関: tandem repeat sequence

WordNet

do over; "They would like to take it over again" (同)take_over
an event that repeats; "the events today were a repeat of yesterdays" (同)repetition
to say again or imitate; "followers echoing the cries of their leaders" (同)echo
to say, state, or perform again; "She kept reiterating her request" (同)reiterate, ingeminate, iterate, restate, retell
one behind the other; "ride tandem on a bicycle built for two"; "riding horses down the path in tandem" (同)in tandem
an arrangement of two or more objects or persons one behind another

PrepTutorEJDIC

〈自分がすでに一度言ったこと)‘を'『繰り返して言う』 / 〈他人の言ったこと〉‘を'おうむ返しに言う;…‘を'他の人に繰り返して言う / …‘を'『暗記して言う』,暗唱する / …‘を'繰り返して行う(do again) / (食べたあとで)〈食物の〉味が残る / 〈小数が〉循環する / 繰り返すこと,反復すること / 繰り返されるもの,(公演の)再演;(番組の)再放送 / 反復楽節;反復記号(∥: :∥)
前後一留に; / 縦並びの,前後に座席のある / 縦につないだ2頭の馬;縦列2頭立ての馬車 / 二人乗り自転車
繰り返して言われる(行われる)

Wikipedia preview

出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2015/05/28 01:01:34」(JST)

wiki en

Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other.^[1] Several protein domains also form tandem repeats within their amino acid primary structure, such as Armadillo repeats. However, in proteins, perfect tandem repeats are unlikely in most in vivo proteins, and most known repeats are in proteins which have been designed.^[2]

An example would be:

ATTCG ATTCG ATTCG

in which the sequence ATTCG is repeated three times.

Terminology

When between 10 and 60 nucleotides are repeated, it is called a minisatellite. Those with fewer are known as microsatellites or short tandem repeats.

When exactly two nucleotides are repeated, it is called a dinucleotide repeat (for example: ACACACAC…). The microsatellite instability in hereditary nonpolyposis colon cancer most commonly affects such regions.^[3]

When three nucleotides are repeated, it is called a trinucleotide repeat (for example: CAGCAGCAGCAG…), and abnormalities in such regions can give rise to trinucleotide repeat disorders.

When the repeat unit copy number is variable in the population being considered, it is called a variable number tandem repeat (VNTR). MeSH classifies variable number tandem repeats under minisatellites.^[4]

Uses

Tandem repeat describes a pattern that helps determine an individual's inherited traits.

Tandem repeats can be very useful in determining parentage. Short tandem repeats are used for certain genealogical DNA tests.

DNA is examined from microsatellites within the chromosomal DNA. Minisatellite is another way of saying special regions of the loci. Polymerase chain reaction (or PCR) is performed on the minisatellite areas. The PCR must be performed on each organism being tested. The amplified material is then run through electrophoresis. By checking the percentage of bands that match, parentage is determined.

Polymorphic tandem repeats (alias VNTRs) are also present in microorganisms and can be used to trace the origin of an outbreak. The corresponding assay in which a collection of VNTRs is typed to characterize a strain is most often called MLVA (Multiple Loci VNTR Analysis).

In the field of Computer Science, tandem repeats in strings (e.g., DNA sequences) can be efficiently detected using suffix trees or suffix arrays.

Studies in 2004 linked the unusual genetic plasticity of dogs to mutations in tandem repeats.^[5]

References

^ Tandem Repeat at the US National Library of Medicine Medical Subject Headings (MeSH)
^ Jorda J, Xue B, Uversky VN, Kajava AV (June 2010). "Protein tandem repeats - the more perfect, the less structured". The FEBS Journal 277 (12): 2673–82. doi:10.1111/j.1742-464X.2010.07684.x. PMC 2928880. PMID 20553501.
^ Oki E, Oda S, Maehara Y, Sugimachi K (March 1999). "Mutated gene-specific phenotypes of dinucleotide repeat instability in human colorectal carcinoma cell lines deficient in DNA mismatch repair". Oncogene 18 (12): 2143–7. doi:10.1038/sj.onc.1202583. PMID 10321739.
^ Variable Number of Tandem Repeats at the US National Library of Medicine Medical Subject Headings (MeSH)
^ Pennisi E (December 2004). "Genetics. A ruff theory of evolution: gene stutters drive dog shape". Science 306 (5705): 2172. doi:10.1126/science.306.5705.2172. PMID 15618495.

External links

Examples:
- VNTRs - info and animated example
Databases:
- The Microorganisms Tandem Repeats Database
- Short Tandem Repeats Database
Search tools:
- Tandem Repeats Finder
- Mreps
- STAR
- TRED - Tandem Repeats over the Edit Distance
- TandemSWAN
- Microsatellite repeats finder
- JSTRING - Java Search for Tandem Repeats in genomes
- Phobos - a tandem repeat search tool for perfect and imperfect repeats - the maximum pattern size depends only on computational power
- UGENE - an ultra fast and memory efficient open-source tandem repeats finder implementation.

UpToDate Contents

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1. DNAによる親子鑑定 parentage testing using dna
2. 非メンデル遺伝のパターン non mendelian inheritance patterns
3. 遺伝的変異の概要 overview of genetic variation
4. 側頭動脈生検の手技 temporal artery biopsy technique
5. 遺伝学用語集 glossary of genetic terms

English Journal

Identification of novel BRCA founder mutations in Middle Eastern breast cancer patients using capture and Sanger sequencing analysis.

Bu R1, Siraj AK1, Al-Obaisi KA1, Beg S1, Al Hazmi M1, Ajarim D2, Tulbah A3, Al-Dayel F4, Al-Kuraya KS1.
International journal of cancer.Int J Cancer.2016 Sep 1;139(5):1091-7. doi: 10.1002/ijc.30143. Epub 2016 May 3.
Ethnic differences of breast cancer genomics have prompted us to investigate the spectra of BRCA1 and BRCA2 mutations in different populations. The prevalence and effect of BRCA 1 and BRCA 2 mutations in Middle Eastern population is not fully explored. To characterize the prevalence of BRCA mutation
PMID 27082205

Complete mitochondrial genome and phylogenic analysis of the mudskipper Scartelaos gigas (Perciformes, Gobiidae).

Li Z1, Zhang Y1, Chen S1, Chen W1, Hong W1.
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis.Mitochondrial DNA A DNA MappSeq Anal.2016 Sep;27(5):3812-4. doi: 10.3109/19401736.2015.1082089. Epub 2015 Oct 5.
In this paper, the complete mitochondrial genome sequence of Scartelaos gigas was firstly determined. The circular genome (16 717 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. The overall base composition of S. gigas is 28.9% for C, 28.3% for A, 26.4% fo
PMID 26436681

Complete mitochondrial genome of yellow-browed tit (Sylviparus modestus).

Wang X1, Huang Y1.
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis.Mitochondrial DNA A DNA MappSeq Anal.2016 Sep;27(5):3358-9. doi: 10.3109/19401736.2015.1018220. Epub 2015 Mar 13.
The complete mitochondrial genome of yellow-browed tit was 17,086 bp in length, and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region. In control region, a 117 bp long tandem repeat was identified, which was the first reported tandem repeats in tits.
PMID 25765087

Japanese Journal

Occurrence of Donor Cell-derived Lymphoid Blast Crisis 24 Years Following Related Bone Marrow Transplantation for Chronic Myeloid Leukemia

Internal Medicine 55(4), 395-397, 2016
NAID 130005125796

3500xL Genetic Analyzer による AmpFlSTR<sup>®</sup> Identifiler<sup>®</sup> PCR Amplification Kit を用いた口腔内細胞からの STR 型検査法の評価

日本法科学技術学会誌 21(1), 47-56, 2016
NAID 130005121052

GlobalFiler による STR 型検査の法科学的評価

日本法科学技術学会誌 21(1), 1-23, 2016
NAID 130005121051

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リンク元	「タンデム反復」「縦列反復」「タンデムリピート」
拡張検索	「short tandem repeat」「tandem repeat sequence」「variable number of tandem repeats」
関連記事	「repeat」「tandem」「repeated」