High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)
June 2016
Authors:
Jessica L. Preston, Ariel E. Royall, Melissa A. Randel, Kristin L. Sikkink, Patrick C. Phillips, and Eric A. Johnson
Info:
Scientists at the University of Oregon developed a new protocol to reduce sequencing and PCR errors, resulting in more accurate SNP detection even for rare variants. Pippin Prep was used for tight sizing of sequencing libraries prior to paired-end Illumina sequencing.
Citation
BMC Genomics 201617:464
DOI: 10.1186/s12864-016-2669-3
Quantitative detection of low-abundance somatic structural variants in normal cells by high-throughput sequencing
June 2016
Authors:
Wilber Quispe-Tintaya, Tatyana Gorbacheva, Moonsook Lee, Sergei Makhortov, Vasily N Popov, Jan Vijg & Alexander Y Maslov
Info:
Scientists report Structural Variant Search, a new method for detecting rare somatic structural variants even with low-coverage sequencing data. The team used PippinHT for automated DNA size selection prior to sequencing with Ion Torrent.
Citation:
Nature Methods
doi:10.1038/nmeth.3893
Long-read sequencing and de novo assembly of a Chinese genome
June 2016
Authors:
Lingling Shi, Yunfei Guo, Chengliang Dong, John Huddleston, Hui Yang, et al.
Info:
Scientists in China and the US analyzed the DNA and RNA of a Chinese individual, using PacBio sequencing and BioNano Genomics maps to produce a high-quality assembly. They report a significant amount of new sequence data and novel gene content, including elements that appear to be specific to the Asian population. The team used BluePippin for size selection prior to genome and transcriptome sequencing with PacBio.
Citation:
Nature Communications
doi:10.1038/ncomms12065
Extensive sequencing of seven human genomes to characterize benchmark reference materials
June 2016
Authors:
Justin M. Zook, David Catoe, Jennifer McDaniel, Lindsay Vang, et al.
Info:
The Genome in a Bottle Consortium used 12 different DNA analysis technologies to generate deep data sets on seven genomes, five of which will become reference materials for the community. BluePippin was used with various platforms, including PacBio and SOLiD.
Citation:
Scientific Data 2016; 3: 160025.
DOI 10.1038/sdata.2016.25
A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations
May 2016
Authors:
Ning Jiang, Fengjun Zhang, Jinhua Wu, Yue Chen, Xiaohua Hu, Ou Fang, Lindsey J. Leach, Di Wang, Zewei Luo
Info:
Scientists in China and the UK developed an optimized RAD-seq protocol that delivers better uniformity of genome coverage. The workflow involves two Pippin Prep size selections.
Citation:
Theor Appl Genet
DOI 10.1007/s00122-016-2736-9