Peer-Reviewed Publication
Cell Genom2026;6(4):101104.April 8, 2026Journal Article
Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers.
Camille A Daniels1, Adetola A Abdulkadir1, Megan H Cleveland2, Jennifer H McDaniel2, David Jáspez3, Luis Alberto Rubio-Rodríguez3, Adrián Muñoz-Barrera3, José Miguel Lorenzo-Salazar3, Carlos Flores4, Byunggil Yoo5, Sayed Mohammad Ebrahim Sahraeian6, Yina Wang7, Massimiliano Rossi7, Arun Visvanath7, Lisa Murray7, Wei-Ting Chen7, Severine Catreux7, James Han7, Rami Mehio7, Gavin Parnaby7, Andrew Carroll8, Pi-Chuan Chang8, Kishwar Shafin8, Daniel Cook8, Alexey Kolesnikov8, Lucas Brambrink8, Mohammed Faizal Eeman Mootor9, Yash Patel9, Takafumi N Yamaguchi9, Paul C Boutros9, Karolina Sienkiewicz10, Jonathan Foox11, Christopher E Mason12, Bryan R Lajoie13, Carlos A Ruiz-Perez13, Semyon Kruglyak13, Justin M Zook14, Nathan D Olson15
1Medical Device Innovation Consortium (MDIC), 1655 N Ft. Myer Drive, Suite 250, Arlington, VA 22209, USA.
2Material Measurement Laboratory, National Institute of Standards and Technology (NIST), 100 Bureau Dr, MS8312, Gaithersburg, MD 20899, USA.
3Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
4Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain; Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Instituto de Investigación Sanitaria de Canarias, Santa Cruz de Tenerife, Spain; CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, Las Palmas de Gran Canaria, Spain.
5Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA.
6Roche Sequencing Solutions, Santa Clara, CA 95050, USA.
7Illumina, Inc., San Diego, CA, USA.
8Google, Inc., Mountain View, CA, USA.
9Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
10Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
11Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
12Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
13Element Biosciences, San Diego, CA, USA.
14Material Measurement Laboratory, National Institute of Standards and Technology (NIST), 100 Bureau Dr, MS8312, Gaithersburg, MD 20899, USA. Electronic address: justin.zook@nist.gov.
15Material Measurement Laboratory, National Institute of Standards and Technology (NIST), 100 Bureau Dr, MS8312, Gaithersburg, MD 20899, USA. Electronic address: nolson@nist.gov.
Abstract
We developed a benchmark set of subclonal variants in the Genome in a Bottle (GIAB) Consortium HG002 reference material (RM) DNA for evaluating lower-frequency variant callsets. We used a somatic variant caller with high-coverage (300×) whole-genome sequencing data from the GIAB Ashkenazi Jewish trio to identify potential subclonal variants in the HG002 RM DNA. Using orthogonal sequencing data and…
Create a free account to keep reading
Free members get 10 full research views every month across publications, clinical trials, FDA clearances, adverse events, and NIH grants. No credit card required.
Want unlimited research access? See Pro plans