Improved Multiple Displacement Amplification (iMDA) and Ultraclean Reagents
June 2014
Authors:
S Timothy Motley, John M Picuri, Chris D Crowder, Jeremiah J Minich, Steven A Hofstadler and Mark W Eshoo
Info:
In this methods paper, researchers from Ibis Biosciences report a superior whole-genome amplification protocol that can be used with very small samples to yield enough DNA for sequencing. Their method showed better efficiency and accuracy than commercially available whole-genome amplification kits for low-input samples. Testing was done on the PGM, and Pippin Prep was used for size selection.
Citation:
BMC Genomics 2014, 15:443
Methylation-capture and Next-Generation Sequencing of free circulating DNA from human plasma
June 2014
Authors:
Kristina Warton, Vita Lin, Tina Navin, Nicola J Armstrong, Warren Kaplan, Kevin Ying, Brian Gloss, Helena Mangs, Shalima S Nair, Neville F Hacker, Robert L Sutherland, Susan J Clark and Goli Samimi1
Info:
This study from the the Garvan Institute and the Kinghorn Cancer Center, and St. Vincent’s Clinical School (Univ of South Wales), in Sydney Australia, suggests a method for collecting and sequencing free circulating DNA from human plasma. The authors were able to capture small amounts of methylated DNA and create sequencing libraries using the Illumina ChIP protocol. The Pippin Prep was used to size select 180bp DNA followed by bisulfate sequencing. The study suggest that high quality genomic data can be obtained with fcDNA for potential clinical applications.
Citation:
BMC Genomics 2014, 15:476
Discovery of transgene insertion sites by high throughput sequencing of mate pair libraries
May 2014
Authors:
Anuj Srivastava, Vivek M Philip, Ian Greenstein, Lucy B Rowe, Mary Barter, Cathleen Lutz and Laura G Reinholdt
Info:
Jackson Laboratory scientists developed a method to characterize and score transgene insertion sites in mice to help researchers more fully understand how these sites function and alter phenotypic outcomes. They used mate-pair sequencing with Illumina and performed size selection with a Pippin Prep.
Citation:
BMC Genomics 2014, 15:367
SimRAD: a R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches
May 2014 (epub ahead of print)
Authors:
Olivier Lepais and Jason T Weir
Info:
This article from Molecular Ecology Resources describes a new software tool designed to help scientists optimize their double-digest RADseq (ddRADseq) experiments by accurately estimating the number of loci generated by a particular method. The tool uses a reference genome to approximate the organism of interest and predicts the number of loci for various protocols, such as tight versus wide size selection with the Pippin Prep.
Citation:
Molecular Ecology Resources 2014
Quality control of next-generation sequencing data without a reference
May 2014
Authors:
Urmi H Trivedi, Timothée Cézard, Stephen Bridgett, Anna Montazam, Jenna Nichols, Mark Blaxter, and Karim Gharbi
Info:
In this paper published in Frontiers in Genetics, scientists at the University of Edinburgh show that it is possible to perform alignment-based quality control on sequence data for organisms that lack a reference genome. They used draft assemblies for organisms representing various genome sizes and found that useful quality control metrics can be inferred from these drafts. The scientists used Illumina sequencing and performed DNA sizing with BluePippin.
Citation:
Front. Genet. 5:111