Selected article for: "sample cost and Supplementary table"
Author: Hayden C. Metsky; Katherine J. Siddle; Adrianne Gladden-Young; James Qu; David K. Yang; Patrick Brehio; Andrew Goldfarb; Anne Piantadosi; Shirlee Wohl; Amber Carter; Aaron E. Lin; Kayla G. Barnes; Damien C. Tully; Björn Corleis; Scott Hennigan; Giselle Barbosa-Lima; Yasmine R. Vieira; Lauren M. Paul; Amanda L. Tan; Kimberly F. Garcia; Leda A. Parham; Ikponmwonsa Odia; Philomena Eromon; Onikepe A. Folarin; Augustine Goba; Etienne Simon-Lorière; Lisa Hensley; Angel Balmaseda; Eva Harris; Douglas Kwon; Todd M. Allen; Jonathan A. Runstadler; Sandra Smole; Fernando A. Bozza; Thiago M. L. Souza; Sharon Isern; Scott F. Michael; Ivette Lorenzana; Lee Gehrke; Irene Bosch; Gregory Ebel; Donald Grant; Christian Happi; Daniel J. Park; Andreas Gnirke; Pardis C. Sabeti; Christian B. Matranga
Title: Capturing diverse microbial sequence with comprehensive and scalable probe design
  • Document date: 2018_3_12
    • ID: a9lkhayg_36
    Snippet: The probe sets we have designed with CATCH, and more broadly capture with comprehensive probe designs, improve the accessibility of metagenomic sequencing in resource-limited settings through smaller capacity platforms. For example, in West Africa we are using the V ALL probe set to characterize LASV and other viruses in patients with undiagnosed fevers by sequencing on a MiSeq (Illumina). This could also be applied on other small machines such a.....
    Document: The probe sets we have designed with CATCH, and more broadly capture with comprehensive probe designs, improve the accessibility of metagenomic sequencing in resource-limited settings through smaller capacity platforms. For example, in West Africa we are using the V ALL probe set to characterize LASV and other viruses in patients with undiagnosed fevers by sequencing on a MiSeq (Illumina). This could also be applied on other small machines such as the iSeq (Illumina) or MinION (Oxford Nanopore) 53 . Further, the increase in viral content enables more samples to be pooled and sequenced on a single run, increasing sample throughput and decreasing per-sample cost relative to unbiased sequencing (Supplementary Table 9 ). Lastly, researchers can use CATCH to quickly design focused probe sets, providing flexibility when it is not necessary to target an exhaustive list of viruses, such as in outbreak response or for targeting pathogens associated with specific clinical syndromes.

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