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Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
...target range using Covaris g-TUBEs (two 30-sec spins at 3000g) and taken forward for library preparation following the instructions for genomic DNA sequencing with the Native Barcoding Kit 24 V14 (Oxford Nanopore Technologies SQK-NBD114.24). Three to four barcoded samples were pooled together for each...
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Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
- Kathleen Zeglinski,
- Christian Montellese,
- Matthew E. Ritchie,
- Monther Alhamdoosh,
- Cédric Vonarburg,
- Rory Bowden,
- Monika Jordi,
- Quentin Gouil,
- Florian Aeschimann,
- and Arthur Hsu
Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
...increase transcriptional efficiency (Han et al. 2021; Sertkaya et al. 2021). It is, therefore, important to have an assay in place that can identify not only the abundance, but also the causes of lentiviral RNA truncation. RNA sequencing using Illumina (Han et al. 2021) and Oxford Nanopore Technologies...
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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
...multiplexed long-read adaptive-sampling genomic sequencing (Oxford Nanopore Technologies) to enrich for and sequence 1 Mb regions around the genomic loci of BRCA1, BRCA2, PALB2, ATM, CHEK2, BARD1, BRIP1, RAD51C, RAD51D, and TP53 (for genomic coordinates, hg38 assembly, see Supplemental Table S2). For each...
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Research: Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
- Taishan Hu,
- Timothy L. Mosbruger,
- Nikolaos G. Tairis,
- Amalia Dinou,
- Pushkala Jayaraman,
- Mahdi Sarmady,
- Kingham Brewster,
- Yang Li,
- Tristan J. Hayeck,
- Jamie L. Duke,
- and Dimitri S. Monos
Genome Res. October 2024 34: 1500-1513; Published in Advance September 26, 2024, doi:10.1101/gr.278588.123
...lines were rather fragmented. Most recently an additional six homozygous for Chromosome 6 BLCLs, with partial coverage for their MHC (Horton et al. 2008), were sequenced using a combination of short and long-read technologies (Illumina, Pacific Biosciences [PacBio] and Oxford Nanopore), accomplishing...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...read length exceeding 10 kb; polymerase-based) or Oxford Nanopore Technologies’ PromethION (potential read length of more than 2 Mb; synthesis-free) (Sone et al. 2019). Long-read sequencing (LRS) in particular is a burgeoning opportunity for repeat disease gene discovery and will be covered in more...
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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
...use our previously published R2C2 method (Volden et al. 2018; Byrne et al. 2019) implemented on the Oxford Nanopore Technologies MinION sequencer to analyze RNA extracted from a human peripheral blood mononuclear cells (PBMC) sample—a mix of mostly monocytes, B cells, and T cells. We analyzed...
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Method: Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly
- Ou Wang,
- Robert Chin,
- Xiaofang Cheng,
- Michelle Ka Yan Wu,
- Qing Mao,
- Jingbo Tang,
- Yuhui Sun,
- Ellis Anderson,
- Han K. Lam,
- Dan Chen,
- Yujun Zhou,
- Linying Wang,
- Fei Fan,
- Yan Zou,
- Yinlong Xie,
- Rebecca Yu Zhang,
- Snezana Drmanac,
- Darlene Nguyen,
- Chongjun Xu,
- Christian Villarosa,
- Scott Gablenz,
- Nina Barua,
- Staci Nguyen,
- Wenlan Tian,
- Jia Sophie Liu,
- Jingwan Wang,
- Xiao Liu,
- Xiaojuan Qi,
- Ao Chen,
- He Wang,
- Yuliang Dong,
- Wenwei Zhang,
- Andrei Alexeev,
- Huanming Yang,
- Jian Wang,
- Karsten Kristiansen,
- Xun Xu,
- Radoje Drmanac,
- and Brock A. Peters
Genome Res. May 2019 29: 798-808; Published in Advance April 2, 2019, doi:10.1101/gr.245126.118
...barcode. This makes stLFR more similar to long read single-molecule sequencing (e.g., Pacific Biosciences [PacBio] SMRT and Oxford Nanopore Technologies [Nanopore] sequencing) than other cobarcoding strategies like Chromium (10x Genomics) that cobarcode multiple long DNA fragments with the same barcode...
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