Computational and Statistical Analyses of Insertional Polymorphic Endogenous Retroviruses in a Non-Model Organism
November 2014
Authors:
Le Bao, Daniel Elleder, Raunaq Malhotra, Michael DeGiorgio, Theodora Maravegias,
Lindsay Horvath, Laura Carrel, Colin Gillin, Tomáš Hron, Helena Fábryová, David R. Hunter and Mary Poss
Info:
Scientists present a computational method for detecting specific integration sites of endogenous retroviruses in a genome, even without the use of a reference genome. They use de novo clustering and statistical models and demonstrate the approach in a study of deer. Pippin Prep sizing was used to narrow the fragment size range to 300-330bp prior to sequencing on the Ion Personal Genome Machine.
Citation:
Computation 2014, 2, 221-245
doi:10.3390/computation2040221
CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer
November 2014
Authors:
Edmond Chipumuro, Eugenio Marco, Camilla L. Christensen, Nicholas Kwiatkowski, Tinghu Zhang,Clark M. Hatheway, Brian J. Abraham, Bandana Sharma, Caleb Yeung, Abigail Altabef, Antonio Perez-Atayde, Kwok-Kin Wong, Guo-Cheng Yuan, Nathanael S. Gray, Richard A. Young, and Rani E. George
Info:
Scientists from Harvard and MIT inhibited cyclindependent kinase 7 (CDK7) in neuroblastoma cells and found significant suppression of MYC oncoproteins. In a mouse model, the effect was notable shrinkage of the tumor. Libraries were size-selected for 200 bp to 400 bp using Pippin Prep prior to sequencing on an Illumina HiSeq 2000.
Citation:
Cell (2014)
dx.doi.org/10.1016/j.cell.2014.10.024
Resolving the complexity of the human genome using single-molecule sequencing
November 2014
Authors:
Mark J. P. Chaisson, John Huddleston, Megan Y. Dennis, Peter H. Sudmant, Maika Malig, Fereydoun Hormozdiari, Francesca Antonacci, Urvashi Surti, Richard Sandstrom, Matthew Boitano, Jane M. Landolin, John A. Stamatoyannopoulos, Michael W. Hunkapiller, Jonas Korlach & Evan E. Eichler
Info:
In this Nature paper, scientists from the University of Washington, University of Bari Aldo Moro, University of Pittsburgh, and Pacific Biosciences used long-read sequencing to close or shrink 55 percent of gaps remaining in the human reference genome. They detected substantial amounts of structural variation not represented in the current reference. The scientists used BluePippin to prepare 20 Kb and 30 Kb libraries for sequencing (see supplementary info).
Citation:
Nature (2014)
dx.doi.org/10.1038/nature13907
Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae
September 2014
Authors:
Sean Conlan, Pamela J. Thomas, Clayton Deming, Morgan Park, Anna F. Lau, John P. Dekker, Evan S. Snitkin, Tyson A. Clark, Khai Luong, Yi Song, Yu-Chih Tsai, Matthew Boitano, Jyoti Dayal, Shelise Y. Brooks, Brian Schmidt, Alice C. Young, James W. Thomas, Gerard G. Bouffard, Robert W. Blakesley, NISC Comparative Sequencing Program, James C. Mullikin, Jonas Korlach, David K. Henderson, Karen M. Frank, Tara N. Palmore, Julia A. Segre
Info:
NIH scientists studied samples of antibiotic-resistant Enterobacteriaceae collected from patients and a hospital environment. They used the PacBio RS II DNA Sequencing System to analyze and assemble the bacterial genomes, and then traced transmission path based on genomic data. BluePippin was used to remove DNA fragments less than 5 Kb from the PacBio library.
Citation:
Sci Transl Med 17 September 2014: Vol. 6, Issue 254
dx.doi.org/10.1126/scitranslmed.3009845
Placental miR-1301 is dysregulated in early-onset preeclampsia and inversely correlated with maternal circulating leptin
September 2014
Authors:
M.S. Weedon-Fekjær, Y. Sheng, M. Sugulle, G.M. Johnsen, F. Herse, C.W. Redman, R. Lyle, R. Dechend, A.C. Staff
Info:
Scientists from Norway, the UK, and Germany used sequenced small RNAs in placenta from patients with and without preeclampsia to determine whether microRNAs have a regulatory role in this condition. They found that miRNAs may be regulating the leptin gene, which affects both maternal blood pressure and newborn weight percentile. cDNA was size selected using Pippin Prep.