PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations
March 2015
Authors:
Min Wang, Christine R Beck, Adam C English, Qingchang Meng, Christian Buhay, Yi Han, Harsha V Doddapaneni, Fuli Yu, Eric Boerwinkle, James R Lupski, Donna M Muzny and Richard A Gibbs
Info:
In this BMC Genomics publication, scientists from Baylor College of Medicine report a new method for targeted sequencing of important structural variations in the human genome with the PacBio platform. Using oligo-based DNA capture with Pippin Prep or BluePippin sizing from Sage Science, the researchers demonstrated successful structural variant analysis at high accuracy and low cost.
Citation:
Wang et al. BMC Genomics (2015) 16:214
DOI 10.1186/s12864-015-1370-2
A phylogenomic analysis of turtles
February 2015
Authors:
Nicholas G Crawford, James F Parham, Anna B Sellas, Brant C Faircloth, Travis C Glenn, Theodore J Papenfuss, James B Henderson, Madison H Hansen, W Brian Simison
Info:
In this Editor’s Choice article from the Molecular Phylogenetics and Evolution journal, researchers provide the first genome-scale analysis of turtle phylogeny using sequence data collected from thousands of ultraconserved elements. Through maximum likelihood, Bayesian, and species tree methods, they produced a single resolved phylogeny. BluePippin was used to prepare the libraries for PCR amplification.
Citation:
Molecular Phylogenetics and Evolution
doi:10.1016/j.ympev.2014.10.021
Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
February 2015
Authors:
Francine E. Garrett-Bakelman, Caroline K. Sheridan, Thadeous J. Kacmarczyk, Jennifer Ishii, Doron Betel, Alicia Alonso, Christopher E. Mason, Maria E. Figueroa, and Ari M. Melnick
Info:
In this publication in the Journal of Visualized Experiments, scientists at Weill Cornell Medical College and the University of Michigan describe a protocol to map DNA methylation patterns across the genome with next-gen sequencing instead of microarrays. Where input amounts allow, the approach calls for automated DNA size selection using Pippin Prep.
Citation:
J Vis Exp. 2015; (96): 52246.
DOI: 10.3791/52246
Assessing the utility of whole genome amplified DNA for next-generation molecular ecology
February 2015
Authors:
Christopher Blair, C. Ryan Campbell, and Anne D. Yoder
Info:
Scientists at Duke University explored whether whole-genome amplification leads to sequence bias by performing a ddRAD-seq study of grey mouse lemurs using multiple displacement amplification. They conclude that MDA enrichment does not cause systematic bias, opening the doors for studies with low-quantity DNA. The team used Pippin Prep for size selection of the ddRAD-seq library.
Citation:
Molecular Ecology Resources (2015) 15, 1079–1090
doi: 10.1111/1755-0998.12376