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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
...average, 280–300 bp), make these important genes challenging to genotype with short-read WGS data.View this table: In this window In a new window Table 1. Summary of immunoglobulin and T cell receptor variable gene lociOne approach employed to genotype complex and repetitive loci is to use combinatorial...
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Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
- Tsung-Kai Hung,
- Wan-Chi Liu,
- Sheng-Kai Lai,
- Hui-Wen Chuang,
- Yi-Che Lee,
- Hong-Ye Lin,
- Chia-Lang Hsu,
- Chien-Yu Chen,
- Ya-Chien Yang,
- Jacob Shujui Hsu,
- and Pei-Lung Chen
Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
...Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pan assemblies Tsung-Kai Hung1, Wan-Chi Liu2, Sheng-Kai Lai3,4, Hui-Wen Chuang1, Yi-Che Lee2, Hong-Ye Lin5, Chia-Lang Hsu1,6, Chien-Yu Chen5, Ya-Chien Yang2,7, Jacob Shujui Hsu1 and Pei-Lung Chen1,3,4,8,9 1Graduate...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...metrics (Gough et al. 2018; Plassais et al. 2019; Dutrow et al. 2022; Morrill et al. 2022).In humans, candidate trait and disease variants are generally identified using a combination of strategies, including multiple species alignment, protein structure predictions, gene mutation tolerance, and machine...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...confirmed (TEC)” and “immunoglobulin (IG) variable chain or T cell receptor (TR) genes” biotypes were removed. In addition, complex loci where alternative promoter or recombined segments are annotated with different gene names but cannot be considered as independent genes were also removed (Jung et al. 2006...
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA Corresponding author: hli@jimmy.harvard.eduAbstractThe human leukocyte antigen (HLA) genes and the killer cell immunoglobulin-like receptor (KIR) genes are critical to immune responses and are associated with many...
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Research: Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression
- Celine L. St. Pierre,
- Juan F. Macias-Velasco,
- Jessica P. Wayhart,
- Li Yin,
- Clay F. Semenkovich,
- and Heather A. Lawson
Genome Res. June 2022 32: 1042-1057; Published in Advance May 2, 2022, doi:10.1101/gr.276193.121
...studies and highlighted how this orthogonal approach can prioritize candidate genes. Untangling the genetic, epigenetic, and environmental mechanisms that govern allele-specific gene regulation is crucial to improving our ability to predict phenotypes from genotypes.ResultsPartitioning allele...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...from 96.5% to 96.9% for C. briggsae isolates and from 98.3% to 99.2% for C. nigoni ones, suggesting that the quality is on par with that of the reference s (Supplemental Table S1). To ensure consistency and minimize potential biases in gene family comparisons, we applied a uniform gene prediction...
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Method: Accurate and efficient detection of gene fusions from RNA sequencing data
- Sebastian Uhrig,
- Julia Ellermann,
- Tatjana Walther,
- Pauline Burkhardt,
- Martina Fröhlich,
- Barbara Hutter,
- Umut H. Toprak,
- Olaf Neumann,
- Albrecht Stenzinger,
- Claudia Scholl,
- Stefan Fröhling,
- and Benedikt Brors
Genome Res. March 2021 31: 448-460; Published in Advance January 13, 2021, doi:10.1101/gr.257246.119
....uhrig@dkfz.de, b.brors@dkfz.deAbstractThe identification of gene fusions from RNA sequencing data is a routine task in cancer research and precision oncology. However, despite the availability of many computational tools, fusion detection remains challenging. Existing methods suffer from poor prediction accuracy...
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Research: Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice
- Yuan Fang,
- Lifen Chen,
- Kande Lin,
- Yilong Feng,
- Pengyue Zhang,
- Xiucai Pan,
- Jennifer Sanders,
- Yufeng Wu,
- Xiu-e Wang,
- Zhen Su,
- Caiyan Chen,
- Hairong Wei,
- and Wenli Zhang
Genome Res. August 2019 29: 1287-1297; Published in Advance July 1, 2019, doi:10.1101/gr.246009.118
...genic loci associated with SO-R-loops, ASO-R-loops, and S/AS-R-loops, respectively.To test if the correspondence between R-loops and gene expression is genic position dependent, we regrouped all expressed genes (FPKM > 0) into two categories (greater or less than 10). We then plotted the normalized read...
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Method: Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
- Artem Mikelov,
- George Nefediev,
- Alexander Tashkeev,
- Oscar L. Rodriguez,
- Diego Aguilar Ortmans,
- Valeriia Skatova,
- Mark Izraelson,
- Alexey N. Davydov,
- Stanislav Poslavsky,
- Souad Rahmouni,
- Corey T. Watson,
- Dmitriy Chudakov,
- Scott D. Boyd,
- and Dmitry Bolotin
Genome Res. December 2024 34: 2293-2303; Published in Advance October 21, 2024, doi:10.1101/gr.278775.123
...making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci. Here, we present a novel algorithm for extrasensitive and specific variable (V) and joining (J) gene allele inference, allowing the reconstruction of individual high...
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