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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...SEQUEL II (HD1, MS1, and MS2) or REVIO (HD2).IgA and IgG FLAIRR-seqRNA was extracted from HD1 and HD2 PBMCs using the AllPrep DNA/RNA Mini Kit (Qiagen). IgG and IgA transcripts were resolved by targeted amplification using FLAIRR-seq as described previously (Ford et al. 2023). FLAIRR-seq cDNA libraries...
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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
...and cDNA sequencing, based on patient-derived DNA and RNA, to systematically evaluate deep intronic variation. We identified all variants across the full genomic loci of targeted genes, applied the in silico tools SpliceAI and Pangolin to predict variants of functional consequence, and then carried out...
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Method: Gene prediction in the immunoglobulin loci
- Vikram Sirupurapu,
- Yana Safonova,
- and Pavel A. Pevzner
Genome Res. June 2022 32: 1152-1169; Published in Advance May 11, 2022, doi:10.1101/gr.276676.122
...@ucsd.eduAbstractThe V(D)J recombination process rearranges the variable (V), diversity (D), and joining (J) genes in the immunoglobulin (IG) loci to generate antibody repertoires. Annotation of these loci across various species and predicting the V, D, and J genes (IG genes) are critical for studies of the adaptive...
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Method: Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing
- Charles Cole,
- Ashley Byrne,
- Matthew Adams,
- Roger Volden,
- and Christopher Vollmers
Genome Res. April 2020 30: 589-601; Published in Advance April 20, 2020, doi:10.1101/gr.257188.119
...,000,000 full-length cDNA sequences at a median accuracy of 97.9% using our nanopore sequencing-based Rolling Circle Amplification to Concatemeric Consensus (R2C2) protocol. We used this data set to (1) show that deep and accurate full-length cDNA sequencing can be used to provide isoform-level transcriptome...
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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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Method: CRISPR-based modular assembly of a UAS-cDNA/ORF plasmid library for more than 5500 Drosophila genes conserved in humans
- Ping Wei,
- Wen Xue,
- Yun Zhao,
- Guang Ning,
- and Jiwu Wang
Genome Res. January 2020 30: 95-106; Published in Advance November 13, 2019, doi:10.1101/gr.250811.119
...plasmids were confirmed by sequencing. The Nhe3 gene was fused with a 3xFLAG tag at its N terminus by Gibson assembly. Briefly, because the SphI site overlaps the Nhe3 start codon, the Nhe3 cDNA clone was linearized by SphI, resulting in a 6792-bp fragment. The overlapping 3FLAG-Nhe3-F and 3FLAG-Nhe3-R...
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Research: ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development
- Charlie Y. Shi,
- Lara E. Elcavage,
- Raghu R. Chivukula,
- Joanna Stefano,
- Benjamin Kleaveland,
- and David P. Bartel
Genome Res. September 2023 33: 1482-1496; Published in Advance August 2, 2023, doi:10.1101/gr.278073.123
...). In another example, a site within the Cyrano lncRNA directs degradation of miR-7, which reduces the level of miR-7 by >97% in some mouse tissues, including the cerebellum (Kleaveland et al. 2018). Two other examples of endogenous TDMD have been reported from studies using cultured mammalian cells (Ghini et...
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Research: Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently
- Sophia David,
- Christophe Rusniok,
- Massimo Mentasti,
- Laura Gomez-Valero,
- Simon R. Harris,
- Pierre Lechat,
- John Lees,
- Christophe Ginevra,
- Philippe Glaser,
- Laurence Ma,
- Christiane Bouchier,
- Anthony Underwood,
- Sophie Jarraud,
- Timothy G. Harrison,
- Julian Parkhill,
- and Carmen Buchrieser
Genome Res. November 2016 26: 1555-1564; Published in Advance September 23, 2016, doi:10.1101/gr.209536.116
...Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently Sophia David 1 , 2 , 9 , Christophe Rusniok 3 , 4 , 9 , Massimo Mentasti 2 , Laura Gomez-Valero 3 , 4 , Simon R. Harris 1...
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ARTICLE: Specific amplification by PCR of rearranged genomic variable regions of immunoglobulin genes from mouse hybridoma cells.
- J Berdoz,
- T P Monath,
- and J P Kraehenbuhl
Genome Res. April 1995 4: 256-264
...heavy chain cDNA in lymphoid cells. Gene 54 : 33 – 40 . 14. Gavilondo-Cowley, J.V., Coloma, M.J. Vazquez, J. Ayala, M. Macias, A. Fry, K.E. and Larrick. J.W. 1990 . Specific amplification of rearranged immunoglobulin variable region genes from mouse hybridoma cells. Hybridoma 9 : 407 – 417 . 15. Leung...
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Methods: Systematic Recovery and Analysis of Full-ORF Human cDNA Clones
- Ágnes Baross,
- Yaron S.N. Butterfield,
- Shaun M. Coughlin,
- Thomas Zeng,
- Malachi Griffith,
- Obi L. Griffith,
- Anca S. Petrescu,
- Duane E. Smailus,
- Jaswinder Khattra,
- Helen L. McDonald,
- Sheldon J. McKay,
- Michelle Moksa,
- Robert A. Holt,
- and Marco A. Marra
Genome Res. October 15, 2004 14: 2083-2092; doi:10.1101/gr.2473704
...clones were selected on agar plates containing 50 μg/mL ampicillin and 10 μg/mL kanamycin. Glycerol stocks were prepared from 24 individual clone isolates per amplified gene and stored in 384-well plates. Restriction Fragment Analysis of cDNA Clones Plasmid DNA was prepared from overnight cultures...

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