Selected article for: "capture sample and viral sequence"
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_15
    Snippet: We also explored the impact of capture on the complete metagenomic diversity within each sample. Metagenomic sequencing generates reads from the host genome as well as background contaminants 40 , and capture ought to reduce the abundance of these taxa. Following capture with V ALL , the fraction of sequence classified as human decreased in patient samples while viral species with a wide range of pre-capture abundances were strongly enriched (Fig.....
    Document: We also explored the impact of capture on the complete metagenomic diversity within each sample. Metagenomic sequencing generates reads from the host genome as well as background contaminants 40 , and capture ought to reduce the abundance of these taxa. Following capture with V ALL , the fraction of sequence classified as human decreased in patient samples while viral species with a wide range of pre-capture abundances were strongly enriched (Fig. 2d) . Moreover, we observed a reduction in the overall number of species detected after capture ( Supplementary Fig. 6a ), suggesting that capture indeed reduces non-targeted taxa. Lastly, analysis of this metagenomic data identified a number of other enriched viral species present in these samples (Supplementary Table 4 ). For example, one HIV-1 sample showed strong evidence of HCV co-infection, an observation consistent with clinical PCR testing.

    Search related documents:
    Co phrase search for related documents
    • clinical PCR testing and patient sample: 1
    • clinical PCR testing and PCR testing: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • co infection and overall number: 1
    • co infection and patient sample: 1, 2, 3, 4, 5
    • metagenomic diversity and patient sample: 1
    • overall number and patient sample: 1