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Clinical-grade validation of whole genome sequencing reveals robust detection of low-frequency variants and copy number alterations in CLL

Klintman, Jenny LU ; Barmpouti, Katerina ; Knight, Samantha J L ; Robbe, Pauline ; Dreau, Hélène ; Clifford, Ruth ; Ridout, Kate ; Burns, Adam ; Timbs, Adele and Bruce, David , et al. (2018) In British Journal of Haematology 182(3). p.412-417
Abstract

The 100 000 Genome Project aims to develop a diagnostics platform by introducing whole genome sequencing (WGS) into clinical practice. Samples from patients with chronic lymphocytic leukaemia were subjected to WGS. WGS detection of single nucleotide variants and insertion/deletions were validated by targeted next generation sequencing showing high concordance (96·3%), also for detection of sub-clonal variants and low-frequency TP53 variants. Copy number alteration detection was verified by fluorescent in situ hybridisation and genome-wide single nucleotide polymorphism array (concordances of 86·7% and 92·9%, respectively), confirming adequate sensitivity by WGS. Our results confirm that WGS can provide comprehensive genomic... (More)

The 100 000 Genome Project aims to develop a diagnostics platform by introducing whole genome sequencing (WGS) into clinical practice. Samples from patients with chronic lymphocytic leukaemia were subjected to WGS. WGS detection of single nucleotide variants and insertion/deletions were validated by targeted next generation sequencing showing high concordance (96·3%), also for detection of sub-clonal variants and low-frequency TP53 variants. Copy number alteration detection was verified by fluorescent in situ hybridisation and genome-wide single nucleotide polymorphism array (concordances of 86·7% and 92·9%, respectively), confirming adequate sensitivity by WGS. Our results confirm that WGS can provide comprehensive genomic characterisation for clinical trials, drug discovery and, ultimately, precision medicine.

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publishing date
type
Contribution to journal
publication status
published
subject
in
British Journal of Haematology
volume
182
issue
3
pages
412 - 417
publisher
Wiley-Blackwell
external identifiers
  • pmid:29808933
  • scopus:85047731241
ISSN
0007-1048
DOI
10.1111/bjh.15406
language
English
LU publication?
no
id
de866cb3-efb0-422f-b53a-04fa6f027668
date added to LUP
2018-11-12 06:04:23
date last changed
2024-04-29 18:05:36
@article{de866cb3-efb0-422f-b53a-04fa6f027668,
  abstract     = {{<p>The 100 000 Genome Project aims to develop a diagnostics platform by introducing whole genome sequencing (WGS) into clinical practice. Samples from patients with chronic lymphocytic leukaemia were subjected to WGS. WGS detection of single nucleotide variants and insertion/deletions were validated by targeted next generation sequencing showing high concordance (96·3%), also for detection of sub-clonal variants and low-frequency TP53 variants. Copy number alteration detection was verified by fluorescent in situ hybridisation and genome-wide single nucleotide polymorphism array (concordances of 86·7% and 92·9%, respectively), confirming adequate sensitivity by WGS. Our results confirm that WGS can provide comprehensive genomic characterisation for clinical trials, drug discovery and, ultimately, precision medicine.</p>}},
  author       = {{Klintman, Jenny and Barmpouti, Katerina and Knight, Samantha J L and Robbe, Pauline and Dreau, Hélène and Clifford, Ruth and Ridout, Kate and Burns, Adam and Timbs, Adele and Bruce, David and Antoniou, Pavlos and Sosinsky, Alona and Becq, Jennifer and Bentley, David and Hillmen, Peter and Taylor, Jenny C and Caulfield, Mark and Schuh, Anna H}},
  issn         = {{0007-1048}},
  language     = {{eng}},
  month        = {{05}},
  number       = {{3}},
  pages        = {{412--417}},
  publisher    = {{Wiley-Blackwell}},
  series       = {{British Journal of Haematology}},
  title        = {{Clinical-grade validation of whole genome sequencing reveals robust detection of low-frequency variants and copy number alterations in CLL}},
  url          = {{http://dx.doi.org/10.1111/bjh.15406}},
  doi          = {{10.1111/bjh.15406}},
  volume       = {{182}},
  year         = {{2018}},
}