Sequencing of human genomes with nanopore technology
April 2019
Authors:
Rory Bowden, Robert W. Davies, Andreas Heger, Alistair T. Pagnamenta, Mariateresa de Cesare, Laura E. Oikkonen, Duncan Parkes, Colin Freema, Fatima Dhalla, Smita Y. Patel, Niko Popitsch, Camilla L.C. Ip, Hannah E. Roberts, Silvia Salatino, Helen Lockstone, Gerton Lunter, Jenny C. Taylor, David Buck, Michael A. Simpson, Peter Donnelly
Info:
The potential of using Oxford Nanopore Technologies MinION sequencer is evaluated for Whole Genome Sequencing (WGS). A reference sample (NA112878) was sequenced alongside an individual with clinical indications. The authors applied novel bioinformatic approaches to the analysis and identify innovations that could significantly improve the platform’s potential for clinical WGS.
BluePippin was used to enrich DNA fragments >6kb using the High-Pass protocol prior to library construction.
Author Affiliations:
Wellcome Centre for Human Genetics, Oxford UK
Hospital for Sick Children, Toronto CA
Oxford University, Oxford UK
National Institute for Health Research, Oxford UK
Children’s Cancer Research Institute, Vienna Austria
Citation:
Nature Communications
DOI: 10.1038/s41467-019-09637-5
Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome
March 2019
Authors:
Jared P. Steranka, Zuojian Tang, Mark Grivainis, Cheng Ran Lisa Huang, Lindsay M. Payer, Fernanda O. R. Rego, Thiago Luiz Araujo Miller, Pedro A. F. Galante, Sitharam Ramaswami, Adriana Heguy, David Fenyö, Jef D. Boeke & Kathleen H. Burns
Info:
A new technique is described; Transposon Insertion Profiling (TIPseq). The method uses vectorette PCR and paired-end Illumina sequencing to map (LINE-1, L1) retrotransposon insertions in the human genome. A detailed protocol is provided.
Pippin Prep is used to remove fragments below 400 bp from libraries prior to sequencing.
Author Affiliations:
Johns Hopkins University School of Medicine, Baltimore, MD
NYU Langone Health, New York, NY,
Hospital Sírio-Libanês, São Paulo, Brazil
Universidade de São Paul, São Paulo, Brazil
Citation:
Mobile DNA
DOI: 10.1186/s13100-019-0148-5
Identification of whole blood mRNA and microRNA biomarkers of tissue damage and immune function resulting from amphetamine exposure or heat stroke in adult male rats
February 2019
Authors:
Luısa Camacho, Camila S. Silva, Joseph P. Hanig, Robert P. Schleimer, Nysia I. George, John F. Bowyer
Info:
A report from the USDA and others evaluate the effect of amphetamine and methamphetamine toxicity on immune systems and tissues using rat models. In particular, hyperthermic effects, due to the drug exposure or environmentally induces were studied. With hyperthermia, an increase in organ related transcripts were indicated and as was possible liver damage. In addition, changes to the immune system suggest modified risk of for HIV and other infections.
The PippinHT was used to isolated small RNA (15-35bp) Illumina libraries prior to sequencing.
Citation:
PLOS One
DOI: 10.1371/journal.pone.0210273
Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development
March 2019
Authors:
Andrea Minio, Mélanie Massonnet, Rosa Figueroa-Balderas, Amanda M. Vondras, Barbara Blanco-Ulate, and Dario Cantu
Info:
Researchers used PacBio’s Iso-Seq method to sequence full-length cDNA transcripts from ripening Cabernet Savignon berries resulting in 1,5000 cultivar-specific genes. The authors discuss using transcriptome profiles for comprehensive referencing as an alternative to costly genome referencing.
The BluePippn was used to size select 1-2 kbp, 2-3 kbp, 3-6 kbp, and 5-10 kbp fractions for cDNA SMRTbell library construction for the Iso-Seq method.
Author Affiliations:
University of California, Davis
Citation:
G3: Genes, Genomes, Genetics
DOI: 10.1534/g3.118.201008
Cancer stem cell–associated miRNAs serve as prognostic biomarkers in colorectal cancer
March 2019
Authors:
Shusuke Toden, Shigeyasu Kunitoshi, Jacob Cardenas, Jinghua Gu, Elizabeth Hutchins, Kendall Van Keuren-Jensen, Hiroyuki Uetake, Yuji Toiyama, and Ajay Goel
Info:
This study evaluates cancer stems cells (CSC) which resist chemotherapy agents and have high tumor initiation capacity. A particular gene variant within these cells, CD44, appears to present a more aggressive phenotype when over expressed. The researchers undertook miRNA profling of the CD44 in a cohort of patients to identify the dysregulated species. They suggest that these miRNAs could be used as prognostic biomarkers or possibly therapeutic targets for patients with colorectal cancer.
For this study, generated several CSC cell lines. ThePippinHT was used to isolate miRNA libraries (148bp).
Author Affiliations:
Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center. Dallas
Baylor Institute for Immunology Research, Dallas
Translational Genomics Research Institute, Phoenix, Arizona
Tokyo Medical and Dental University, Tokyo
Mie University Graduate School of Medicine, Mie, Japan
Citation:
Journal of Clinical Investigation Insight