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

by Sedlazeck, Fritz J. , Mootor, Mohammed Faizal Eeman , Boutros, Paul C. , Harris, Lindsay , Rubio-Rodríguez, Luis A. , Xiao, Chunlin , McDaniel, Jennifer , Freed, Donald , Lorenzo-Salazar, José M. , Sahraeian, Sayed Mohammad Ebrahim , Olson, Nathan D. , Flores, Carlos , Wilson, Melissa , Murray, Lisa , Jáspez, David , Carroll, Andrew , Byrska-Bishop, Marta , Pinto, Brendan J. , Zook, Justin M. , Fontana, Peter , Lake, Juniper A. , Muñoz-Barrera, Adrián , Shafin, Kishwar , Narzisi, Giuseppe , Evani, Uday S. , Wagner, Justin , Greenberg, Craig

in 45/23 / 631/114/2785 / 631/208/212 / 631/208/514/1948 / Assemblies / Benchmarking / Benchmarks / Chromosomes / Chromosomes, Human, X - genetics / Chromosomes, Human, Y - genetics / Copy number / DNA Copy Number Variations / Genetic Variation / Genome, Human / Genomes / Genomics - methods / Humanities and Social Sciences / Humans / Male / multidisciplinary / Phenotypes / Ploidy / Science / Science (multidisciplinary) / Sex / Sex chromosomes / Somatic chromosomes / Technology assessment / Y chromosomes

2025

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2025

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2025

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Journal Article

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

Sedlazeck, Fritz J.,

Mootor, Mohammed Faizal Eeman,

Boutros, Paul C.,

Harris, Lindsay,

Rubio-Rodríguez, Luis A.,

Xiao, Chunlin,

McDaniel, Jennifer,

Freed, Donald,

Lorenzo-Salazar, José M.,

Sahraeian, Sayed Mohammad Ebrahim,

Olson, Nathan D.,

Flores, Carlos,

Wilson, Melissa,

Murray, Lisa,

Jáspez, David,

Carroll, Andrew,

Byrska-Bishop, Marta,

Pinto, Brendan J.,

Zook, Justin M.,

Fontana, Peter,

Lake, Juniper A.,

Muñoz-Barrera, Adrián,

Shafin, Kishwar,

Narzisi, Giuseppe,

Evani, Uday S.,

Wagner, Justin,

Greenberg, Craig

2025

Overview

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. The paper describes a Genome in a Bottle benchmark for the X and Y chromosomes enabled by complete chromosome assemblies. This benchmark enables users to evaluate small variant accuracy in challenging repetitive regions of the sex chromosomes.

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Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio

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