a031b47638667e81781d1c72d480245e pmc_9406074.pdf 6df199b6da8ba21fc7c0427e1d2df2e47d5da143 pmc_9406074.pdf cdc726befecb1e7a26f67d972dd689e76dd04e1368a358200fcb703519e52f40 pmc_9406074.pdf Title: Ultra Deep Sequencing of Circulating Cell-Free DNA as a Potential Tool for Hepatocellular Carcinoma Management Subject: Background: Cell-free DNA (cfDNA) concentrations have been described to be inversely correlated with prognosis in cancer. Mutations in HCC-associated driver genes in cfDNA have been reported, but their relation with patient’s outcome has not been described. Our aim was to elucidate whether mutations found in cfDNA could be representative from those present in HCC tissue, providing the rationale to use the cfDNA to monitor HCC. Methods: Tumoral tissue, paired nontumor adjacent tissue and blood samples were collected from 30 HCC patients undergoing curative therapies. Deep sequencing targeting HCC driver genes was performed. Results: Patients with more than 2 ng/L of cfDNA at diagnosis had higher mortality (mean OS 24.6 vs. 31.87 months, p = 0.01) (AUC = 0.782). Subjects who died during follow-up, had a significantly higher number of mutated genes (p = 0.015) and number of mutations (p = 0.015) on cfDNA. Number of mutated genes (p = 0.001), detected mutations (p = 0.001) in cfDNA and ratio (number of mutations/cfDNA) (p = 0.003) were significantly associated with recurrence. However, patients with a ratio (number of mutations/cfDNA) above 6 (long-rank p = 0.0003) presented a higher risk of recurrence than those with a ratio under 6. Detection of more than four mutations in cfDNA correlated with higher risk of death (long-rank p = 0.042). Conclusions: In summary, cfDNA and detection of prevalent HCC mutations could have prognostic implications in early-stage HCC patients Keywords: liquid biopsy; cfDNA; HCC; biomarkers Author: Mónica Higuera, Elena Vargas-Accarino, María Torrens, Josep Gregori, María Teresa Salcedo, Joan Martínez-Campreciós, Gloria Torres, María Bermúdez-Ramos, Itxarone Bilbao, Mercedes Guerrero-Murillo, Xavier Serres-Créixams, Xavier Merino, Francisco Rodríguez-Frías, Josep Quer and Beatriz Mínguez Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Thu Aug 11 10:30:08 2022 CEST ModDate: Thu Aug 11 10:37:40 2022 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 17 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 2100740 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- HKBJPQ+VnURWPalladioL Type 1 Custom yes yes 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no 168 0 GLHPAH+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 171 0 GLIAFC+PalatinoLinotype,BoldItalic TrueType WinAnsi yes yes no 174 0 GLHOPE+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 190 0 GLHOPF+PalatinoLinotype CID TrueType Identity-H yes yes yes 193 0 GLHOPG+PalatinoLinotype TrueType WinAnsi yes yes no 199 0 GLHPAH+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 202 0 GLHOPE+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 220 0 GLHOPG+PalatinoLinotype TrueType WinAnsi yes yes no 223 0 GLHPAH+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 226 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-09-27 02:37:34 CEST RepresentationInformation: pmc_9406074.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-09-23 02:18:01 CEST Size: 2100740 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 449 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Item: Title: Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Children: Item: Title: Study Design and Participants Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Item: Title: Sample Collection Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: DNA Extraction and Quantification Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: Primer Design and PCR Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Item: Title: Library Preparation and Next-Generation Sequencing Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Item: Title: Data Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Item: Title: Statistical Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77f99a05 Children: Item: Title: Study Design and Patient Characteristics Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@63440df3 Item: Title: Quantification of cfDNA in HCC Patients Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3aeaafa6 Item: Title: Mutations Identified in Plasma cfDNA and Matched HCC Tissue DNA Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@76a3e297 Item: Title: Variant Characteristics in Plasma and HCC Tissue Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4d3167f4 Item: Title: Early Detection of Mutations in Driver Genes Prior to HCC Diagnosis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ed9d034 Item: Title: Dynamics of cfDNA and Mutations during HCC Progression Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6121c9d6 Item: Title: Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@87f383f Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4eb7f003 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@eafc191 Info: Title: Ultra Deep Sequencing of Circulating Cell-Free DNA as a Potential Tool for Hepatocellular Carcinoma Management Author: Mónica Higuera, Elena Vargas-Accarino, María Torrens, Josep Gregori, María Teresa Salcedo, Joan Martínez-Campreciós, Gloria Torres, María Bermúdez-Ramos, Itxarone Bilbao, Mercedes Guerrero-Murillo, Xavier Serres-Créixams, Xavier Merino, Francisco Rodríguez-Frías, Josep Quer and Beatriz Mínguez Subject: Background: Cell-free DNA (cfDNA) concentrations have been described to be inversely correlated with prognosis in cancer. Mutations in HCC-associated driver genes in cfDNA have been reported, but their relation with patient’s outcome has not been described. Our aim was to elucidate whether mutations found in cfDNA could be representative from those present in HCC tissue, providing the rationale to use the cfDNA to monitor HCC. Methods: Tumoral tissue, paired nontumor adjacent tissue and blood samples were collected from 30 HCC patients undergoing curative therapies. Deep sequencing targeting HCC driver genes was performed. Results: Patients with more than 2 ng/L of cfDNA at diagnosis had higher mortality (mean OS 24.6 vs. 31.87 months, p = 0.01) (AUC = 0.782). Subjects who died during follow-up, had a significantly higher number of mutated genes (p = 0.015) and number of mutations (p = 0.015) on cfDNA. Number of mutated genes (p = 0.001), detected mutations (p = 0.001) in cfDNA and ratio (number of mutations/cfDNA) (p = 0.003) were significantly associated with recurrence. However, patients with a ratio (number of mutations/cfDNA) above 6 (long-rank p = 0.0003) presented a higher risk of recurrence than those with a ratio under 6. Detection of more than four mutations in cfDNA correlated with higher risk of death (long-rank p = 0.042). 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