Enhanced detection of circulating tumor DNA by fragment size analysis
November 2018
Authors:
Florent Mouliere et al.
Info:
This study from Cancer Research UK and a large team of collaborators is a continuation of work evaluating circulating tumor DNA (ctDNA) and the significance of sub-167 base pair cell-free DNA as a marker for tumors. Samples from a cohort of 200 patients were tested and show significantly improved detection of ctDNA by size selecting DNA between 90-150 bp, and using the TAm-Seq technique to detect mutations. PippinHT was used for DNA size selection.
Citation:
Science Translational Medicine
DOI: 10.1126/scitranslmed.aat4921
Small-seq for single-cell small-RNA sequencing
September 2018
Authors:
Michael Hagemann-Jensen, Ilgar Abdullayev, Rickard Sandberg and Omid R Faridani
Info:
A new protocol from researchers at the Karolinska Institutet and the Ludwig Institute for Cancer Research outline a method for making small RNA sequencing libraries from a single mammalian cell. The method increases sensitivity compared with other methods by using a oligonucleotides to mask ribosomal RNA rather than using a pulldown strategy. Pippin Prep is recommended to isolated miRNA away from other small RNAs.
Citation:
Nature Protocols 13, pages2407–2424 (2018)
10.1038/s41596-018-0049-y
Genomic and epidemiological monitoring of yellow fever virus transmission potential
August 2018
Authors:
N.R. Faria, et al.
Info:
A large collaboration between international and Brazilian researchers used a suite of epidemiological, spatial, and genomic approaches to characterize Yellow Fever virus transmission in Brazil. The study potentially establishes a framework for monitoring the disease in real time to prevent future epidemics. Pippin Prep used to size select RNA-seq libraries for paired end Illumina sequencing.
Citation:
Science 361 (6405), 894-899
doi: 10.1126/science.aat7115
Highly sensitive detection of mutations in CHO cell recombinant DNA using multi‐parallel single molecule real‐time DNA sequencing
June 2018
Authors:
Joseph Cartwright, Karin Anderson, Joseph Longworth, Philip Lobb, and David James
Info:
To improve the quantitative assessment of recombinant DNA in cell lines, University of Sheffield scientists and collaborators developed a PacBio-based method for high-throughput rDNA sequence analysis. The protocol can sequence 40,000 individual recombinant DNA molecules at once to find point mutations. BluePippin was used for purification prior to sequencing.
Citation:
Biotechnology and Bioengineering
doi: 10.1002/bit.26561
A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination
May 2018
Authors:
Kranti Konganti, Felix Guerrero, Faye Schilkey, Peter Ngam, et al.
Info:
Researchers sequenced, assembled, and annotated the genome of horn fly, a blood-feeding insect that preys on cattle. The 1.14 Gb assembly shows the fly is most closely related to Musca domestica and Drosophila melanogaster. BluePippin was used to size-select mate-pair libraries for genome and transcriptome sequencing using Illumina.
Citation:
G3: Genes, Genomes, Genetics
vol. 8 no. 5 1675-1686