Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing

Sharjeel H. Sabir, Savitri Krishnamurthy, Sanjay Gupta, Gordon Mills, Wei Wei, Andrea C. Cortes, Kenna R. Mills Shaw, Rajyalakshmi Luthra, Michael J. Wallace

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Purpose Determine the characteristics of percutaneous core biopsies that are adequate for a next generation sequencing (NGS) genomic panel. Materials and methods All patients undergoing percutaneous core biopsies in interventional radiology (IR) with samples evaluated for a 46-gene NGS panel during 1-year were included in this retrospective study. Patient and procedure variables were collected. An imaging-based likelihood of adequacy score incorporating targeting and sampling factors was assigned to each biopsied lesion. Univariate and multivariate logistic regression was performed. Results 153 patients were included (58.2% female, average age 59.5 years). The most common malignancy was lung cancer (40.5%), most common biopsied site was lung (36%), and average size of biopsied lesions was 3.8 cm (+/- 2.7). Adequacy for NGS was 69.9%. Univariate analysis showed higher likelihood of adequacy score (p = 0.004), primary malignancy type (p = 0.03), and absence of prior systemic therapy (p = 0.018) were associated with adequacy for NGS. Multivariate analysis showed higher adequacy for lesions with likelihood of adequacy scored 3 (high) versus lesions scored 1 (low) (OR, 7.82; p = 0.002). Melanoma lesions had higher adequacy for NGS versus breast cancer lesions (OR 9.5; p = 0.01). Absence of prior systemic therapy (OR, 6.1; p = 0.02) and systemic therapy </ = 3 months (OR 3.24; p = 0.01) compared to systemic therapy >3 months before biopsy yielded greater adequacy for NGS. Lesions <3 cm had greater adequacy for NGS than larger lesions (OR 2.72, p = 0.02). Conclusion As targeted therapy becomes standard for more cancers, percutaneous biopsy specimens adequate for NGS genomic testing will be needed. An imaging-based likelihood of adequacy score assigned by IR physicians and other pre-procedure variables can help predict the likelihood of biopsy adequacy for NGS.

Original languageEnglish (US)
Article numbere0189651
JournalPLoS One
Volume12
Issue number12
DOIs
StatePublished - Dec 1 2017
Externally publishedYes

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Biopsy
lesions (animal)
biopsy
genomics
Interventional Radiology
Radiology
therapeutics
radiology
Imaging techniques
Neoplasms
Therapeutics
image analysis
Logistics
Melanoma
Lung Neoplasms
Multivariate Analysis
Retrospective Studies
Genes
Logistic Models
Breast Neoplasms

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Sabir, S. H., Krishnamurthy, S., Gupta, S., Mills, G., Wei, W., Cortes, A. C., ... Wallace, M. J. (2017). Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing. PLoS One, 12(12), [e0189651]. https://doi.org/10.1371/journal.pone.0189651

Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing. / Sabir, Sharjeel H.; Krishnamurthy, Savitri; Gupta, Sanjay; Mills, Gordon; Wei, Wei; Cortes, Andrea C.; Mills Shaw, Kenna R.; Luthra, Rajyalakshmi; Wallace, Michael J.

In: PLoS One, Vol. 12, No. 12, e0189651, 01.12.2017.

Research output: Contribution to journalArticle

Sabir, SH, Krishnamurthy, S, Gupta, S, Mills, G, Wei, W, Cortes, AC, Mills Shaw, KR, Luthra, R & Wallace, MJ 2017, 'Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing', PLoS One, vol. 12, no. 12, e0189651. https://doi.org/10.1371/journal.pone.0189651
Sabir, Sharjeel H. ; Krishnamurthy, Savitri ; Gupta, Sanjay ; Mills, Gordon ; Wei, Wei ; Cortes, Andrea C. ; Mills Shaw, Kenna R. ; Luthra, Rajyalakshmi ; Wallace, Michael J. / Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing. In: PLoS One. 2017 ; Vol. 12, No. 12.
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abstract = "Purpose Determine the characteristics of percutaneous core biopsies that are adequate for a next generation sequencing (NGS) genomic panel. Materials and methods All patients undergoing percutaneous core biopsies in interventional radiology (IR) with samples evaluated for a 46-gene NGS panel during 1-year were included in this retrospective study. Patient and procedure variables were collected. An imaging-based likelihood of adequacy score incorporating targeting and sampling factors was assigned to each biopsied lesion. Univariate and multivariate logistic regression was performed. Results 153 patients were included (58.2{\%} female, average age 59.5 years). The most common malignancy was lung cancer (40.5{\%}), most common biopsied site was lung (36{\%}), and average size of biopsied lesions was 3.8 cm (+/- 2.7). Adequacy for NGS was 69.9{\%}. Univariate analysis showed higher likelihood of adequacy score (p = 0.004), primary malignancy type (p = 0.03), and absence of prior systemic therapy (p = 0.018) were associated with adequacy for NGS. Multivariate analysis showed higher adequacy for lesions with likelihood of adequacy scored 3 (high) versus lesions scored 1 (low) (OR, 7.82; p = 0.002). Melanoma lesions had higher adequacy for NGS versus breast cancer lesions (OR 9.5; p = 0.01). Absence of prior systemic therapy (OR, 6.1; p = 0.02) and systemic therapy 3 months before biopsy yielded greater adequacy for NGS. Lesions <3 cm had greater adequacy for NGS than larger lesions (OR 2.72, p = 0.02). Conclusion As targeted therapy becomes standard for more cancers, percutaneous biopsy specimens adequate for NGS genomic testing will be needed. An imaging-based likelihood of adequacy score assigned by IR physicians and other pre-procedure variables can help predict the likelihood of biopsy adequacy for NGS.",
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N2 - Purpose Determine the characteristics of percutaneous core biopsies that are adequate for a next generation sequencing (NGS) genomic panel. Materials and methods All patients undergoing percutaneous core biopsies in interventional radiology (IR) with samples evaluated for a 46-gene NGS panel during 1-year were included in this retrospective study. Patient and procedure variables were collected. An imaging-based likelihood of adequacy score incorporating targeting and sampling factors was assigned to each biopsied lesion. Univariate and multivariate logistic regression was performed. Results 153 patients were included (58.2% female, average age 59.5 years). The most common malignancy was lung cancer (40.5%), most common biopsied site was lung (36%), and average size of biopsied lesions was 3.8 cm (+/- 2.7). Adequacy for NGS was 69.9%. Univariate analysis showed higher likelihood of adequacy score (p = 0.004), primary malignancy type (p = 0.03), and absence of prior systemic therapy (p = 0.018) were associated with adequacy for NGS. Multivariate analysis showed higher adequacy for lesions with likelihood of adequacy scored 3 (high) versus lesions scored 1 (low) (OR, 7.82; p = 0.002). Melanoma lesions had higher adequacy for NGS versus breast cancer lesions (OR 9.5; p = 0.01). Absence of prior systemic therapy (OR, 6.1; p = 0.02) and systemic therapy 3 months before biopsy yielded greater adequacy for NGS. Lesions <3 cm had greater adequacy for NGS than larger lesions (OR 2.72, p = 0.02). Conclusion As targeted therapy becomes standard for more cancers, percutaneous biopsy specimens adequate for NGS genomic testing will be needed. An imaging-based likelihood of adequacy score assigned by IR physicians and other pre-procedure variables can help predict the likelihood of biopsy adequacy for NGS.

AB - Purpose Determine the characteristics of percutaneous core biopsies that are adequate for a next generation sequencing (NGS) genomic panel. Materials and methods All patients undergoing percutaneous core biopsies in interventional radiology (IR) with samples evaluated for a 46-gene NGS panel during 1-year were included in this retrospective study. Patient and procedure variables were collected. An imaging-based likelihood of adequacy score incorporating targeting and sampling factors was assigned to each biopsied lesion. Univariate and multivariate logistic regression was performed. Results 153 patients were included (58.2% female, average age 59.5 years). The most common malignancy was lung cancer (40.5%), most common biopsied site was lung (36%), and average size of biopsied lesions was 3.8 cm (+/- 2.7). Adequacy for NGS was 69.9%. Univariate analysis showed higher likelihood of adequacy score (p = 0.004), primary malignancy type (p = 0.03), and absence of prior systemic therapy (p = 0.018) were associated with adequacy for NGS. Multivariate analysis showed higher adequacy for lesions with likelihood of adequacy scored 3 (high) versus lesions scored 1 (low) (OR, 7.82; p = 0.002). Melanoma lesions had higher adequacy for NGS versus breast cancer lesions (OR 9.5; p = 0.01). Absence of prior systemic therapy (OR, 6.1; p = 0.02) and systemic therapy 3 months before biopsy yielded greater adequacy for NGS. Lesions <3 cm had greater adequacy for NGS than larger lesions (OR 2.72, p = 0.02). Conclusion As targeted therapy becomes standard for more cancers, percutaneous biopsy specimens adequate for NGS genomic testing will be needed. An imaging-based likelihood of adequacy score assigned by IR physicians and other pre-procedure variables can help predict the likelihood of biopsy adequacy for NGS.

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