medRxivGenetic & Genomic MedicinePreprint
High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs
John E. GorzynskiiD, Hannah N. De JongiD, David AmariD, Chris HughesiD, Alexander G. IoannidisiD, Rob BiermaniD, Dawei LiuiD, Yosuke TanigawaiD, Amy L. KistleriD, Jack KammiD, Jaehee KimiD, Lorenzo CappelloiD, Norma F NeffiD, Simone RubinacciiD, Olivier DelaneauiD, Massa J. ShouraiD, Kinya SeoiD, Anna KirillovaiD, Archana Natarajan RajaiD, Shirley C. SuttoniD, ChunHong HuangiD, Malaya Kumar SahooiD, Kalyan C. Mallempati, Gonzalo Montero-MartíniD, Kazutoyo OsoegawaiD, , Victoria Nicole ParikhiD
Abstract
During COVID19 and other viral pandemics, rapid generation of host and pathogen genomic data is critical to tracking infection and informing therapies. There is an urgent need for efficient approaches to this data generation at scale. We have developed a scalable, high throughput approach to generate high fidelity low pass whole genome and HLA sequencing, viral genomes, and representation of human transcriptome from single nasopharyngeal swabs of COVID19 patients.
- organism: human
- assay: whole-genome sequencing
- assay: whole-exome sequencing
- assay: spatial transcriptomics
- research focus: variant calling
- research focus: gene regulatory network inference
- research focus: cell type annotation
- approach: experimental assay
- Citations
- 8
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