ライフサイエンスコーパス: FFPE

1 A total of 22 FFPE liver specimens, 21 with hepatocellular carcinoma (

2 We confirmed accuracy using 249 FFPE cancer specimens characterized by established assay

3 For example, TMA analysis of 300 FFPE cores would typically require 6 h of total time thr

4 tion of a gene rearrangement panel using 319 FFPE samples showed 100% sensitivity (95% confidence lim

5 nine different areas microdissected from 32 FFPE UMs.

6 n tissue-derived prognostic signatures in 42 FFPE CRC samples measured by both platforms.

7 ) could extract fungal DNA from 69 of the 74 FFPE tissues from which a housekeeping gene could be amp

8 Tissue samples from 78 FFPE specimens with both histopathology and correspondin

9 n 3 cohorts, including 18 snap-frozen and 83 FFPE tissues.

10 140 samples, 47 fresh frozen samples and 93 FFPE samples, on HU133_Plus_2.0 and HuEx_1.0_st arrays,

11 Liver allograft FFPE C4d staining: (a) can help classify liver allograft

12 oducible microdissection of nuclei across an FFPE rat brain tissue section in milliseconds.

13 jor recommendations include submission of an FFPE block, whole blood, and serial serum or plasma from

14 The ability to retrospectively analyze FFPE tissues for DNA adducts may provide clues to the or

15 plicons both in snap-frozen (P = 0.0006) and FFPE (P = 0.0152) tissues.

16 profiles of a matched 10-year-old frozen and FFPE breast cancer sample.

17 mber alterations from small fresh-frozen and FFPE clinical tumor specimens, although some care must b

18 d in comparable yields from fresh-frozen and FFPE preserved tissues of rodents treated with the proca

19 mplification (WGA) kit to amplify frozen and FFPE tissue for use in array CGH (aCGH).

20 ingle short amplicon between snap-frozen and FFPE tissues was only 36%.

21 A from cell lines, fresh frozen material and FFPE samples to assess copy number variation.

22 h known CN, including tonsil, placentae, and FFPE melanoma cell lines.

23 t for each platform, gene or transcript, and FFPE processing regime.

24 and risk group in 108 (98%) of 110 archival FFPE biopsies.

25 ut high-quality DNA extraction from archival FFPE tissue specimens remains complex and time-consuming

26 aCGH application to a set of archival FFPE samples of skin squamous cell carcinomas detected a

27 teomics using very small amounts of archived FFPE tissue.

28 Eighty-one archived FFPE tissues with a positive Gomori methenamine silver (

29 We extracted DNA from 140 long-term archived FFPE samples using a simple but effective deparaffinizat

30 and X (13|X PRT) were tested using archived FFPE pathology samples with known CN, including tonsil,

31 nical diagnosis and prognosis using archived FFPE tissue.

32 ce most pathologic specimens are archived as FFPE samples, the ability to use them to generate expres

33 Because FFPE is a routine diagnostic sample preparation, the fea

34 that resulted in strong correlations between FFPE and frozen biospecimens may provide guidance when o

35 mbedded (FFPE) samples and validated in both FFPE and frozen tissues.

36 perience with performing AMP on 986 clinical FFPE samples, we show its potential as both a robust cli

37 ostate cancer patients and a set of clinical FFPE samples.

38 ured in tissue microarrays (TMAs) containing FFPE samples from two independent lung cancer cohorts (n

39 s of LISH-based assays using patient-derived FFPE tissue.

40 undertaken on routinely collected diagnostic FFPE tissue into stratification schemes for medulloblast

41 imens are formalin-fixed, paraffin embedded (FFPE) archival samples, making this type of tissue a pot

42 Formalin-fixed paraffin embedded (FFPE) material is the most widely available source of tu

43 ng formaldehyde fixed and paraffin embedded (FFPE) samples allows the utilization of the vast majorit

44 eserved in formalin fixed paraffin embedded (FFPE) sections, making it easier to identify cell types

45 Formalin-fixed, paraffin embedded (FFPE) tissue samples provide an invaluable resource for

46 (CN) using formalin fixed paraffin embedded (FFPE) tissue.

47 contrast, formalin-fixed paraffin embedded (FFPE) tissues frequently are accessible for biomarker di

48 ively from formalin fixed paraffin embedded (FFPE) tissues, signifying FFPE tissues can serve as bios

49 markers in formalin fixed paraffin embedded (FFPE) tissues.

50 Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is import

51 o utilize formalin-fixed, paraffin-embedded (FFPE) archival specimens reliably for high-resolution mo

52 available formalin-fixed paraffin-embedded (FFPE) biopsies.

53 PD-L1 on formalin-fixed, paraffin-embedded (FFPE) biopsy specimens from 48 cervical SCCs and 23 vulv

54 lied to 46 formalin-fixed/paraffin-embedded (FFPE) biopsy tissue specimens from well-characterized pa

55 including formalin-fixed paraffin-embedded (FFPE) blocks.

56 nes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identi

57 outine formalin-fixed and paraffin-embedded (FFPE) clinical specimens.

58 ofiles of formalin-fixed, paraffin-embedded (FFPE) clinical trial samples.

59 l archival formalin-fixed paraffin-embedded (FFPE) congenital cutaneous and hepatic hemangiomas, 4/8

60 orted that formalin-fixed paraffin-embedded (FFPE) DNA samples can yield spurious CNV calls in real-t

61 archival formalin-fixed, paraffin-embedded (FFPE) human tissue sections while preserving the microan

62 es and formalin-fixed and paraffin-embedded (FFPE) human tumors, as well as their functional role in

63 or are formalin-fixed and paraffin-embedded (FFPE) in order to maintain tissue morphology for histolo

64 Formalin-fixed, paraffin-embedded (FFPE) material tends to yield degraded DNA and is thus s

65 en and 23 formalin-fixed, paraffin-embedded (FFPE) MTCs was used for validation by RT-qPCR.

66 g from formalin-fixed and paraffin-embedded (FFPE) primary tumor specimens.

67 elapse in formalin-fixed, paraffin-embedded (FFPE) prostate cancers, through gene expression profilin

68 veloped in formalin-fixed paraffin-embedded (FFPE) samples and validated in both FFPE and frozen tiss

69 d from formalin-fixed and paraffin-embedded (FFPE) samples of 121 human gastrointestinal stromal tumo

70 nalysis of formalin-fixed paraffin-embedded (FFPE) samples, which largely precludes the analysis of m

71 regions of formalin-fixed paraffin-embedded (FFPE) sections underwent macrodissection, DNA extraction

72 cies from formalin-fixed, paraffin-embedded (FFPE) skin biopsy specimens.

73 archived formalin-fixed, paraffin-embedded (FFPE) specimens contain valuable molecular insight into

74 ic biopsy formalin-fixed, paraffin-embedded (FFPE) specimens from 120 patients with CUP were collecte

75 ing of formalin-fixed and paraffin-embedded (FFPE) specimens, banked from completed clinical trials a

76 d from 132 formalin-fixed paraffin-embedded (FFPE) specimens.

77 processed formalin-fixed, paraffin-embedded (FFPE) specimens.

78 input from formalin-fixed paraffin-embedded (FFPE) specimens.

79 Formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens are a valuable resource for mo

80 Archived formalin-fixed paraffin-embedded (FFPE) tissue collections represent a valuable informatio

81 ession and formalin-fixed paraffin-embedded (FFPE) tissue datasets.

82 Using formalin-fixed paraffin-embedded (FFPE) tissue for immunohistochemistry, fluorescent in si

83 ns such as formalin-fixed paraffin-embedded (FFPE) tissue for molecular mechanisms of disease progres

84 ulatum in formalin-fixed, paraffin-embedded (FFPE) tissue is described.

85 A from formalin-fixed and paraffin-embedded (FFPE) tissue remains a challenge, despite numerous attem

86 Formalin-fixed paraffin-embedded (FFPE) tissue samples are a potentially valuable resource

87 matin from formalin-fixed paraffin-embedded (FFPE) tissue samples for accurate detection of histone m

88 nalysis of formalin-fixed paraffin-embedded (FFPE) tissue samples.

89 processed formalin-fixed, paraffin-embedded (FFPE) tissue section soaked in a polyethylene glycol sol

90 tion from formalin-fixed, paraffin-embedded (FFPE) tissue sections.

91 vered from formalin-fixed paraffin-embedded (FFPE) tissue slides are suitable for scDNase-seq assays.

92 tings, formalin-fixed and paraffin-embedded (FFPE) tissue specimens are collected routinely and there

93 ng of (1) formalin-fixed, paraffin-embedded (FFPE) tissue; (2) blood and its components; and (3) fres

94 RNAs)) in formalin-fixed, paraffin-embedded (FFPE) tissues and cultured cells, using locked nucleic a

95 fresh and formalin-fixed, paraffin-embedded (FFPE) tissues and sterile body fluids with known diagnos

96 Formalin-fixed paraffin-embedded (FFPE) tissues are important resources for molecular medi

97 this onto formalin-fixed paraffin-embedded (FFPE) tissues for MALDI imaging of N-glycans.

98 ction from formalin-fixed paraffin-embedded (FFPE) tissues is difficult and requires special protocol

99 contrast, formalin-fixed paraffin-embedded (FFPE) tissues with clinical diagnosis are readily access

100 acking on formalin-fixed, paraffin-embedded (FFPE) tissues, and particularly for microRNA (miRNA) ana

101 ization in formalin-fixed paraffin-embedded (FFPE) tissues, we developed multicolor miRNA FISH.

102 ohilum in formalin-fixed, paraffin-embedded (FFPE) tissues.

103 yeasts in formalin-fixed paraffin-embedded (FFPE) tissues.

104 archived, formalin-fixed paraffin-embedded (FFPE) tumor samples for massive parallel sequencing has

105 ort of 41 formalin-fixed, paraffin-embedded (FFPE) uveal melanomas, whose chromosome 3 status had bee

106 formed on formalin-fixed, paraffin-embedded (FFPE) whole tumor sections from 19 disomy 3 metastasizin

107 mples are Formalin-Fixed, Paraffin-Embedded (FFPE).

108 ia formalin fixation and paraffin embedding (FFPE).

109 by formalin-fixation and paraffin-embedding (FFPE).

110 utral phosphate-buffered formalin, pH 7) for FFPE tissue across trials.

111 ewly developed and validated MCL35 assay for FFPE biopsies uses the proliferation signature to define

112 d a reliable rapid DNA extraction method for FFPE tissue specimens.

113 ch include: the designing of PCR primers for FFPE tumor tissue samples versus normal blood samples, d

114 igh-throughput gene expression profiling for FFPE samples.

115 ance when optimizing molecular protocols for FFPE use; however, discrepancies reported for similar as

116 efficiency and reliability were reduced for FFPE DNA when compared with fresh samples, closer examin

117 are high-quality cDNA from highly fragmented FFPE-RNA, previously precluded from high-throughput anal

118 n material (Pearson's R(2) = 0.898) and from FFPE (R(2) = 0.883).

119 We demonstrate that FiT-seq data from FFPE specimens are concordant with ChIP-seq data from fr

120 (LOH), and copy number for DNA derived from FFPE tissues using oligonucleotide microarrays containin

121 fungal assay identifies fungi directly from FFPE tissues and can be a useful adjunct to traditional

122 -PCR analysis of p15, RNA was extracted from FFPE sections from 14 nevus and melanoma samples via mac

123 aid in the diagnosis of histoplasmosis from FFPE tissue.

124 thod to quantitatively retrieve dA-AL-I from FFPE tissue.

125 ddition, sequence variations identified from FFPE RNA show 99.67% concordance with that from exome se

126 on individual cell populations isolated from FFPE tissue sections using laser capture microdissection

127 ity RNA samples, such as those isolated from FFPE tissue, remains a challenge.

128 ing as little as 5 ng starting material from FFPE (R(2) = 0.918).

129 enomic and expression profiles obtained from FFPE biospecimens accurately reflect the physiologic con

130 ntly high quality RNA could be obtained from FFPE tumor tissues to detect frozen tissue-derived progn

131 7-oligo-dT24-VN-DNA sequences, obtained from FFPE-RNA, are used as primers for the RT of complementar

132 ocols for DNA extraction and processing from FFPE tissues utilizing DNase processing to generate rand

133 analysis to generate proteomic profiles from FFPE samples of intestinal-type gastric cancer, metaplas

134 Capture transcriptome profiling from FFPE revealed two oncogenic fusions: the pathognomonic N

135 ldwide, can be recovered quantitatively from FFPE tissues.

136 the technology of DNA adduct retrieval from FFPE tissue clear the way for use of archived pathology

137 for the extraction and isolation of RNA from FFPE samples.

138 Recovery of good quality RNA from FFPE sections can be challenging, however, recent studie

139 specific at discriminating each species from FFPE controls of unrelated bacterial, viral, protozoan,

140 ve for expression profiling in heterogeneous FFPE tissues for cancer diagnosis/prognosis biomarker di

141 oString technology, RNA from 40 stage II-III FFPE primary melanomas was analyzed and a 53-immune-gene

142 and CISH analyses of genetic aberrations in FFPE tissue, including TMAs.

143 oof of principle for copy number analysis in FFPE samples.

144 reater sensitivity than nested PCR assays in FFPE tissues and provides an effective method to specifi

145 efore, PRTs are suitable for analyzing CN in FFPE tissues.

146 High expression of CXCL1 in FFPE samples from explant cultures of CRC patients-deriv

147 antigens, and PCR identified Exserohilum in FFPE and fresh tissues.

148 lar detection and identification of fungi in FFPE tissue.

149 sensitive method for detection of fungus in FFPE tissues, demonstrating both hyphal forms and granul

150 alence and characteristics of HPV genomes in FFPE tissue from the cervices of 99 women undergoing hys

151 GenomePlex kit) in FFPE normal and tumor tissue specimens.

152 aristolochic acids (AAs) can be measured in FFPE tissues at a level of sensitivity comparable to fre

153 studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation seq

154 it may not detect certain abundant miRNAs in FFPE tissue.

155 zation of differentially expressed miRNAs in FFPE tumor tissues.

156 In an effort to detect various mutations in FFPE tissue samples among multiple solid tumor types for

157 PA can detect monosomy 3 cell populations in FFPE whole tumor sections previously missed by FISH perf

158 describe a protocol for analyzing protein in FFPE-TMAs using matrix-assisted laser desorption/ionizat

159 he possibility of long RNA quantification in FFPE tissues, we selected 14 target RNAs (8 mRNAs and 6

160 er, long-chain RNA analysis is restricted in FFPE tissues due to high levels of degradation.

161 PCR (LD-PCR) for the detection of HCV RNA in FFPE liver tissue.

162 apping short amplicons for 14 target RNAs in FFPE tissues.

163 ozen tissue-derived prognostic signatures in FFPE CRC samples, we evaluated the expression of 516 gen

164 nes with high sensitivity and specificity in FFPE biopsy tissue specimens.

165 novel MSI method to image protein targets in FFPE tissue samples.

166 high correlation between frozen and matched FFPE samples (R(2) between 0.82 and 0.89), while the sig

167 er tumors archived for >11 years as 5 microm FFPE sections and matched germline DNA.

168 ) and ITS4 primers yielded a product in most FFPE tissues.

169 We used mouse FFPE inner ear sections to procure distinct populations

170 Thus, a method developed using mouse FFPE tissue can be applied to human archival temporal bo

171 Multiple FFPE core biopsies can be assembled in a single block to

172 A 40-mum FFPE tissue section from each specimen was digested with

173 ion data for colon and lung tumor and normal FFPE samples and matched frozen samples and found a high

174 ature genes from tumor versus matched normal FFPE tissue from colon and lung were identified as cance

175 PE DNA on the microarrays better than age of FFPE sample.

176 The tumor samples show differing amounts of FFPE damaged DNA sequencing reads revealed as relatively

177 detectable by direct T7 IVT-amplification of FFPE-RNA.

178 ming genome-wide deep sequencing analysis of FFPE archived tumors of limited sample size such as resi

179 ble to carry out gene expression analysis of FFPE material.

180 LISH analysis of FFPE RNA is a novel methodology with broad applications

181 alternative methodology for the analysis of FFPE RNA.

182 The direct analysis of FFPE-TMA tissue using IMS allows direct analysis of mult

183 chniques to examine the molecular content of FFPE tissue, mass spectrometry imaging (MSI) is the most

184 rrays (TMAs) consisting of multiple cores of FFPE material are being used to enable simultaneous anal

185 a workflow for rapid analysis of hundreds of FFPE tissue specimens.

186 nally reduced once the CT value for 10 ng of FFPE DNA increased above 30 cycles, reflecting importanc

187 ifying PCR test predicted the performance of FFPE DNA on the microarrays better than age of FFPE samp

188 ce somatic mutations even in the presence of FFPE induced DNA damage.

189 ss protocol reliability over a wide range of FFPE samples.

190 RK-10 shows staining in the tumor regions of FFPE tissues where the SP263 kit does not.

191 gnostic archives are an enormous resource of FFPE tissue, but extracted DNA is of poor quality and ma

192 Overall, 71 samples of FFPE tissue from cases of cervical SCCs (n = 48) and vul

193 measured in 10-mum thick tissue-sections of FFPE kidney from patients with upper urinary tract cance

194 nd follow this up with data from a series of FFPE biopsies and surgical samples.

195 Study limitations include the use of FFPE samples, which do not always provide high-quality D

196 We also tested the method described above on FFPE sections from human crista ampullaris.

197 otein expression at the single-cell level on FFPE patient samples.

198 histochemistry for alphaSMA was performed on FFPE sections and subsequently quantified via digital im

199 ue proteomic analyses have been performed on FFPE tissues using advanced mass spectrometry (MS) techn

200 tation of the immunofluorescence workflow on FFPE sections milled at histological thickness, cellular

201 ent copy number and LOH profiles from paired FFPE and fresh frozen tumor samples.

202 Single endoscopic pinch FFPE biopsies (n = 41) were sampled at both active and i

203 ing were developed for blood, serum, plasma, FFPE, and fresh/frozen tissue.

204 lated on split-sample (portion fresh/portion FFPE) of colorectal tumor samples.

205 ng short amplicons in standardized-preserved FFPE tissues.

206 The locked assay was applied to pretreatment FFPE lymph node biopsies from an independent cohort of 1

207 and that the model can be applied to routine FFPE tissue from initial diagnostic biopsies.

208 enotypes microdissected from within the same FFPE sample.

209 N-linked glycans and proteins from the same FFPE tissue section.

210 Methods Forty-seven FFPE biopsies were used to train an assay on the NanoStr

211 paraffin embedded (FFPE) tissues, signifying FFPE tissues can serve as biospecimens for carcinogen DN

212 the lack of antibodies suitable for staining FFPE tissue, primarily due to the inaccessibility of the

213 The FFPE process results in fragmentation and chemical modif

214 For the normalized copy number analysis, the FFPE process caused none or very minimal bias.

215 form hybrids with HCV RNAs released from the FFPE tissue.

216 in formalin-fixed paraffin-embedded tissues (FFPE) from donor-specific antibody-positive (DSA+) renal

217 of formalin-fixed paraffin-embedded tissues (FFPE) is increasingly recognized as a strategy for the d

218 The protocols are applied to FFPE clinical samples of varied tumor types, from multip

219 conversion that should extend, generally, to FFPE and other types of samples intended for any analyti

220 us strains (DMV, PWMV and novel CeMVs) using FFPE samples from 1996 to 2011.

221 w accepted that proteomics can be done using FFPE tissue and can generate similar results as snap-fro

222 xpression profiling assay was feasible using FFPE biopsy specimens and identified a putative tissue o

223 Assay validation was performed using FFPE preparations of cell lines with known SOX2 expressi

224 correspondence with disease phenotype, using FFPE diagnostic surgical pathology specimens.

225 esions by generating proteome profiles using FFPE samples.

226 Thus, proteomic profiling using FFPE samples has led to the identification of two novel

227 and confidence in the results obtained with FFPE biospecimens.

228 validating protocols optimized for use with FFPE specimens with a case-matched fresh or frozen cohor

229 hat the Mapping 500K arrays can be used with FFPE-derived samples to produce genotype, copy number, a