Ahmed N. Alkanaq, Kohei Hamanaka, Futoshi Sekiguchi, Masataka Taguri, Atsushi Takata, Noriko Miyake, Satoko Miyatake, Takeshi Mizuguchi, Naomichi Matsumot
The genotypes of mitochondrial DNA variants are compared using both short-read (Illumina Hi-SeqX10) and long-read (PacBio Sequel) sequencing. DNA samples from three individuals with mitochondrial disease used for the study. The authors conclude that although long reads have higher error rates (though random) and short-read have higher accuracy (but with systemic errors), PacBio sequencing can overcome is error bias with 37 reads.
BluePippin was used to select >10kb SMRTbell libraries using the High-Pass protocol.
Yokohama City University
Journal of Human Genetics
Hojatollah Rezaei Nejad, Bruno C. M. Oliveira, Aydin Sadeqi, Amin Dehkharghani, Ivanela Kondova Jan A. M. Langermans, Jeffrey S. Guasto, Saul Tzipori, Giovanni Widmer, Sameer R. Sonkusale
From Engineering and Nano Labs at Tufts University, and a consortium of Veterinary groups from the Netherlands, Brazil, and Tufts. A 3D printed micro-engineered pill with osmotic pumping technology was developed to sample the gut microbiome in animals. The pill was coated to resist exposure to the stomach microbiome and can be magnetically held in the upper intestinal track until sampling is complete.
The system was validated in vitro and in vivo. The Pippin Prep was used to size select 16S amplicons prior to Illumina sequencing.
Advanced Intelligent Systems
Min Young Lee, David Baxter, Kelsey Scherler , Taek-Kyun Kim, Xiaogang Wu , Duna Abu-Amara, Janine Flory, Rachel Yehuda, Charles Marma, Marti Jett, Inyoul Lee, Kai Wang, and Leroy Hood
Researchers report on studies that profile circulating miRNAs in combat veterans suffering from Post Traumatic Stress Disorder (PTSD). Previous studies had shown that circulating miRNA spectra in extra cellular vesicles (EV) in patients suffering from psychiatric disorders. The authors confirm that miRNA profiles differ between PTSD and non-PTSD patients in both EV and EV-depleted fractions of plasma. Further study is recommended to understand the utility of these findings.
PippinHT was used to isolate modified Illumina small RNA sequencing libraries (134-162bp size selection for 20-22 bp inserts). The method (Giraldez et al. 2019) uses custom degenerate adapters (4N adapters) and increased polyethylene glycol (PEG) during the ligation process. This reduces bias and optimizes several other parameters to make it appropriate for use specifically with plasma RNA.
Institute for Systems Biology, Seattle
Steven and Alexandra Cohen Veterans Center for Posttraumatic Stress and Traumatic Brain Injury, New York University, New York
Icahn School of Medicine at Mount Sinai, New York
James J. Peters VA Medical Center, New Yourk
Integrative Systems Biology, US Army Center for Environmental Health Research, Frederick, MD
Journal of Clinical Medicine
De Coster Wouter, De Rijk Peter, De Roeck Arne, De Pooter Tim, D’Hert Svenn, Strazisar Mojca, Kristel Sleegers and Van Broeckhoven Christine
Researchers from VIB Center for Molecular Neurology, Antwerp Belgium and University of Antwerp assess using the ONT Promethion for Structural Varian detection in the genome of Yoruban reference individual NA19240. Several variant calling tools were evaluated and compared to short-read sequencing variant calls. A scalable workflow is discussed and future study is considered.
The BluePippin was used for High Pass DNA size selection prior to library construction.
Effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the differentiation of embryonic stem cells towards pancreatic lineage and pancreatic beta cell function
John A. Kubi, Andy C.H. Chen, Sze Wan Fong, Keng Po Lai, Chris K.C. Wong,
William S.B. Yeung, Kai Fai Lee, Yin Lau Lee
From the University of Hong Kong and Hong Kong Baptist University, this study examines the effect of low exposure of a dioxin (TCDD) on embryonic stem cells. Previous animal studies had linked high dioxin exposure to susceptibility to type 2 diabetes. Results indicated altered methylation patterns in stem cell genes associated with insulin secretion. The authors suggest that early embryonic exposure to TCDD may affect pancreatogenesis.
The BluePippin was used to size select libraries prior to bisulfite conversion and reduced representation bisulfite sequencing.