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Difference between revisions of "Molecular pathology"
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→Overview: tweak pricing, FISH $$ > DNA $$
(→See also: +link) |
m (→Overview: tweak pricing, FISH $$ > DNA $$) |
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| PCR, sequencing machine | | PCR, sequencing machine | ||
| any (small) DNA change in the genome; does not account for post-transcriptional changes (one cannot definitively infer protein level change) | | any (small) DNA change in the genome; does not account for post-transcriptional changes (one cannot definitively infer protein level change) | ||
| | | $$$ | ||
| gold standard; will not detect large scale changes unless the break points/fusion regions are sequenced | | gold standard; will not detect large scale changes unless the break points/fusion regions are sequenced | ||
|- | |- | ||
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| any change in the mRNA (post-splicing); useful for infering protein level changes | | any change in the mRNA (post-splicing); useful for infering protein level changes | ||
| $$$ | | $$$ | ||
| less costly than DNA sequencing - as extrons are not sequenced | | slightly less costly than DNA sequencing - as the extrons are not sequenced | ||
|- | |- | ||
| Restriction fragment length polymorphism (RFLP) | | Restriction fragment length polymorphism (RFLP) | ||
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| gel electrophoresis, hybridization probe with label | | gel electrophoresis, hybridization probe with label | ||
| useful for finding a specific known change, quantifying gene copy number | | useful for finding a specific known change, quantifying gene copy number | ||
| $$$$ | | $$$$$ | ||
| -rarely done<br>-does '''not''' use PCR<br>-considered the gold standard for clonality<ref name=pmid10583924>{{Cite journal | last1 = Medeiros | first1 = LJ. | last2 = Carr | first2 = J. | title = Overview of the role of molecular methods in the diagnosis of malignant lymphomas. | journal = Arch Pathol Lab Med | volume = 123 | issue = 12 | pages = 1189-207 | month = Dec | year = 1999 | doi = 10.1043/0003-9985(1999)1231189:OOTROM2.0.CO;2 | PMID = 10583924 }}</ref><br>-most labs consider fresh or frozen tissue a requirement<ref name=pmid11070157>{{Cite journal | last1 = Reinartz | first1 = JJ. | last2 = McCormick | first2 = SR. | last3 = Ikier | first3 = DM. | last4 = Mellgen | first4 = AM. | last5 = Bonham | first5 = SC. | last6 = Strickler | first6 = JG. | last7 = Mendiola | first7 = JR. | title = Immunoglobulin heavy-chain gene rearrangement studies by Southern blot using DNA extracted from formalin-fixed, paraffin-embedded tissue. | journal = Mol Diagn | volume = 5 | issue = 3 | pages = 227-33 | month = Sep | year = 2000 | doi = 10.1054/modi.2000.19808 | PMID = 11070157 }}</ref> | | -rarely done<br>-does '''not''' use PCR<br>-considered the gold standard for clonality<ref name=pmid10583924>{{Cite journal | last1 = Medeiros | first1 = LJ. | last2 = Carr | first2 = J. | title = Overview of the role of molecular methods in the diagnosis of malignant lymphomas. | journal = Arch Pathol Lab Med | volume = 123 | issue = 12 | pages = 1189-207 | month = Dec | year = 1999 | doi = 10.1043/0003-9985(1999)1231189:OOTROM2.0.CO;2 | PMID = 10583924 }}</ref><br>-most labs consider fresh or frozen tissue a requirement<ref name=pmid11070157>{{Cite journal | last1 = Reinartz | first1 = JJ. | last2 = McCormick | first2 = SR. | last3 = Ikier | first3 = DM. | last4 = Mellgen | first4 = AM. | last5 = Bonham | first5 = SC. | last6 = Strickler | first6 = JG. | last7 = Mendiola | first7 = JR. | title = Immunoglobulin heavy-chain gene rearrangement studies by Southern blot using DNA extracted from formalin-fixed, paraffin-embedded tissue. | journal = Mol Diagn | volume = 5 | issue = 3 | pages = 227-33 | month = Sep | year = 2000 | doi = 10.1054/modi.2000.19808 | PMID = 11070157 }}</ref> | ||
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| probes label two parts of a (normal) gene; the two markers straddle (common) break points | | probes label two parts of a (normal) gene; the two markers straddle (common) break points | ||
| gene fragmentation consistent with translocation; one may find: gene duplication (or chromosomal duplication), gene loss (or chromosome loss) | | gene fragmentation consistent with translocation; one may find: gene duplication (or chromosomal duplication), gene loss (or chromosome loss) | ||
| $$$ | | $$$$ | ||
| can detect translocations - without knowing the specific fusion product | | can detect translocations - without knowing the specific fusion product | ||
|- | |- | ||
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| probes label different genes (that are not adjacent) | | probes label different genes (that are not adjacent) | ||
| translocation involving the two genes labeled; one may find: gene duplication (or chromosomal duplication), gene loss (or chromosome loss) | | translocation involving the two genes labeled; one may find: gene duplication (or chromosomal duplication), gene loss (or chromosome loss) | ||
| $$$ | | $$$$ | ||
| can detect one specific translocation | | can detect one specific translocation | ||
|- | |- | ||
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| probe labels one region (gene) | | probe labels one region (gene) | ||
| gene duplication (or chromosomal duplication), gene loss (or chromosome loss) | | gene duplication (or chromosomal duplication), gene loss (or chromosome loss) | ||
| $$ | | $$$ | ||
| | | | ||
|- | |- | ||
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| metaphase nuclei | | metaphase nuclei | ||
| large scale changes (fusions, deletions, translocations) | | large scale changes (fusions, deletions, translocations) | ||
| $$$ | | $$$$ | ||
| gives the "big picture" view of all the (nuclear) DNA | | gives the "big picture" view of all the (nuclear) DNA | ||
|- | |- | ||
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| probe labels one region (one colour) ''or'' probes label two parts of a (normal) gene (two colours) ''or'' probes label different genes (two colours) | | probe labels one region (one colour) ''or'' probes label two parts of a (normal) gene (two colours) ''or'' probes label different genes (two colours) | ||
| gene duplication, gene loss, translocations | | gene duplication, gene loss, translocations | ||
| $$$$ | | $$$$$ | ||
| rarely done; follows karyotyping to better characterize unusual cases; can be thought of as a karyotype and a simultaneous ISH | | rarely done; follows karyotyping to better characterize unusual cases; can be thought of as a karyotype and a simultaneous ISH | ||
|} | |} | ||