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The diagnostic utility of DNA copy number analysis of core needle biopsies from soft tissue and bone tumors

Köster, Jan LU ; Piccinelli, Paul LU ; Arvidsson, Linda ; Vult von Steyern, Fredrik LU ; Bedeschi Rego De Mattos, Camila LU orcid ; Almquist, Martin LU ; Nilsson, Jenny LU ; Magnusson, Linda LU and Mertens, Fredrik LU (2022) In Laboratory Investigation 102(8). p.838-845
Abstract

Morphologic and immunohistochemical analysis of preoperative core needle biopsies (CNB) is important in the management of patients with soft tissue and bone tumors (STBTs). Most SBTB subtypes have more or less extensive DNA copy number aberrations (CNA), potentially providing useful diagnostic information. To evaluate the technical feasibility of single nucleotide polymorphism (SNP) array analysis and the diagnostic usefulness of the copy number profiles, we studied CNBs from 171 patients with suspected STBTs. SNP array analysis could be performed on 168 (98%) of the samples. The CNA profile was compatible with the CNB diagnosis in 87% of the cases. Discrepant cases were dominated by false-negative results due to nonrepresentative... (More)

Morphologic and immunohistochemical analysis of preoperative core needle biopsies (CNB) is important in the management of patients with soft tissue and bone tumors (STBTs). Most SBTB subtypes have more or less extensive DNA copy number aberrations (CNA), potentially providing useful diagnostic information. To evaluate the technical feasibility of single nucleotide polymorphism (SNP) array analysis and the diagnostic usefulness of the copy number profiles, we studied CNBs from 171 patients with suspected STBTs. SNP array analysis could be performed on 168 (98%) of the samples. The CNA profile was compatible with the CNB diagnosis in 87% of the cases. Discrepant cases were dominated by false-negative results due to nonrepresentative material or contamination with normal cells. 70 genomic profiles were indicative of specific histopathologic tumor entities and in agreement with the corresponding CNB diagnoses in 83%. In 96 of the cases with aberrant CNA profiles, the SNP profiles were of sufficient quality for segmentation, allowing clustering analysis on the basis of the Jaccard similarity index. The analysis of these segment files showed three major CNA clusters, based on the complexity levels and the predominance of gains versus losses. For 43 of these CNB samples, we had SNP array data also from their corresponding surgical samples. In 33 of these pairs, the two corresponding samples clustered next to each other, with Jaccard scores ranging from 0.61 to 0.99 (median 0.96). Also, for those tumor pairs that did not cluster together, the Jaccard scores were relatively high (median 0.9). 10 cases showed discrepant results, mainly due to varying degrees of normal cell contamination or technical issues. Thus, the copy number profile seen in a CNB is typically highly representative of the major cell population in the tumor.

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author
; ; ; ; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Biopsy, Large-Core Needle, Bone Neoplasms/diagnosis, DNA Copy Number Variations, Humans, Retrospective Studies, Soft Tissue Neoplasms/diagnosis, sarcoma
in
Laboratory Investigation
volume
102
issue
8
pages
8 pages
publisher
Nature Publishing Group
external identifiers
  • scopus:85126886563
  • pmid:35318454
ISSN
0023-6837
DOI
10.1038/s41374-022-00770-2
language
English
LU publication?
yes
id
b483f324-2ede-4cdb-bbd6-676f048476a0
date added to LUP
2022-04-19 15:59:28
date last changed
2025-03-23 22:48:41
@article{b483f324-2ede-4cdb-bbd6-676f048476a0,
  abstract     = {{<p>Morphologic and immunohistochemical analysis of preoperative core needle biopsies (CNB) is important in the management of patients with soft tissue and bone tumors (STBTs). Most SBTB subtypes have more or less extensive DNA copy number aberrations (CNA), potentially providing useful diagnostic information. To evaluate the technical feasibility of single nucleotide polymorphism (SNP) array analysis and the diagnostic usefulness of the copy number profiles, we studied CNBs from 171 patients with suspected STBTs. SNP array analysis could be performed on 168 (98%) of the samples. The CNA profile was compatible with the CNB diagnosis in 87% of the cases. Discrepant cases were dominated by false-negative results due to nonrepresentative material or contamination with normal cells. 70 genomic profiles were indicative of specific histopathologic tumor entities and in agreement with the corresponding CNB diagnoses in 83%. In 96 of the cases with aberrant CNA profiles, the SNP profiles were of sufficient quality for segmentation, allowing clustering analysis on the basis of the Jaccard similarity index. The analysis of these segment files showed three major CNA clusters, based on the complexity levels and the predominance of gains versus losses. For 43 of these CNB samples, we had SNP array data also from their corresponding surgical samples. In 33 of these pairs, the two corresponding samples clustered next to each other, with Jaccard scores ranging from 0.61 to 0.99 (median 0.96). Also, for those tumor pairs that did not cluster together, the Jaccard scores were relatively high (median 0.9). 10 cases showed discrepant results, mainly due to varying degrees of normal cell contamination or technical issues. Thus, the copy number profile seen in a CNB is typically highly representative of the major cell population in the tumor.</p>}},
  author       = {{Köster, Jan and Piccinelli, Paul and Arvidsson, Linda and Vult von Steyern, Fredrik and Bedeschi Rego De Mattos, Camila and Almquist, Martin and Nilsson, Jenny and Magnusson, Linda and Mertens, Fredrik}},
  issn         = {{0023-6837}},
  keywords     = {{Biopsy, Large-Core Needle; Bone Neoplasms/diagnosis; DNA Copy Number Variations; Humans; Retrospective Studies; Soft Tissue Neoplasms/diagnosis; sarcoma}},
  language     = {{eng}},
  number       = {{8}},
  pages        = {{838--845}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Laboratory Investigation}},
  title        = {{The diagnostic utility of DNA copy number analysis of core needle biopsies from soft tissue and bone tumors}},
  url          = {{http://dx.doi.org/10.1038/s41374-022-00770-2}},
  doi          = {{10.1038/s41374-022-00770-2}},
  volume       = {{102}},
  year         = {{2022}},
}