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Research: Genotype imputation from low-coverage data for medical and population genetic analyses
- Simone Andrea Biagini,
- Sara Becelaere,
- Mio Aerden,
- Tatjana Jatsenko,
- Laurens Hannes,
- Philip Van Damme,
- Jeroen Breckpot,
- Koenraad Devriendt,
- Bernard Thienpont,
- Joris Robert Vermeesch,
- Isabelle Cleynen,
- and Toomas Kivisild
Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
...to the genotype called from the high coverage data. This motivated us to carry out systematic revisions of conflicts between the GT and GP values, which could be characteristic only for ultralow coverage data, and to focus our search for optimal solutions in the GDI design on the combination of INFO score, GP...
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Method: System-wide analyses of the fission yeast poly(A)⁺ RNA interactome reveal insights into organization and function of RNA–protein complexes
- Cornelia Kilchert,
- Tea Kecman,
- Emily Priest,
- Svenja Hester,
- Ebru Aydin,
- Krzysztof Kus,
- Oliver Rossbach,
- Alfredo Castello,
- Shabaz Mohammed,
- and Lidia Vasiljeva
Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
...-values) of protein enrichment in the noCL-normalized interactome. (F) Distribution of proteins annotated with a classical RBD (left), GO function “mRNA binding” (middle), or GO process “mRNA metabolic process” (right) in the WCE-normalized RNA interactome designated in black, using symbols to indicate protein...
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Method: MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome
- Dechao Tian,
- Ruochi Zhang,
- Yang Zhang,
- Xiaopeng Zhu,
- and Jian Ma
Genome Res. February 2020 30: 227-238; Published in Advance January 6, 2020, doi:10.1101/gr.250316.119
...of modules (i.e., clusters). We develop a new algorithm, MOCHI (motif clustering in heterogeneous interactomes), that can effectively uncover such network modules, which we call heterogeneous interactome modules (HIMs), based on network motif clustering using a four-node motif specifically designed to reveal...
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Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
- Jonas A. Gustafson,
- Sophia B. Gibson,
- Nikhita Damaraju,
- Miranda P.G. Zalusky,
- Kendra Hoekzema,
- David Twesigomwe,
- Lei Yang,
- Anthony A. Snead,
- Phillip A. Richmond,
- Wouter De Coster,
- Nathan D. Olson,
- Andrea Guarracino,
- Qiuhui Li,
- Angela L. Miller,
- Joy Goffena,
- Zachary B. Anderson,
- Sophie H.R. Storz,
- Sydney A. Ward,
- Maisha Sinha,
- Claudia Gonzaga-Jauregui,
- Wayne E. Clarke,
- Anna O. Basile,
- André Corvelo,
- Catherine Reeves,
- Adrienne Helland,
- Rajeeva Lochan Musunuri,
- Mahler Revsine,
- Karynne E. Patterson,
- Cate R. Paschal,
- Christina Zakarian,
- Sara Goodwin,
- Tanner D. Jensen,
- Esther Robb,
- The 1000 Genomes ONT Sequencing Consortium,
- University of Washington Center for Rare Disease Research (UW-CRDR),
- Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
- William Richard McCombie,
- Fritz J. Sedlazeck,
- Justin M. Zook,
- Stephen B. Montgomery,
- Erik Garrison,
- Mikhail Kolmogorov,
- Michael C. Schatz,
- Richard N. McLaughlin, Jr.,
- Harriet Dashnow,
- Michael C. Zody,
- Matt Loose,
- Miten Jain,
- Evan E. Eichler,
- and Danny E. Miller
Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
...patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37× and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...University, Beijing 100871, China; 3School of Life Sciences, Peking University, Beijing 100871, China Corresponding authors: gaoyq@pku.edu.cn, yanyi@pku.edu.cnAbstractThe interactome networks at the DNA, RNA, and protein levels are crucial for cellular functions, and the diverse variations of these networks...
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Resource: Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony
- Jacqueline A. Robinson,
- Saurabh Belsare,
- Shifra Birnbaum,
- Deborah E. Newman,
- Jeannie Chan,
- Jeremy P. Glenn,
- Betsy Ferguson,
- Laura A. Cox,
- and Jeffrey D. Wall
Genome Res. May 2019 29: 848-856; Published in Advance March 29, 2019, doi:10.1101/gr.247122.118
...designations in the pedigree were concordant with genetic assignments and to determine whether any of the founders showed evidence of hybrid origin. The original founders of the SNPRC colony were captured near what is now known to be a large admixture zone between olive and yellow baboons in Eastern Africa...
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Resource: Low-coverage sequencing: Implications for design of complex trait association studies
- Yun Li,
- Carlo Sidore,
- Hyun Min Kang,
- Michael Boehnke,
- and Gonçalo R. Abecasis
Genome Res. June 2011 21: 940-951; Published in Advance April 1, 2011, doi:10.1101/gr.117259.110
...Low-coverage sequencing: Implications for design of complex trait association studies Yun Li 1 , 4 , Carlo Sidore 2 , 3 , 4 , Hyun Min Kang 4 , Michael Boehnke 4 and Gonçalo R. Abecasis 4 , 5 1Department of Genetics...
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Method: Leveraging family data to design Mendelian randomization that is provably robust to population stratification
- Nathan LaPierre,
- Boyang Fu,
- Steven Turnbull,
- Eleazar Eskin,
- and Sriram Sankararaman
Genome Res. July 2023 33: 1032-1041; Published in Advance May 17, 2023, doi:10.1101/gr.277664.123
..., as well as the confounding effects of population stratification and horizontal pleiotropy. Here, we show that family data can be leveraged to design MR tests that are provably robust to confounding from population stratification, assortative mating, and dynastic effects. We show in simulations that our...
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Research: Sequence determinants of improved CRISPR sgRNA design
- Han Xu,
- Tengfei Xiao,
- Chen-Hao Chen,
- Wei Li,
- Clifford A. Meyer,
- Qiu Wu,
- Di Wu,
- Le Cong,
- Feng Zhang,
- Jun S. Liu,
- Myles Brown,
- and X. Shirley Liu
Genome Res. August 2015 25: 1147-1157; Published in Advance June 10, 2015, doi:10.1101/gr.191452.115
.... Leveraging the information from multiple designs, we derived a new sequence model for predicting sgRNA efficiency in CRISPR/Cas9 knockout experiments. Our model confirmed known features and suggested new features including a preference for cytosine at the cleavage site. The model was experimentally validated...
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Research: Interactome mapping suggests new mechanistic details underlying Alzheimer's disease
- Montserrat Soler-López,
- Andreas Zanzoni,
- Ricart Lluís,
- Ulrich Stelzl,
- and Patrick Aloy
Genome Res. March 2011 21: 364-376; Published in Advance December 16, 2010, doi:10.1101/gr.114280.110
...no significant difference (10.3, 11.7, and 10.3 interactions per protein on average, respectively), although the use of different Y2H setups specially designed to deal with transmembrane proteins might indeed increase the coverage (Snider et al. 2010). Thus, in this particular study, failure to detect...

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