TY - JOUR
T1 - Accurate detection of copy number aberrations in FFPE samples using the mFAST-SeqS approach
AU - Jary, Aude
AU - Kim, Yongsoo
AU - Rozemeijer, Kirsten
AU - Eijk, Paul P.
AU - van der Zee, Ramon P.
AU - Bleeker, Maaike C.G.
AU - Wilting, Saskia M.
AU - Steenbergen, Renske D.M.
N1 - Publisher Copyright: © 2024 The Authors
PY - 2024/6
Y1 - 2024/6
N2 - Background: Shallow whole genome sequencing (Shallow-seq) is used to determine the copy number aberrations (CNA) in tissue samples and circulating tumor DNA. However, costs of NGS and challenges of small biopsies ask for an alternative to the untargeted NGS approaches. The mFAST-SeqS approach, relying on LINE-1 repeat amplification, showed a good correlation with Shallow-seq to detect CNA in blood samples. In the present study, we evaluated whether mFAST-SeqS is suitable to assess CNA in small formalin-fixed paraffin-embedded (FFPE) tissue specimens, using vulva and anal HPV-related lesions. Methods: Seventy-two FFPE samples, including 36 control samples (19 vulva;17 anal) for threshold setting and 36 samples (24 vulva; 12 anal) for clinical evaluation, were analyzed by mFAST-SeqS. CNA in vulva and anal lesions were determined by calculating genome-wide and chromosome arm-specific z-scores in comparison with the respective control samples. Sixteen samples were also analyzed with the conventional Shallow-seq approach. Results: Genome-wide z-scores increased with the severity of disease, with highest values being found in cancers. In vulva samples median and inter quartile ranges [IQR] were 1[0–2] in normal tissues (n = 4), 3[1–7] in premalignant lesions (n = 9) and 21[13–48] in cancers (n = 10). In anal samples, median [IQR] were 0[0–1] in normal tissues (n = 4), 14[6–38] in premalignant lesions (n = 4) and 18[9–31] in cancers (n = 4). At threshold 4, all controls were CNA negative, while 8/13 premalignant lesions and 12/14 cancers were CNA positive. CNA captured by mFAST-SeqS were mostly also found by Shallow-seq. Conclusion: mFAST-SeqS is easy to perform, requires less DNA and less sequencing reads reducing costs, thereby providing a good alternative for Shallow-seq to determine CNA in small FFPE samples.
AB - Background: Shallow whole genome sequencing (Shallow-seq) is used to determine the copy number aberrations (CNA) in tissue samples and circulating tumor DNA. However, costs of NGS and challenges of small biopsies ask for an alternative to the untargeted NGS approaches. The mFAST-SeqS approach, relying on LINE-1 repeat amplification, showed a good correlation with Shallow-seq to detect CNA in blood samples. In the present study, we evaluated whether mFAST-SeqS is suitable to assess CNA in small formalin-fixed paraffin-embedded (FFPE) tissue specimens, using vulva and anal HPV-related lesions. Methods: Seventy-two FFPE samples, including 36 control samples (19 vulva;17 anal) for threshold setting and 36 samples (24 vulva; 12 anal) for clinical evaluation, were analyzed by mFAST-SeqS. CNA in vulva and anal lesions were determined by calculating genome-wide and chromosome arm-specific z-scores in comparison with the respective control samples. Sixteen samples were also analyzed with the conventional Shallow-seq approach. Results: Genome-wide z-scores increased with the severity of disease, with highest values being found in cancers. In vulva samples median and inter quartile ranges [IQR] were 1[0–2] in normal tissues (n = 4), 3[1–7] in premalignant lesions (n = 9) and 21[13–48] in cancers (n = 10). In anal samples, median [IQR] were 0[0–1] in normal tissues (n = 4), 14[6–38] in premalignant lesions (n = 4) and 18[9–31] in cancers (n = 4). At threshold 4, all controls were CNA negative, while 8/13 premalignant lesions and 12/14 cancers were CNA positive. CNA captured by mFAST-SeqS were mostly also found by Shallow-seq. Conclusion: mFAST-SeqS is easy to perform, requires less DNA and less sequencing reads reducing costs, thereby providing a good alternative for Shallow-seq to determine CNA in small FFPE samples.
KW - Anal lesions
KW - Copy number aberrations
KW - FFPE
KW - HPV-related diseases
KW - LINE-1
KW - Shallow sequencing
KW - Vulva lesions
KW - mFAST-SeqS
UR - http://www.scopus.com/inward/record.url?scp=85194430285&partnerID=8YFLogxK
U2 - 10.1016/j.yexmp.2024.104906
DO - 10.1016/j.yexmp.2024.104906
M3 - Article
C2 - 38820761
SN - 0014-4800
VL - 137
JO - Experimental and Molecular Pathology
JF - Experimental and Molecular Pathology
M1 - 104906
ER -