Citations

ATAC-seq with unique molecular identifiers improves quantification and footprinting

November 2020

Authors:
Tao Zhu, Keyan Liao, Rongfang Zhou, Chunjiao Xia & Weibo Xie

Info:
The authors suggest an improvement on the ATAC-seq method (Assay for Transposase-Accessible Chromatin with high-throughput sequencing). By using unique molecular identifiers to distinguish between transposase insertions and PCR duplicates. They go on to demonstrate the UMI-ATAC-seq method more accurately quantifies chromatin accessibility and improve the sensitivity of identifying transcription footprints.

The PippinHT was used to size select libraries prior to sequencing.

Author Affiliations:
Huazhong Agricultural University, Wuhan China

Citation:
Nature Communications Biology
DOI: 10.1038/s42003-020-01403-4

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Complete and haplotype-specific sequence assembly of segmental duplication-mediated genome rearrangements using targeted CRISPR-targeted ultra-long read sequencing (CTLR-Seq)

October 2020

Authors:
Bo Zhou, GiWon Shin, Stephanie U. Greer, Lisanne Vervoort, Yiling Huang, Reenal Pattni, Marcus Ho, Wing H. Wong, Joris R. Vermeesch, Hanlee P. Ji, Alexander E. Urban
Info:

In this preprint the authors report on a method, CTLR-Seq, that combines Sage Science’s HLS-CATCH with low input Oxford Nanopore sequencing(using the MinION platform). The researchers are studying complex and highly repetitive genomic regions associated with neuropsychiatric disorders (mutations at 22q11.2 and at 16p11.2). Long read nanopore sequencing is used to resolve large segmental duplications, copy number variations, and large deletions.

Author Affiliations:
Stanford University, Stanford CA
KU Leuven, Flanders Belgium

Citation:
BioRxiv Preprint
DOI:10.1101/2020.10.23.349621

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Ultra-low input single tube linked-read library method enables short-read second-generation sequencing systems to generate highly accurate and economical long-range sequencing information routinely generate highly accurate and economical long-range sequencing information

June 2020

Authors:
Zhoutao Chen, Long Pham, Tsai-Chin Wu, Guoya Mo, Yu Xia, Peter L Chang, Devin Porter, Tan Phan, Huu Che, Hao Tran, Vikas Bansal, Justin Shaffer, Pedro Belda-Ferre, Gregory Humphrey, Rob Knight, Pavel Pevzner, Son Pham, Yong Wang and Ming Lei

Info:
This study describes the TELL-Seq™ barcode linked read method developed by Universal Sequencing Technology Corp, and presents validation data for the process. TELL-Seq uses a transposase enzyme method that is linked to a bead (TELL-Bead) to insert an 18 bp molecular barcode into illumina sequencing libraries. The method allows economical analysis of haplotype phasing and structural variation in genomes or metagenomic analyses. The workflow requires low DNA input (0.1-5 ng) and is completed in a single tube.

Author Affiliations:
Universal Sequencing Technology, Canton MA
Bioturing, Inc., San Diego CA
University of California, San Diego

Citation:
Genome Research
DOI: 10.1101/gr.260380.119

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CRISPR–Cas9/long-read sequencing approach to identify cryptic mutations in BRCA1 and other tumour suppressor genes

October 2020

Authors:
Tom Walsh, Silvia Casadei, Katherine M Munson, Mary Eng, Jessica B Mandell, Suleyman Gulsuner, Mary-Claire King

Info:
In this short report, researchers studying young-onset breast cancer used the SageHLS and HLS-CATCH method to purify high molecular weight targets containing the BRCA1 locus. Affected individuals in this study showed normal sequence based on gene panel and whole exome sequencing. Using long read (~10kb) and low input PacBio® HiFi™ sequencing on the HMW targets the researchers identified an SVA retrotransposon insertion in intronic regions of the BRCA1 locus that are homologous to a region on chr1. They were further able to show how BRCA1 transcription was affected.

Author Affiliations:
University of Washington, Seattle WA

Citation:
Journal of Medical Genetics
DOI:10.1136/jmedgenet-2020-107320

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A long-read RNA-seq approach to identify novel transcripts of very large genes

July 2020

Authors:
Prech Uapinyoying, Jeremy Goecks, Susan M. Knoblach, Karuna Panchapakesan, Carsten G. Bonnemann, Terence A. Partridge, Jyoti K. Jaiswal, and Eric P. Hoffman

Info:
Scientists researching muscular disorders present a method for studying gene expression of large RNA transcripts. The PacBio Iso-Seq method allows the sequencing of large transcripts for the identification of isoforms and alternative splicing. However, it has not been amenable to accurate quantitation of expression. Here the scientists combine Iso-Seq with PacBio’s HiFi high consensus accuracy method to show differential gene expression of large transcripts in muscles as well as identify and quantitate previously unannotated ones.

BluePippin was used to size select 5-10kb cDNA fragments for PacBio Iso-Seq library construction, and a second size selection step to remove unligated adapters.

Author Affiliations:
Center for Genetic Medicine Research, Children’s Research Institute, Washington D.C.

Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C.
National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD

Computational Biology Program, Oregon Health and Science University, Portland, OR

Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY

Citation:
Genome Research
DOI: 10.1101/gr.259903.119.

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