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Difference between revisions of "Molecular pathology"
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[[Image:G-Storm thermal cycler.jpg|thumb| | [[Image:G-Storm thermal cycler.jpg|thumb|300px|right|A thermal cycler used for PCR-based molecular testing. ([[WC]])]] | ||
'''Molecular pathology''' is the study of disease at the molecular level. It is becoming increasingly important in pathology. | '''Molecular pathology''' is the study of disease at the molecular level. It is becoming increasingly important in pathology. | ||
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| 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 | ||
|} | |} | ||
==Data formats== | |||
Human gene naming is provided by the HUGO Gene Nomenclature Committee: https://www.genenames.org/ | |||
DNA data repositories | |||
* NCBI: National Center for Biotechnology Information | |||
**Standard sequencing data is usually located in Nucleotide database: https://www.ncbi.nlm.nih.gov/nuccore | |||
**Next-gen sequencing data is in short read archive: https://www.ncbi.nlm.nih.gov/sra/docs/submit/ | |||
* EMBL: European Molecular Biology Laboratory | |||
* DDBJ: DNA Data Bank of Japan | |||
DNA sequence data formats | |||
* GenBank: human readable, can be processed by computer (fixed width, first 10 characters are an identifier). | |||
** NCBI Reference Sequence (RefSeq) project provides sequence records and related information. | |||
** Prefix AC_ in acession number is for genomic data, NM_ is for mRNA. | |||
* FASTA: Sequence information | |||
** Header starts with > and is followed by a sequence ID. | |||
** Sequence lines should wrap always at the same width. | |||
** Lower-case letters may indicate repetitive regions. | |||
* FASTQ: Current standard for sequencing data | |||
** It is essentially FASTA with quality values for the sequence. | |||
** Quality is on a scale from 0 - 40 and represented by a distinct character. | |||
** Upper case letters ABCDEFGHI means high quality. | |||
** Special letters !"#$%&'()*+,-. mean low quality. | |||
==Polymerase chain reaction-based techniques== | ==Polymerase chain reaction-based techniques== | ||
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:''PCR'' redirects here | :''PCR'' redirects here | ||
===General=== | ===General=== | ||
*A molecular technique to duplicate DNA molecules ("amplify") and allow the DNA sequence to be determined. | *A molecular technique to duplicate DNA (or RNA) molecules ("amplify") and allow the DNA (or RNA) sequence to be determined. | ||
Utility? | Utility? | ||
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==Miscellaneous stuff== | ==Miscellaneous stuff== | ||
===World protein databank=== | ===World protein databank=== | ||
The protein databank's goal is to maintain a free and publicly available archive.<ref>Worldwide Protein Data Bank. URL: [http://www.wwpdb.org/faq.html http://www.wwpdb.org/faq.html] Accessed on: April 22, 2009.</ref> Ironically, its announcement is in a pay-for-access journal (''Nature Structual Biology'').<ref name=pmid14634627>{{cite journal |author=Berman H, Henrick K, Nakamura H |title=Announcing the worldwide Protein Data Bank |journal=Nat. Struct. Biol. |volume=10 |issue=12 |pages=980 |year=2003 |month=December |pmid=14634627 |doi=10.1038/nsb1203-980 |url=}}</ref> | |||
===Wnt/beta-catenin pathway=== | ===Wnt/beta-catenin pathway=== | ||