Results 1 to 10 of about 2,613,419 (309)

Demystifying the Discussion of Sequencing Panel Size in Oncology Genetic Testing

European Medical Journal, 2022
Clinical laboratories worldwide are implementing next-generation sequencing (NGS) to identify cancer genomic variants and ultimately improve patient outcomes. The ability to massively sequence the entire genome or exome of tumour cells has been critical
Cecília Durães, Carla Pereira Gomes, Jose Luis Costa, Luca Quagliata   +3 more
doaj   +1 more source

BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing

BMC Bioinformatics, 2018
Background Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each DNA molecule prior pooling them ...
Panu Somervuo, Patrik Koskinen, Peng Mei, Liisa Holm, Petri Auvinen, Lars Paulin   +5 more
doaj   +1 more source

The GENESTAR manual for biospecimen collection biobanking and omics data generation from commercial space missions

npj Microgravity
The surge in commercial and civilian spaceflight enables the systematic and longitudinal, large-scale biospecimen collection to understand the prospective effects of space travel on human health.
Aparna Krishnavajhala, Marie-Claude Gingras, Emmanuel Urquieta, Hsu Chao, Dilrukshi Bandaranaike, Yi Chen, Sravya Bhamidipati, Viktoriya Korchina, S. Michelle Griffin, Michal M. Masternak, Hannah Moreno, Javid Mohammed, Mullai Murugan, Jennifer E. Posey, Jimmy H. Wu, Donna Muzny, Richard A. Gibbs, Harsha Doddapaneni   +17 more
doaj   +1 more source

Deconstructing the Polymerase Chain Reaction II: an improved workflow and effects on artifact formation and primer degeneracy [PDF]

PeerJ, 2019
Polymerase chain reaction (PCR) amplification of complex microbial genomic DNA templates with degenerate primers can lead to distortion of the underlying community structure due to inefficient primer-template interactions leading to bias.
Ankur Naqib, Silvana Poggi, Stefan J. Green   +2 more
doaj   +2 more sources

Complete genomic characterization of global pathogens respiratory syntical virus and human norovirus using probe based capture enrichment

Scientific Reports
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in children worldwide, while human noroviruses (HuNoV) are a leading cause of epidemic and sporadic acute gastroenteritis.
Sravya V Bhamidipati, Anil Surathu, Hsu Chao, Daniel P. Agustinho, Qin Xiang, Kavya Kottapalli, Abirami Santhanam, Zeineen Momin, Kimberly Walker, Vipin K. Menon, George Weissenberger, Nathanael Emerick, Faria Mahjabeen, Qingchang Meng, Jianhong Hu, Richard Sucgang, David Henke, Fritz J. Sedlazeck, Ziad M. Khan, Ginger A. Metcalf, Vasanthi Avadhanula, Pedro A. Piedra, Sasirekha Ramani, Robert L. Atmar, Mary K. Estes, Joseph F. Petrosino, Richard A. Gibbs, Donna M. Muzny, Sara Cregeen Javornik, Harsha Doddapaneni   +29 more
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Efficient Method for Molecular Characterization of the 5′ and 3′ Ends of the Dengue Virus Genome

Viruses, 2020
Dengue is a mosquito-borne disease that is of major importance in public health. Although it has been extensively studied at the molecular level, sequencing of the 5′ and 3′ ends of the untranslated regions (UTR) commonly requires specific approaches for
Alicia Rosales-Munar, Diego Alejandro Alvarez-Diaz, Katherine Laiton-Donato, Dioselina Peláez-Carvajal, Jose A. Usme-Ciro   +4 more
doaj   +1 more source

K-mer analysis of long-read alignment pileups for structural variant genotyping

Nature Communications
Accurately genotyping structural variant (SV) alleles is crucial to genomics research. We present a novel method (kanpig) for genotyping SVs that leverages variant graphs and k-mer vectors to rapidly generate accurate SV genotypes.
Adam C. English, Fabio Cunial, Ginger A. Metcalf, Richard A. Gibbs, Fritz J. Sedlazeck   +4 more
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Tracking updates in clinical databases increases efficiency for variant reanalysis

Genetics in Medicine Open
Purpose: Variant interpretation, guided by American College of Medical Genetics and Genomics guidelines, can inform clinical decision-making. However, interpretations may change over time for a variety of reasons.
Lele Li, Xia Tian, Vaughan Woodzell, Richard A. Gibbs, Bo Yuan, Eric Venner   +5 more
doaj   +1 more source

Characterization and Engineering of Two Novel Strand-Displacing B Family DNA Polymerases from Bacillus Phage SRT01hs and BeachBum

Biomolecules
Polymerase-coupled nanopore sequencing requires DNA polymerases with strong strand displacement activity and high processivity to sustain continuous signal generation.
Yaping Sun, Kang Fu, Wu Lin, Jie Gao, Xianhui Zhao, Yun He, Hui Tian   +6 more
doaj   +1 more source

Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)

BMC Biology, 2017
Background The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications.
Peter A. Larsen, R. Alan Harris, Yue Liu, Shwetha C. Murali, C. Ryan Campbell, Adam D. Brown, Beth A. Sullivan, Jennifer Shelton, Susan J. Brown, Muthuswamy Raveendran, Olga Dudchenko, Ido Machol, Neva C. Durand, Muhammad S. Shamim, Erez Lieberman Aiden, Donna M. Muzny, Richard A. Gibbs, Anne D. Yoder, Jeffrey Rogers, Kim C. Worley   +19 more
doaj   +1 more source