Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients
Elsie Cheruba, Ramya Viswanathan, Pui-Mun Wong, Howard John Womersley,
Shuting Han, Brenda Tay, Yiting Lau, Anna Gan, Polly S. Y. Poon, Anders Skanderup,
Sarah B. Ng, Aik Yong Chok, Dawn Qingqing Chong, Iain Beehuat Tan, Lih Feng Cheow
The authors outline a method (Heatrich-BS) for enriching GC-rich regions (CpG islands) in cell free DNA by heating the sequencing libraries prior to performing bisulfite sequencing. Since methylation profiles are key biomarkers for many cancers, this method provides a low cost and scalable method for clinical assays. The authors also provide an algorithm for monitoring response to colorectal cancer treatment in patients.
BluePippin was used size select the libraries prior to sequencing.
Department of Biomedical Engineering, National University of Singapore
Institute for Health Innovation and Technology, National University of Singapore
Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore
Division of Medical Oncology, National Cancer Centre Singapore,
Department of Colorectal Surgery, Singapore General Hospital, Singapore
Medical School, National University of Singapore, Singapore
Manuel Hotz, Nathaniel H. Thayer, David G. Hendrickson, Elizabeth L. Schinski, Jun Xu, and Daniel E. Gottschling
The authors propose a new mechanism for aging and lifespan determination in budding yeast.
The researchers “discovered a previously unappreciated relationship between the number of copies of the ribosomal RNA gene present in its chromosomal array and replicative lifespan (RLS). Specifically, the chromosomal ribosomal DNA (rDNA) copy number (rDNA CN) positively correlated with RLS and this interaction explained over 70% of variability in RLS among a series of wild-type strains. In strains with low rDNA CN, SIR2 expression was attenuated and extra chromosomal rDNA circle (ERC) accumulation was increased, leading to shorter lifespan.”
Pippin Prep was used for DNA size selection for ATAC-seq analysis.
Calico Life Sciences LLC, South San Francisco, CA
Catherine D. Aimone, Steen Hoyer, Anna E. Dye, David O. Deppong, Siobain Duffy, Ignazio Carbone, Linda Hanley-Bowdoin
The authors provide a protocol for analyzing single stranded DNA (ssDNA) from begomoviruses, which cause significant damage to many crops (e.g. cassava and tomato), and is transmitted by whiteflies. The ssDNA is enriched from both plants and whiteflies and combined rolling circle amplification (RCA) and DNA size selection to prepare samples for sequencing and analysis of the viral genomes. The authors suggest that this method can be used to examine viral DNA as it moves from host to vector and be used for viral DNA population studies.
BluePippin was used for DNA size selection.
Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC,
Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ
Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC
Journal of Virological Methods
Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye
The authors report on a high quality genome assembly of the model plant species Arabidopsis include two telomere-to-telomere assemblies (Chr 3 and 5). PacBio’s HiFi, Oxford Nanopore ultra-long reads and Hi-C (Illumina) were used.
BluePippin was used to size select large fragments from genomic extracts and for Hi-FI library construction. The SageHLS was used to collect DNA fragments >50kb for Oxford Nanopore ultra-long library prep (Genome Center of Grandomics [Wuhan, China]). .
Xi’an Jiaotong University, Xi’an, China
Genomics, Proteomics & Bioinformatics
Ashley Jones ,Cynthia Torkel,David Stanley,Jamila Nasim,Justin Borevitz,Benjamin Schwessinger
The authors provide a protocol for preparing high molecular weight DNA sequencing libraries with a particular focus on difficult plant and fungal tissues, and also can be used with animals and microbes. The libraries can be used for PacBio or Oxford Nanopore sequencing, includes clean up and size selection recommendations, in a manner that is economical and scalable.
The PippinHT was used for the DNA size selection recommendations.
Australian National University, Canberra, Australian Capital Territory, Australia