Assessing structural variation in a personal genome—towards a human reference diploid genome
April 2015
Authors:
Adam C English, William J Salerno, Oliver A Hampton, Claudia Gonzaga-Jauregui, Shruthi Ambreth, Deborah I Ritter, Christine R Beck, Caleb F Davis, Mahmoud Dahdouli, Singer Ma, Andrew Carroll, Narayanan Veeraraghavan, Jeremy Bruestle, Becky Drees, Alex Hastie, Ernest T Lam, Simon White, Pamela Mishra, Min Wang, Yi Han, Feng Zhang, Pawel Stankiewicz, David A Wheeler, Jeffrey G Reid, Donna M Muzny, Jeffrey Rogers, Aniko Sabo, Kim C Worley, James R Lupski, Eric Boerwinkle and Richard A Gibbs
Info:
In this BMC Genomics paper, scientists characterize structural variation across a human genome using Parliament, a new structural variant-calling pipeline developed at Baylor. They found that long reads are critical to detecting structural variants. BluePippin was used to prepare 20 Kb libraries for the PacBio sequencer.
Citation:
BMC Genomics 2015, 16:286
doi:10.1186/s12864-015-1479-3
Improved transposon-based library preparation for the Ion Torrent platform
April 2015
Authors:
Tatyana Gorbacheva, Wilber Quispe-Tintaya, Vasily N. Popov, Jan Vijg, and Alexander Y. Maslov
Info:
In this Biotechniques paper, scientists from the Albert Einstein College of Medicine in New York describe MuPlus, a new transposon-based method for barcoded library prep compatible with Ion Torrent sequencers. The protocol eliminates self-complementary regions, increasing sequencing efficiency. Pippin Prep was used for automated size selection of a mouse library.
Citation:
BioTechniques, Vol. 58, No. 4, April 2015, pp. 200–202
Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa
March 2015
Authors:
Matthew H Stremlau, Kristian G Andersen, Onikepe A Folarin, Jessica N Grove, Ikponmwonsa Odia, Philomena E Ehiane, Omowunmi Omoniwa, Omigie Omoregie, Pan-Pan Jiang, Nathan L Yozwiak, Christian B Matranga, Xiao Yang, Stephen K Gire, Sarah Winnicki, Ridhi Tariyal, Stephen F Schaffner, Peter O Okokhere, Sylvanus Okogbenin, George O Akpede, Danny A. Asogun, Dennis E. Agbonlahor, Peter J Walker, Robert B Tesh, Joshua Z Levin, Robert F Garry, Pardis C Sabeti, Christian T Happi
Info:
In this PLOS Neglected Tropical Diseases paper, researchers utilized next-generation sequencing to identify RNA viruses in the blood of 195 patients with unexplained acute febrile illness and compared them with those found in 328 apparently healthy control individuals, all from communities in southeastern Nigeria. The researchers suggest that human infection with rhabdoviruses might be common. Carrier RNA was removed after cDNA synthesis using Pippin Prep size selection.
Citation:
PLoS Negl Trop Dis
9(3): e0003631. doi:10.1371/journal.pntd.0003631
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