Searching journal content for articles similar to Clifford et al. 10 (8): 1259.

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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...We obtained unaligned HiFi LRS data for the HG002 individual from PacBio (https://downloads.pacbcloud.com/public/revio/2022Q4/). We obtained ONT R10 stereo duplex LRS data for HG002 from the Human Pangenomics Project (https://human-pangenomics.s3.amazonaws.com/index.html?prefix=submissions/0CB931D5-AE0C-4187...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...(ESHRE 2025), accounting for >2.5% of live births in the United States (CDC 2024b) and many other Western countries (Katagiri et al. 2023; Smeenk et al. 2023). This number has risen steadily over the past decade (CDC 2024a) and is projected to grow further owing to rising infertility rates (Nugent...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...(or recall) of clusters in the sample group. The three axes separate clusters based on complexity, frequency of observations, and Jaccard score or recall. The frequencies of specific Jaccard scores are displayed in the orange projection, showing that the vast majority of samples have a high Jaccard...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
....Data accessAll raw and processed sequencing data generated in this study have been submitted to the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) under accession number PRJNA1201891. The assemblies and annotations are openly available on the Figshare database (https://doi.org/10.6084/m9...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...to UV mutagenesis. However, the impact of genomic context and chromatin architecture on CPD deamination rates in cells remains poorly understood. Here, we develop a method known as dCPD-seq to map deaminated CPDs (dCPDs) across the of repair-deficient yeast cells at single-nucleotide resolution. Our d...
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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
...sequencing-based map of normal patterns of human genetic variation for filtering and prioritizing candidate disease-causing variants (International HapMap Consortium 2005; The 1000 Genomes Project Consortium 2015; Byrska-Bishop et al. 2022). The impact of 1KGP on our understanding of human genetic diversity...
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Resource: Proactive functional classification of all possible missense single-nucleotide variants in KCNQ4
- Honglan Zheng,
- Xinhao Yan,
- Guanluan Li,
- Hengwei Lin,
- Siqi Deng,
- Wenhui Zhuang,
- Fuqiang Yao,
- Yu Lu,
- Xin Xia,
- Huijun Yuan,
- Li Jin,
- and Zhiqiang Yan
Genome Res. August 2022 32: 1573-1584; Published in Advance June 27, 2022, doi:10.1101/gr.276562.122
...on variant pathogenicity interpretation. A total of 509 KCNQ4 missense variants were collected from multiple data sources, such as the Deafness Variation Database (DVD) (Azaiez et al. 2018), ClinVar (Landrum et al. 2016), the 1000 Genomes Project (The 1000 Genomes Project Consortium 2012), and gnomAD (Lek et...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...generating crucial control data sets: the 1000 Genomes Project ONT Sequencing Consortium is producing LRS data from 1kGP samples to aid in filtering and prioritizing SNVs and SVs (Gustafson et al. 2024), while the All of Us (AoU) initiative has begun a long-read arm to sequence blood samples from Americans...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...: chirag@iisc.ac.inAbstractAffordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single-nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference is unreliable in highly polymorphic...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...DNA array encoding 18S, 5.8S, and 28S rRNAs, we first searched the 45S rDNA representative repeat unit of 7197 nt (Supplemental Table S5) for single-nucleotide variants (SNVs) that could distinguish the positions of each 45S rDNA unit variant within the array. We aligned 3322 PacBio HiFi reads to the 45S r...
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