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_25
Snippet: Because viruses often have extensive within-host viral nucleotide variation that can inform studies of transmission and within-host virus evolution 41-44 , we examined the impact of capture on estimating within-host variant frequencies. We used three DENV samples that yielded high read depth (Supplementary Table 3 ). Using both V ALL and V WAFR , we found 9 . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for.....
Document: Because viruses often have extensive within-host viral nucleotide variation that can inform studies of transmission and within-host virus evolution 41-44 , we examined the impact of capture on estimating within-host variant frequencies. We used three DENV samples that yielded high read depth (Supplementary Table 3 ). Using both V ALL and V WAFR , we found 9 . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/279570 doi: bioRxiv preprint that frequencies of all within-host variants were consistent with pre-capture levels (Fig. 3d , Supplementary Table 6 ; concordance correlation coefficient is 0.996 for V ALL and 0.997 for V WAFR ). These estimates were consistent for both low and high frequency variants. Since capture preserves frequencies so well, it should enable measurement of within-host diversity that is both sensitive and cost-effective.
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