Molecular pathology - Revision history

Michael at 20:24, 11 October 2023

2023-10-11T20:24:01Z

2019-05-03T11:02:18Z

Data formats: NCBI repositories

← Older revision		Revision as of 11:02, 3 May 2019
Line 126:		Line 126:
	DNA data repositories		DNA data repositories
	* NCBI: National Center for Biotechnology Information		* 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		* EMBL: European Molecular Biology Laboratory
	* DDBJ: DNA Data Bank of Japan		* DDBJ: DNA Data Bank of Japan

2019-05-03T10:58:10Z

Molecular data formats: Some basic informations

← Older revision		Revision as of 10:58, 3 May 2019
Line 119:		Line 119:
	\| 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
			* 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==

2015-07-24T17:52:49Z

World protein databank: tweak

← Older revision		Revision as of 17:52, 24 July 2015
Line 169:		Line 169:
	==Miscellaneous stuff==		==Miscellaneous stuff==
	===World protein databank===		===World protein databank===
	~~I can't help think it is ironic that the~~ protein databank 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> ~~yet the~~ announcement is in 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>		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===

2015-07-24T17:50:37Z

← Older revision		Revision as of 17:50, 24 July 2015
Line 1:		Line 1:
	[[Image:G-Storm thermal cycler.jpg\|thumb\|~~200px~~\|right\|A thermal cycler used for PCR-based molecular testing. ([[WC]])]]		[[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.

2015-07-24T17:49:41Z

Polymerase chain reaction-based techniques

← Older revision		Revision as of 17:49, 24 July 2015
Line 124:		Line 124:
	:''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?

2015-07-24T17:48:21Z

Polymerase chain reaction-based techniques

← Older revision		Revision as of 17:48, 24 July 2015
Line 122:		Line 122:
	==Polymerase chain reaction-based techniques==		==Polymerase chain reaction-based techniques==
	:Abbreviated ''PCR-based techniques''		:Abbreviated ''PCR-based techniques''
			:''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 molecules ("amplify") and allow the DNA sequence to be determined.

2015-07-24T17:48:00Z

Polymerase chain reaction-based techniques

← Older revision		Revision as of 17:48, 24 July 2015
Line 121:		Line 121:

	==Polymerase chain reaction-based techniques==		==Polymerase chain reaction-based techniques==
	:Abbreviated ''PCR-based techniques''.		:Abbreviated ''PCR-based techniques''
	===General===		===General===
	*A molecular technique to duplicate DNA molecules ("amplify") and allow the DNA sequence to be determined.		*A molecular technique to duplicate DNA molecules ("amplify") and allow the DNA sequence to be determined.

2015-07-24T17:46:56Z

Polymerase chain reaction-based techniques

← Older revision		Revision as of 17:46, 24 July 2015
Line 121:		Line 121:

	==Polymerase chain reaction-based techniques==		==Polymerase chain reaction-based techniques==
	:Abbreviated ''PCR'''.		:Abbreviated ''PCR-based techniques''.
	===General===		===General===
	*A molecular technique to duplicate DNA molecules ("amplify") and allow the DNA sequence to be determined.		*A molecular technique to duplicate DNA molecules ("amplify") and allow the DNA sequence to be determined.

2015-07-24T17:46:28Z

PCR-based techniques: tweak

← Older revision		Revision as of 17:46, 24 July 2015
Line 120:		Line 120:
	\|}		\|}

	==~~PCR~~-based techniques==		==Polymerase chain reaction-based techniques==
			:Abbreviated ''PCR'''.
	===General===		===General===
	~~What~~?		*A molecular technique to duplicate DNA molecules ("amplify") and allow the DNA sequence to be determined.
	*~~Very~~ small changes - submicroscopic.
			Utility?
			*Detect very small molecular changes - submicroscopic.
	**Changes in sequence - may be as small as one base pair.		**Changes in sequence - may be as small as one base pair.
	*Used to confirmation [[chromosomal translocation]]s that are, in clinical practice, usually found with other techniques.		*Used to confirmation [[chromosomal translocation]]s that are, in clinical practice, usually found with other techniques.