eprintid: 1501080
rev_number: 34
eprint_status: archive
userid: 608
dir: disk0/01/50/10/80
datestamp: 2016-06-23 10:27:41
lastmod: 2022-01-10 00:20:54
status_changed: 2016-06-23 10:27:41
type: article
metadata_visibility: show
creators_name: Bartram, J
creators_name: Mountjoy, E
creators_name: Brooks, T
creators_name: Hancock, J
creators_name: Williamson, H
creators_name: Wright, G
creators_name: Moppett, J
creators_name: Goulden, N
creators_name: Hubank, M
title: Accurate sample assignment in a multiplexed, ultrasensitive, high-throughput sequencing assay for minimal residual disease
ispublished: pub
divisions: UCL
divisions: B02
divisions: D13
note: © 2016 Published by Elsevier Inc. on behalf of the American Society for Investigative Pathology and the Association for Molecular Pathology. All rights reserved.
abstract: High-throughput sequencing (HTS) (next-generation sequencing) of the rearranged Ig and T-cell receptor genes promises to be less expensive and more sensitive than current methods of monitoring minimal residual disease (MRD) in patients with acute lymphoblastic leukemia. However, the adoption of new approaches by clinical laboratories requires careful evaluation of all potential sources of error and the development of strategies to ensure the highest accuracy. Timely and efficient clinical use of HTS platforms will depend on combining multiple samples (multiplexing) in each sequencing run. Here we examine the Ig heavy-chain gene HTS on the Illumina MiSeq platform for MRD. We identify errors associated with multiplexing that could potentially impact the accuracy of MRD analysis. We optimize a strategy that combines high-purity, sequence-optimized oligonucleotides, dual indexing, and an error-aware demultiplexing approach to minimize errors and maximize sensitivity. We present a probability-based, demultiplexing pipeline Error-Aware Demultiplexer that is suitable for all MiSeq strategies and accurately assigns samples to the correct identifier without excessive loss of data. Finally, using controls quantified by digital PCR, we show that HTS-MRD can accurately detect as few as 1 in 10(6) copies of specific leukemic MRD.
date: 2016-05-13
date_type: published
official_url: http://dx.doi.org/10.1016/j.jmoldx.2016.02.008
oa_status: green
full_text_type: other
language: eng
primo: open
primo_central: open_green
article_type_text: JOURNAL ARTICLE
verified: verified_manual
elements_id: 1137809
doi: 10.1016/j.jmoldx.2016.02.008
pii: S1525-1578(16)30045-9
language_elements: ENG
lyricists_name: Bartram, Jack
lyricists_name: Hubank, Michael
lyricists_id: JLBAR39
lyricists_id: MJFHU53
actors_name: Bartram, Jack
actors_name: Poirier, Elizabeth
actors_id: JLBAR39
actors_id: EPPOI23
actors_role: owner
actors_role: impersonator
full_text_status: public
publication: Journal of Molecular Diagnostics
volume: 18
number: 4
pagerange: 494-506
issn: 1943-7811
citation:        Bartram, J;    Mountjoy, E;    Brooks, T;    Hancock, J;    Williamson, H;    Wright, G;    Moppett, J;         ... Hubank, M; + view all <#>        Bartram, J;  Mountjoy, E;  Brooks, T;  Hancock, J;  Williamson, H;  Wright, G;  Moppett, J;  Goulden, N;  Hubank, M;   - view fewer <#>    (2016)    Accurate sample assignment in a multiplexed, ultrasensitive, high-throughput sequencing assay for minimal residual disease.                   Journal of Molecular Diagnostics , 18  (4)   pp. 494-506.    10.1016/j.jmoldx.2016.02.008 <https://doi.org/10.1016/j.jmoldx.2016.02.008>.       Green open access   
 
document_url: https://discovery.ucl.ac.uk/id/eprint/1501080/1/Bartram_JMolDiagnostics_final.pdf