Variant calling in low-coverage whole genome sequencing of a Native American population sample
January 2014
Authors:
Chris Bizon, Michael Spiegel, Scott A Chasse, Ian R Gizer, Yun Li, Ewa P Malc, Piotr A Mieczkowski, Josh K Sailsbery, Xiaoshu Wang, Cindy L Ehlers and Kirk C Wilhelmsen
Info:
Scientists from the University of North Carolina at Chapel Hill tested Thunder, a linkage disequilibrium-aware variant caller, on a community sample of Native Americans and determined that low-coverage whole genome sequencing is better at finding novel variants and associations than fixed-content genotyping arrays. They used Pippin Prep to select fragments of 300 base pairs for sequencing on the HiSeq 2000.
Citation:
BMC Genomics 2014, 15:85
Transcriptome Analysis in Venom Gland of the Predatory Giant Ant Dinoponera quadriceps: Insights into the Polypeptide Toxin Arsenal of Hymenopterans
January 2014
Authors:
Alba F. C. Torres, Chen Huang, Cheong-Meng Chong, Siu Wai Leung, Alvaro R. B. Prieto-da-Silva, Alexandre Havt, Yves P. Quinet, Alice M. C. Martins, Simon M. Y. Lee, and Gandhi Radis-Baptista
Info:
Scientists from Brazil and Macao performed a transcriptome analysis of Dinoponera quadriceps, a predatory giant ant, to learn more about its venom. They found novel sequences that contribute to knowledge about the function and biological makeup of the venom’s toxins. The team used Pippin Prep to target 330 bp fragments, which were then sequenced on the Ion Torrent PGM.
Citation:
PLoS ONE 9(1): e87556. doi:10.1371/journal.pone.0087556
Semiconductor-based DNA sequencing of histone modification states
October 2013
Authors:
Christine S. Cheng, Kunal Rai, Manuel Garber, Andrew Hollinger, Dana Robbins, Scott Anderson, Alyssa Macbeth, Austin Tzou, Mauricio O. Carneiro, Raktima Raychowdhury, Carsten Russ, Nir Hacohen, Jeffrey E. Gershenwald, Niall Lennon, Chad Nusbaum, Lynda Chin, Aviv Regev & Ido Amit
Info:
Researchers at the Broad Institute and collaborators at several institutions provide optimized sample preparation protocols for the generation of ChIP-seq libraries on the Ion Torrent PGM. They showed that Pippin size selection was required to generate usable libraries, even down to sub-nanogram input. Results were comparable to results from Illumina Chip-Seq workflow.
Citation:
Nature Communications 4:2672
Mitochondrial Sequence Variation in African-American Primary Open-Angle Glaucoma Patients
October 2013
Authors:
David W. Collins, Harini V. Gudiseva, Benjamin T. Trachtman, Matthew Jerrehian, Thomasine Gorry, William T. Merritt III, Allison L. Rhodes, Prithvi S. Sankar, Meredith Regina, Eydie Miller-Ellis, Joan M.
O’Brien
Info:
Researchers at the University of Pennsylvania deep-sequenced mitochondrial DNA of patients with primary open-angle glaucoma, plus a control group for comparison. They testing a theory implicating variation in mtDNA in this disease, but it could not be confirmed. Pippin Prep was used for size selection of Ion PGM libraries, per the Ion Express protocol.
Citation:
PLoS ONE 8(10): e76627
Genetic Basis for the Biosynthesis of the Pharmaceutically Important Class of Epoxyketone Proteasome Inhibitors
October 2013
Authors:
Michelle Schorn, Judith Zettler, Joseph P. Noel, Pieter C. Dorrestein, Bradley S. Moore, and Leonard Kaysser
Info:
Scientists from California and Germany teamed up to study genes that encode for the biosynthesis of an important component of certain proteasome inhibitors used for cancer treatment. The Ion PGM was used to sequence gene clusters in two microbial strains, reporting the first successful characterization of a region producing natural peptidyl-epoxyketones. For this project, libraries were prepared from genomic DNA sheared to 100 bp to 250 bp, after which sequencing material was separated and extracted using Pippin Prep.
Citation:
ACS Chem. Biol. October 2013