Prospective Evaluation of Unprocessed Core Needle Biopsy DNA and RNA Yield from Lung, Liver, and Kidney Tumors: Implications for Cancer Genomics
Context. Targeted needle biopsies are increasingly performed for the genetic characterization of cancer. While the nucleic acid content of core needle biopsies after standard pathology processing (i.e., formalin fixation and paraffin embedding (FFPE)) has been previously reported, little is known ab...
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| Format: | Article |
| Language: | English |
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Wiley
2018-01-01
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| Series: | Analytical Cellular Pathology |
| Online Access: | http://dx.doi.org/10.1155/2018/2898962 |
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| author | Mikhail T. Silk Nina Mikkilineni Tarik C. Silk Emily C. Zabor Irina Ostrovnaya Ari A. Hakimi James J. Hsieh Etay Ziv Natasha Rekhtman Stephen B. Solomon Jeremy C. Durack |
| author_facet | Mikhail T. Silk Nina Mikkilineni Tarik C. Silk Emily C. Zabor Irina Ostrovnaya Ari A. Hakimi James J. Hsieh Etay Ziv Natasha Rekhtman Stephen B. Solomon Jeremy C. Durack |
| author_sort | Mikhail T. Silk |
| collection | DOAJ |
| description | Context. Targeted needle biopsies are increasingly performed for the genetic characterization of cancer. While the nucleic acid content of core needle biopsies after standard pathology processing (i.e., formalin fixation and paraffin embedding (FFPE)) has been previously reported, little is known about the potential yield for molecular analysis at the time of biopsy sample acquisition. Objectives. Our objective was to improve the understanding of DNA and RNA yields from commonly used core needle biopsy techniques prior to sample processing. Methods. We performed 552 ex vivo 18 and 20G core biopsies in the lungs, liver, and kidneys. DNA and RNA were extracted from fresh-frozen core samples and quantified for statistical comparisons based on needle gauge, biopsy site, and tissue type. Results. Median tumor DNA yields from all 18G and 20G samples were 5880 ng and 2710 ng, respectively. Median tumor RNA yields from all 18G and 20G samples were 1100 ng and 230 ng, respectively. A wide range of DNA and RNA quantities (1060–13,390 ng and 370–6280 ng, respectively) were acquired. Median DNA and RNA yields from 18G needles were significantly greater than those from 20G needles across all organs (p<0.001). Conclusions. Core needle biopsy techniques for cancer diagnostics yield a broad range of DNA and RNA for molecular pathology, though quantities are greater than what has been reported for FFPE processed material. Since non-formalin-fixed DNA is advantageous for molecular studies, workflows that optimize core needle biopsy yield for molecular characterization should be explored. |
| format | Article |
| id | doaj-art-35526f9264c549efb8becb26b3f0eaa1 |
| institution | Kabale University |
| issn | 2210-7177 2210-7185 |
| language | English |
| publishDate | 2018-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Analytical Cellular Pathology |
| spelling | doaj-art-35526f9264c549efb8becb26b3f0eaa12025-02-03T01:26:24ZengWileyAnalytical Cellular Pathology2210-71772210-71852018-01-01201810.1155/2018/28989622898962Prospective Evaluation of Unprocessed Core Needle Biopsy DNA and RNA Yield from Lung, Liver, and Kidney Tumors: Implications for Cancer GenomicsMikhail T. Silk0Nina Mikkilineni1Tarik C. Silk2Emily C. Zabor3Irina Ostrovnaya4Ari A. Hakimi5James J. Hsieh6Etay Ziv7Natasha Rekhtman8Stephen B. Solomon9Jeremy C. Durack10Interventional Radiology Section, Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USADepartment of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USAInterventional Radiology Section, Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USADepartment of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USADepartment of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USADepartment of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USADivision of Oncology, Department of Medicine, Washington University Medical School, USAInterventional Radiology Section, Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USADepartment of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USAInterventional Radiology Section, Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USAInterventional Radiology Section, Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USAContext. Targeted needle biopsies are increasingly performed for the genetic characterization of cancer. While the nucleic acid content of core needle biopsies after standard pathology processing (i.e., formalin fixation and paraffin embedding (FFPE)) has been previously reported, little is known about the potential yield for molecular analysis at the time of biopsy sample acquisition. Objectives. Our objective was to improve the understanding of DNA and RNA yields from commonly used core needle biopsy techniques prior to sample processing. Methods. We performed 552 ex vivo 18 and 20G core biopsies in the lungs, liver, and kidneys. DNA and RNA were extracted from fresh-frozen core samples and quantified for statistical comparisons based on needle gauge, biopsy site, and tissue type. Results. Median tumor DNA yields from all 18G and 20G samples were 5880 ng and 2710 ng, respectively. Median tumor RNA yields from all 18G and 20G samples were 1100 ng and 230 ng, respectively. A wide range of DNA and RNA quantities (1060–13,390 ng and 370–6280 ng, respectively) were acquired. Median DNA and RNA yields from 18G needles were significantly greater than those from 20G needles across all organs (p<0.001). Conclusions. Core needle biopsy techniques for cancer diagnostics yield a broad range of DNA and RNA for molecular pathology, though quantities are greater than what has been reported for FFPE processed material. Since non-formalin-fixed DNA is advantageous for molecular studies, workflows that optimize core needle biopsy yield for molecular characterization should be explored.http://dx.doi.org/10.1155/2018/2898962 |
| spellingShingle | Mikhail T. Silk Nina Mikkilineni Tarik C. Silk Emily C. Zabor Irina Ostrovnaya Ari A. Hakimi James J. Hsieh Etay Ziv Natasha Rekhtman Stephen B. Solomon Jeremy C. Durack Prospective Evaluation of Unprocessed Core Needle Biopsy DNA and RNA Yield from Lung, Liver, and Kidney Tumors: Implications for Cancer Genomics Analytical Cellular Pathology |
| title | Prospective Evaluation of Unprocessed Core Needle Biopsy DNA and RNA Yield from Lung, Liver, and Kidney Tumors: Implications for Cancer Genomics |
| title_full | Prospective Evaluation of Unprocessed Core Needle Biopsy DNA and RNA Yield from Lung, Liver, and Kidney Tumors: Implications for Cancer Genomics |
| title_fullStr | Prospective Evaluation of Unprocessed Core Needle Biopsy DNA and RNA Yield from Lung, Liver, and Kidney Tumors: Implications for Cancer Genomics |
| title_full_unstemmed | Prospective Evaluation of Unprocessed Core Needle Biopsy DNA and RNA Yield from Lung, Liver, and Kidney Tumors: Implications for Cancer Genomics |
| title_short | Prospective Evaluation of Unprocessed Core Needle Biopsy DNA and RNA Yield from Lung, Liver, and Kidney Tumors: Implications for Cancer Genomics |
| title_sort | prospective evaluation of unprocessed core needle biopsy dna and rna yield from lung liver and kidney tumors implications for cancer genomics |
| url | http://dx.doi.org/10.1155/2018/2898962 |
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