Pathology materials useful for epidemiologic studies of lymphoid neoplasms
| Applications . | Material needed . | Preferred specimen(s) . | Collection media . | Method(s) . |
|---|---|---|---|---|
| Tumor cell phenotyping | Protein | Tumor tissue, blood lymphocytes, bone marrow aspirates, malignant effusions | FFPE tissue, frozen tissue, fresh cells in tissue culture media, or glass tubes with anticoagulant (EDTA or heparin) | Flow cytometry or immunohistochemistry |
| Chromosomal abnormalities, such as translocations, gains, deletions, gene amplifications | DNA | Tumor tissue | FFPE tissue, fresh tissue, blood cells, bone marrow aspirates | FISH, genomic SNP/CN arrays, real-time PCR, LDI-PCR, genome sequencing |
| Detection of tumor oncogene products, receptors for growth factors, cytokines | Protein | Tumor tissue, tissue microarrays | FFPE tissue, fresh or frozen tissue | Immunohistochemistry, Western blot, flow cytometry, real-time PCR |
| Quantitative gene expression | mRNA, cDNA | Tumor tissue | FFPE tissue, fresh or frozen tissue or cells; use of RNA preservative, such as RNA trizol | Real-time PCR, cDNA microarrays, other hybridization platforms, transcriptome sequencing |
| Detect single-stranded RNAs (typically 21-23 nucleotides long) that regulate gene expression | Micro-RNAs | Tumor tissue | FFPE tissue, fresh or frozen tissue or cells | Real-time PCR, quantitative PCR, Northern blot, miRNA-profiling |
| Detection of gene polymorphisms; single-nucleotide polymorphisms (SNPs); DNA sequencing | DNA | Blood leukocytes, buccal smears | Blood clots, buffy coats, buccal cell samples | Multiple genotyping and sequencing platforms |
| Viral antibody detection | Serum or plasma | Clotted blood or serum | Blood-collection tubes with EDTA or ACD | ELISA, real-time PCR, immunofluorescence |
| Serum markers, such as cytokines, growth factors, vitamin levels, chemicals, etc. | Serum or plasma | Peripheral blood | Blood-collection tube, glass with EDTA or ACD | ELISA, mass spectroscopy |
| Proteomic biomarkers | Serum or plasma | Peripheral blood | Blood-collection tube, glass with EDTA or ACD | Mass spectroscopy |
| Applications . | Material needed . | Preferred specimen(s) . | Collection media . | Method(s) . |
|---|---|---|---|---|
| Tumor cell phenotyping | Protein | Tumor tissue, blood lymphocytes, bone marrow aspirates, malignant effusions | FFPE tissue, frozen tissue, fresh cells in tissue culture media, or glass tubes with anticoagulant (EDTA or heparin) | Flow cytometry or immunohistochemistry |
| Chromosomal abnormalities, such as translocations, gains, deletions, gene amplifications | DNA | Tumor tissue | FFPE tissue, fresh tissue, blood cells, bone marrow aspirates | FISH, genomic SNP/CN arrays, real-time PCR, LDI-PCR, genome sequencing |
| Detection of tumor oncogene products, receptors for growth factors, cytokines | Protein | Tumor tissue, tissue microarrays | FFPE tissue, fresh or frozen tissue | Immunohistochemistry, Western blot, flow cytometry, real-time PCR |
| Quantitative gene expression | mRNA, cDNA | Tumor tissue | FFPE tissue, fresh or frozen tissue or cells; use of RNA preservative, such as RNA trizol | Real-time PCR, cDNA microarrays, other hybridization platforms, transcriptome sequencing |
| Detect single-stranded RNAs (typically 21-23 nucleotides long) that regulate gene expression | Micro-RNAs | Tumor tissue | FFPE tissue, fresh or frozen tissue or cells | Real-time PCR, quantitative PCR, Northern blot, miRNA-profiling |
| Detection of gene polymorphisms; single-nucleotide polymorphisms (SNPs); DNA sequencing | DNA | Blood leukocytes, buccal smears | Blood clots, buffy coats, buccal cell samples | Multiple genotyping and sequencing platforms |
| Viral antibody detection | Serum or plasma | Clotted blood or serum | Blood-collection tubes with EDTA or ACD | ELISA, real-time PCR, immunofluorescence |
| Serum markers, such as cytokines, growth factors, vitamin levels, chemicals, etc. | Serum or plasma | Peripheral blood | Blood-collection tube, glass with EDTA or ACD | ELISA, mass spectroscopy |
| Proteomic biomarkers | Serum or plasma | Peripheral blood | Blood-collection tube, glass with EDTA or ACD | Mass spectroscopy |
Abbreviations: FFPE, formalin-fixed paraffin embedded; FISH, fluorescence in situ hybridization; SNP, single-nucleotide polymorphism; CN, copy number; PCR, polymerase chain reaction; LDI-PCR, long-distance-inverse PCR; miRNA, micro-RNA; ACD, acid citrate dextrose; EDTA, ethylenediamine tetra-acetic acid; ELISA, enzyme-linked immunosorbent assay.