Identifying the true number of specimens of the extinct blue antelope (Hippotragus leucophaeus)
Jan 2021
Authors:
Elisabeth Hempel, Faysal Bibi, J. Tyler Faith, James S. Brink, Daniela C. Kalthoff, Pepijn Kamminga, Johanna L. A. Paijmans, Michael V. Westbury, Michael Hofreiter & Frank E. Zachos
Info:
In an effort to better understand the mechanisms leading to the extinction of the only large African mammal in modern times, scientists sampled existing museum specimens. These were subject to genomic and mitochondrial sequencing. After using DNA extraction methods designed for ancient specimens, the Pippin Prep was used to exclude DNA fragments (<165 bp) from specimens that yielded very short fragments. This resulted in several-fold more mappable endogenous regions. The authors report that only four of the sixteen specimens were in fact blue antelope and highlight how genetics can be used to identify rare museum species.
Author Affiliations:
Evolutionary Adaptive Genomics, Universität Potsdam, Potsdam Germany
Museum Für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin Germany
Natural History Museum of Utah, University of Utah, Salt Lake City UT
Natural History Museum of Utah, University of Utah, Salt Lake City UT
Florisbad Quaternary Research Station and Department, National Museum, Republic of South Africa
Centre for Environmental Management, University of the Free State, Republic of South Africa
Swedish Museum of Natural History, Stockholm, Sweden
Naturalis Biodiversity Center, Leiden, The Netherlands
Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Denmark
Nature Scientific Reports
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
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
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
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