title: Filter Paper-based Nucleic Acid Storage in High-throughput Solid Tumor Genotyping.
abstract: Molecular testing of tumors from formalin-fixed paraffin-embedded (FFPE) tissue blocks is central to clinical practice; however, it requires histology support and increases test turnaround time. Prospective fresh frozen tissue collection requires special handling, additional storage space, and may not be feasible for small specimens. Filter paper-based collection of tumor DNA reduces the need for histology support, requires little storage space, and preserves high-quality nucleic acid. We investigated the performance of tumor smears on filter paper in solid tumor genotyping, as compared with paired FFPE samples. Whatman FTA Micro Card (FTA preps) smears were prepared from 21 fresh tumor samples. A corresponding cytology smear was used to assess tumor cellularity and necrosis. DNA was isolated from FTA preps and FFPE core samples using automated methods and quantified using SYBR green dsDNA detection. Samples were genotyped for 471 mutations on a mass spectrophotometry-based platform (Sequenom). DNA concentrations from FTA preps and FFPE correlated for untreated carcinomas but not for mesenchymal tumors (Spearman σ=0.39 and σ=-0.1, respectively). Average DNA concentrations were lower from FTA preps as compared with FFPE, but DNA quality was higher with less fragmentation. Seventy-six percent of FTA preps and 86% of FFPE samples generated adequate DNA for genotyping. FTA preps tended to perform poorly for collection of DNA from pretreated carcinomas and mesenchymal neoplasms. Of the 16 paired DNA samples that were genotyped, 15 (94%) gave entirely concordant results. Filter paper-based sample preservation is a feasible alternative to FFPE for use in automated, high-throughput genotyping of carcinomas.
authors.affiliation: *Brigham and Women's Hospital and Harvard Medical School †Dana Farber Cancer Institute, Boston, MA ‡Case Western Reserve School of Medicine, Cleveland, OH §University of Vermont College of Medicine, Burlington, VT ∥Mount Sinai Medical Center, New York, NY.
authors.forename: Matthew
authors.initials: M
authors.lastname: Stachler
authors.forename: Yonghui
authors.initials: Y
authors.lastname: Jia
authors.forename: Nematullah
authors.initials: N
authors.lastname: Sharaf
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Wade
authors.forename: Janina
authors.initials: J
authors.lastname: Longtine
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Garcia
authors.forename: Lynette M
authors.initials: LM
authors.lastname: Sholl
mesh_terms: D000230:Adenocarcinoma / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D052160:Benzothiazoles; D002294:Carcinoma, Squamous Cell / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D003110:Colonic Neoplasms / Q000175:diagnosis / Q000235:genetics / Q000473:pathology; D004273:DNA, Neoplasm / Q000302:isolation & purification*; D003959:Diamines; D005456:Fluorescent Dyes / Q000737:chemistry; D005557:Formaldehyde; D005838:Genotype; D060005:Genotyping Techniques / Q000592:standards*; D057166:High-Throughput Screening Assays; D006801:Humans; D007680:Kidney Neoplasms / Q000175:diagnosis / Q000235:genetics / Q000473:pathology; D008175:Lung Neoplasms / Q000175:diagnosis / Q000235:genetics / Q000473:pathology; D009930:Organic Chemicals / Q000737:chemistry; D010190:Pancreatic Neoplasms / Q000175:diagnosis / Q000235:genetics / Q000473:pathology; D010209:Paper; D011804:Quinolines; D011934:Reagent Strips / Q000737:chemistry*; D016610:Tissue Embedding; D016707:Tissue Fixation
chemical_list: D052160:Benzothiazoles; D004273:DNA, Neoplasm; D003959:Diamines; D005456:Fluorescent Dyes; D009930:Organic Chemicals; D011804:Quinolines; D011934:Reagent Strips; C098022:SYBR Green I; D005557:Formaldehyde