Peer-Reviewed Publication
bioRxiv2025December 16, 2025Journal Article
Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance.
Monika Cechova1,2, Tamara A Potapova3, Andreas Rechtsteiner4, Glenn Hickey1, Rebecca Serra Mari5,6, Mira Mastoras1, Julian Menendez1, Nikol Poláková2, Prajna Hebbar1, Fedor Ryabov1,7, Hailey Loucks1, Aljona Groot4, Tomáš Pavlík2, Mobin Asri1, Shihua Dong8, Stephanie M Yan9, Julian K Lucas1, Steven J Solar10, Matthew Borchers3, Mark Mattingly3, Sean McKinney3, Marie Krátká2,11, Catherine Mikhailova1, Ondřej Hanák2, Sohinee Tiffany Saha1, Emily Xu1, Dmitry Antipov10, Sergey Koren10, Jordan M Eizenga1, Brandy McNulty1, Joshua M V Gardner1, Todd Hillaker1, Ivo Violich1, Christopher Markovic12, Semyon Kruglyak13, Shawn Levy13, Trevor Wolf13, Matthew W Mitchell14, Laura Scheinfeldt14, Haoyu Cheng15, Ivan A Alexandrov16, Rajiv C McCoy9, Benedict Paten1, Adam M Phillippy10, Justin M Zook17, Jennifer L Gerton3, Robert S Fulton13, Nathan O Stitziel18, Ting Wang8, Tobias Marschall5,6, Carol W Greider4, Karen H Miga1
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
2Faculty of Informatics, Masaryk University, Brno, Czech Republic.
3Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.
4Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
5Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
6Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
7International Laboratory of Bioinformatics, HSE University, Moscow, Russia.
8Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
9Department of Biology, Johns Hopkins University, Baltimore, MD, USA 21218.
10Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
11National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
12McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
13Element Biosciences, San Diego, CA 92121, USA.
14Coriell Institute for Medical Research, Camden, NJ 08103, USA.
15Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT, USA.
16Department of Anatomy and Anthropology & Department of Human Molecular Genetics and Biochemistry, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
17Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.
18Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
Abstract
Pedigree analysis remains the gold standard for rare disease diagnostics, yet whole genome sequencing studies typically omit critical regions like centromeres, telomeres, and acrocentric chromosome p-arms. Here, we present telomere-to-telomere (T2T) reference genomes for four self-identified African American individuals of admixed ancestry spanning three generations. Our parent-of-origin assigned,…
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