchmarks to difficult regions, but highlight remaining challenges benchmarking variants in long homopolymers and tandem repeats, complex gene conversions, copy number variable gene arrays, and human satellites.

Date: 2025
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-024-55710-z

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DOI: 10.1038/s41467-024-55710-z

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