SNP array: Difference between revisions

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{{See also|DNA microarray|SNP genotyping}}

{{expert needed|Computational Biology|date=April 2016}}

In [[molecular biology]], '''SNP array''' is a type of [[DNA microarray]] which is used to detect [[Polymorphism (biology)|polymorphisms]] within a population. A [[single nucleotide polymorphism]] (SNP), a variation at a single site in [[DNA]], is the most frequent type of variation in the genome. Around 325 million SNPs have been identified in the [[human genome]],<ref>{{cite web|title=dbSNP Summary|url=https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi|website=www.ncbi.nlm.nih.gov|accessdate=4 October 2017}}</ref> 15 million of which are present at frequencies of 1% or higher across different populations worldwide.<ref name="DurbinAltshuler2010">{{cite journal|last1=Durbin|first1=Richard M.|last2=Altshuler|first2=David L.|last3=Durbin|first3=Richard M.|last4=Abecasis|first4=Gonçalo R.|last5=Bentley|first5=David R.|last6=Chakravarti|first6=Aravinda|last7=Clark|first7=Andrew G.|last8=Collins|first8=Francis S.|last9=De La Vega|first9=Francisco M.|last10=Donnelly|first10=Peter|last11=Egholm|first11=Michael|last12=Flicek|first12=Paul|last13=Gabriel|first13=Stacey B.|last14=Gibbs|first14=Richard A.|last15=Knoppers|first15=Bartha M.|last16=Lander|first16=Eric S.|last17=Lehrach|first17=Hans|last18=Mardis|first18=Elaine R.|last19=McVean|first19=Gil 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In [[molecular biology]], '''SNP array''' is a type of [[DNA microarray]] which is used to detect [[Polymorphism (biology)|polymorphisms]] within a population. A [[single nucleotide polymorphism]] (SNP), a variation at a single site in [[DNA]], is the most frequent type of variation in the genome. Around 325 million SNPs have been identified in the [[human genome]],<ref>{{cite web|title=dbSNP Summary|url=https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi|website=www.ncbi.nlm.nih.gov|accessdate=4 October 2017}}</ref> 15 million of which are present at frequencies of 1% or higher across different populations worldwide.<ref>{{cite journal|author=The 1000 Genomes Project Consortium|title=A map of human genome variation from population-scale sequencing|journal=Nature|date=28 October 2010|volume=467|issue=7319|pages=1061–1073|doi=10.1038/nature09534}}</ref>

==Principles==

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# A detection system that records and interprets the [[DNA-DNA hybridization|hybridization]] signal.

The ASO probes are often chosen based on sequencing of a representative panel of individuals: positions found to vary in the panel at a specified frequency are used as the basis for probes. SNP chips are generally described by the number of SNP positions they assay. Two probes must be used for each SNP position to detect both alleles; if only one probe were used, experimental failure would be indistinguishable from [[homozygosity]] of the non-probed allele.<ref>{{cite book|first1=ed. by Ralph| last1=Rapley|first2=Stuart|last2=Harbron|title=Molecular analysis and genome discovery|date=2004|publisher=Wiley|___location=Chichester [u.a.]|isbn=0-471-49919-6}}</ref>

==Applications==

[[File:LRR and BAF profiles for the T47D breast cancer cell line top.svg|right|thumb|DNA copy number profile for the T47D breast cancer cell line (Affymetrix SNP Array)]]

[[File:LRR and BAF profiles for the T47D breast cancer cell line bottom.svg|thumb|LOH profile for the T47D breast cancer cell line (Affymetrix SNP Array)]]

An SNP array is a useful tool for studying slight variations between whole [[genomes]]. The most important clinical applications of SNP arrays are for determining disease susceptibility<ref>{{cite journal|last1=Schaaf|first1=Christian P.|last2=Wiszniewska|first2=Joanna|last3=Beaudet|first3=Arthur L.|title=Copy Number and SNP Arrays in Clinical Diagnostics|journal=Annual Review of Genomics and Human Genetics|date=22 September 2011|volume=12|issue=1|pages=25–51|doi=10.1146/annurev-genom-092010-110715}}</ref> and for measuring the efficacy of drug therapies designed specifically for individuals.<ref>{{cite journal|last1=Alwi|first1=Zilfalil Bin|title=The Use of SNPs in Pharmacogenomics Studies|journal=The Malaysian Journal of Medical Sciences : MJMS|date=2005|volume=12|issue=2|pages=4–12|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3349395/|issn=1394-195X}}</ref> In research, SNP arrays are most frequently used for [[genome-wide association studies]].<ref name="GibbsBelmont2003">{{cite journal|authorlast1=TheGibbs|first1=Richard InternationalA.|last2=Belmont|first2=John HapMapW.|last3=Hardenbol|first3=Paul|last4=Willis|first4=Thomas ConsortiumD.|last5=Yu|first5=Fuli|last6=Zhang|first6=Houcan|last7=Zeng|first7=Changqing|last8=Matsuda|first8=Ichiro|last9=Fukushima|first9=Yoshimitsu|last10=Macer|first10=Darryl R.|last11=Suda|first11=Eiko|last12=Stein|first12=Lincoln D.|last13=Cunningham|first13=Fiona|last14=Kanani|first14=Ardavan|last15=Thorisson|first15=Gudmundur A.|last16=Chakravarti|first16=Aravinda|last17=Chen|first17=Peter E.|last18=Cutler|first18=David J.|last19=Kashuk|first19=Carl S.|last20=Donnelly|first20=Peter|last21=Marchini|first21=Jonathan|last22=McVean|first22=Gilean A. T.|last23=Myers|first23=Simon R.|last24=Cardon|first24=Lon R.|last25=Abecasis|first25=Gonçalo R.|last26=Morris|first26=Andrew|last27=Weir|first27=Bruce S.|last28=Mullikin|first28=James C.|last29=Sherry|first29=Stephen T.|last30=Feolo|first30=Michael|last31=Altshuler|first31=David|last32=Daly|first32=Mark J.|last33=Schaffner|first33=Stephen F.|last34=Qiu|first34=Renzong|last35=Kent|first35=Alastair|last36=Dunston|first36=Georgia M.|last37=Kato|first37=Kazuto|last38=Niikawa|first38=Norio|last39=Knoppers|first39=Bartha M.|last40=Foster|first40=Morris W.|last41=Clayton|first41=Ellen Wright|last42=Wang|first42=Vivian Ota|last43=Watkin|first43=Jessica|last44=Gibbs|first44=Richard A.|last45=Belmont|first45=John W.|last46=Sodergren|first46=Erica|last47=Weinstock|first47=George M.|last48=Wilson|first48=Richard K.|last49=Fulton|first49=Lucinda L.|last50=Rogers|first50=Jane|last51=Birren|first51=Bruce W.|last52=Han|first52=Hua|last53=Wang|first53=Hongguang|last54=Godbout|first54=Martin|last55=Wallenburg|first55=John C.|last56=L'Archevêque|first56=Paul|last57=Bellemare|first57=Guy|last58=Todani|first58=Kazuo|last59=Fujita|first59=Takashi|last60=Tanaka|first60=Satoshi|last61=Holden|first61=Arthur L.|last62=Lai|first62=Eric H.|last63=Collins|first63=Francis S.|last64=Brooks|first64=Lisa D.|last65=McEwen|first65=Jean E.|last66=Guyer|first66=Mark S.|last67=Jordan|first67=Elke|last68=Peterson|first68=Jane L.|last69=Spiegel|first69=Jack|last70=Sung|first70=Lawrence M.|last71=Zacharia|first71=Lynn F.|last72=Kennedy|first72=Karen|last73=Dunn|first73=Michael G.|last74=Seabrook|first74=Richard|last75=Shillito|first75=Mark|last76=Skene|first76=Barbara|last77=Stewart|first77=John G.|last78=Valle|first78=David L.|last79=Clayton|first79=Ellen Wright|last80=Jorde|first80=Lynn B.|last81=Belmont|first81=John W.|last82=Chakravarti|first82=Aravinda|last83=Cho|first83=Mildred K.|last84=Duster|first84=Troy|last85=Foster|first85=Morris W.|last86=Jasperse|first86=Marla|last87=Knoppers|first87=Bartha M.|last88=Kwok|first88=Pui-Yan|last89=Licinio|first89=Julio|last90=Long|first90=Jeffrey C.|last91=Marshall|first91=Patricia A.|last92=Ossorio|first92=Pilar N.|last93=Wang|first93=Vivian Ota|last94=Rotimi|first94=Charles N.|last95=Royal|first95=Charmaine D. M.|last96=Spallone|first96=Patricia|last97=Terry|first97=Sharon F.|last98=Lander|first98=Eric S.|last99=Lai|first99=Eric H.|last100=Nickerson|first100=Deborah A.|last101=Abecasis|first101=Gonçalo R.|last102=Altshuler|first102=David|last103=Bentley|first103=David R.|last104=Boehnke|first104=Michael|last105=Cardon|first105=Lon R.|last106=Daly|first106=Mark J.|last107=Deloukas|first107=Panos|last108=Douglas|first108=Julie A.|last109=Gabriel|first109=Stacey B.|last110=Hudson|first110=Richard R.|last111=Hudson|first111=Thomas J.|last112=Kruglyak|first112=Leonid|last113=Kwok|first113=Pui-Yan|last114=Nakamura|first114=Yusuke|last115=Nussbaum|first115=Robert L.|last116=Royal|first116=Charmaine D. M.|last117=Schaffner|first117=Stephen F.|last118=Sherry|first118=Stephen T.|last119=Stein|first119=Lincoln D.|last120=Tanaka|first120=Toshihiro|display-authors=6|title=The International HapMap Project|journal=Nature|date=18 December 2003|volume=426|issue=6968|year=2003|pages=789–796|issn=0028-0836|doi=10.1038/nature02168}}</ref> Each individual has many SNPs. SNP-based [[genetic linkage]] analysis can be used to map disease loci, and determine disease susceptibility genes in individuals. The combination of SNP maps and high density SNP arrays allows SNPs to be used as markers for genetic diseases that have complex traits. For example, [[genome-wide association studies]] have identified SNPs associated with diseases such as [[rheumatoid arthritis]],<ref>{{cite journal|last1=Walsh|first1=Alice M.|last2=Whitaker|first2=John W.|last3=Huang|first3=C. Chris|last4=Cherkas|first4=Yauheniya|last5=Lamberth|first5=Sarah L.|last6=Brodmerkel|first6=Carrie|last7=Curran|first7=Mark E.|last8=Dobrin|first8=Radu|title=Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations|journal=Genome Biology|date=30 April 2016|volume=17|issue=1|doi=10.1186/s13059-016-0948-6}}</ref> [[prostate cancer]],<ref>{{cite journal|last1=Amin Al Olama|first1=A.|last2=Kote-Jarai|first2=Z.|last3=Schumacher|first3=F. R.|last4=Wiklund|first4=F.|last5=Berndt|first5=S. I.|last6=Benlloch|first6=S.|last7=Giles|first7=G. G.|last8=Severi|first8=G.|last9=Neal|first9=D. E.|last10=Hamdy|first10=F. C.|last11=Donovan|first11=J. L.|last12=Hunter|first12=D. J.|last13=Henderson|first13=B. E.|last14=Thun|first14=M. J.|last15=Gaziano|first15=M.|last16=Giovannucci|first16=E. L.|last17=Siddiq|first17=A.|last18=Travis|first18=R. C.|last19=Cox|first19=D. G.|last20=Canzian|first20=F.|last21=Riboli|first21=E.|last22=Key|first22=T. J.|last23=Andriole|first23=G.|last24=Albanes|first24=D.|last25=Hayes|first25=R. B.|last26=Schleutker|first26=J.|last27=Auvinen|first27=A.|last28=Tammela|first28=T. L. J.|last29=Weischer|first29=M.|last30=Stanford|first30=J. L.|last31=Ostrander|first31=E. A.|last32=Cybulski|first32=C.|last33=Lubinski|first33=J.|last34=Thibodeau|first34=S. N.|last35=Schaid|first35=D. J.|last36=Sorensen|first36=K. D.|last37=Batra|first37=J.|last38=Clements|first38=J. A.|last39=Chambers|first39=S.|last40=Aitken|first40=J.|last41=Gardiner|first41=R. A.|last42=Maier|first42=C.|last43=Vogel|first43=W.|last44=Dork|first44=T.|last45=Brenner|first45=H.|last46=Habuchi|first46=T.|last47=Ingles|first47=S.|last48=John|first48=E. M.|last49=Dickinson|first49=J. L.|last50=Cannon-Albright|first50=L.|last51=Teixeira|first51=M. R.|last52=Kaneva|first52=R.|last53=Zhang|first53=H.-W.|last54=Lu|first54=Y.-J.|last55=Park|first55=J. Y.|last56=Cooney|first56=K. A.|last57=Muir|first57=K. R.|last58=Leongamornlert|first58=D. 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C.|last95=Corral|first95=R.|last96=Aly|first96=M.|last97=Isaacs|first97=W.|last98=Adolfsson|first98=J.|last99=Xu|first99=J.|last100=Zheng|first100=S. L.|last101=Wahlfors|first101=T.|last102=Taari|first102=K.|last103=Kujala|first103=P.|last104=Klarskov|first104=P.|last105=Nordestgaard|first105=B. G.|last106=Roder|first106=M. A.|last107=Frikke-Schmidt|first107=R.|last108=Bojesen|first108=S. E.|last109=FitzGerald|first109=L. M.|last110=Kolb|first110=S.|last111=Kwon|first111=E. M.|last112=Karyadi|first112=D. M.|last113=Orntoft|first113=T. F.|last114=Borre|first114=M.|last115=Rinckleb|first115=A.|last116=Luedeke|first116=M.|last117=Herkommer|first117=K.|last118=Meyer|first118=A.|last119=Serth|first119=J.|last120=Marthick|first120=J. R.|last121=Patterson|first121=B.|last122=Wokolorczyk|first122=D.|last123=Spurdle|first123=A.|last124=Lose|first124=F.|last125=McDonnell|first125=S. K.|last126=Joshi|first126=A. D.|last127=Shahabi|first127=A.|last128=Pinto|first128=P.|last129=Santos|first129=J.|last130=Ray|first130=A.|last131=Sellers|first131=T. A.|last132=Lin|first132=H.-Y.|last133=Stephenson|first133=R. A.|last134=Teerlink|first134=C.|last135=Muller|first135=H.|last136=Rothenbacher|first136=D.|last137=Tsuchiya|first137=N.|last138=Narita|first138=S.|last139=Cao|first139=G.-W.|last140=Slavov|first140=C.|last141=Mitev|first141=V.|last142=Chanock|first142=S.|last143=Gronberg|first143=H.|last144=Haiman|first144=C. A.|last145=Kraft|first145=P.|last146=Easton|first146=D. F.|last147=Eeles|first147=R. A.|display-authors=6|title=A meta-analysis of genome-wide association studies to identify prostate cancer susceptibility loci associated with aggressive and non-aggressive disease|journal=Human Molecular Genetics|date=12 October 2012|volume=22|issue=2|pages=408–415|doi=10.1093/hmg/dds425}}</ref> and [[type 2 diabetes]].<ref>{{cite journal|last1=Billings|first1=Liana K.|last2=Florez|first2=Jose C.|title=The genetics of type 2 diabetes: what have we learned from GWAS?|journal=Annals of the New York Academy of Sciences|date=November 2010|volume=1212|issue=1|pages=59–77|doi=10.1111/j.1749-6632.2010.05838.x}}</ref> A SNP array can also be used to generate a virtual [[karyotype]] using software to determine the copy number of each SNP on the array and then align the SNPs in chromosomal order.<ref>{{cite journal|last1=Sato-Otsubo|first1=Aiko|last2=Sanada|first2=Masashi|last3=Ogawa|first3=Seishi|title=Single-Nucleotide Polymorphism Array Karyotyping in Clinical Practice: Where, When, and How?|journal=Seminars in Oncology|date=February 2012|volume=39|issue=1|pages=13–25|doi=10.1053/j.seminoncol.2011.11.010}}</ref>

SNPs can also be used to study genetic abnormalities in cancer. For example, SNP arrays can be used to study [[loss of heterozygosity]] (LOH). LOH occurs when one allele of a gene is mutated in a deleterious way and the normally-functioning allele is lost. LOH occurs commonly in oncogenesis. For example, tumor suppressor genes help keep cancer from developing. If a person has one mutated and dysfunctional copy of a tumor suppressor gene and his second, functional copy of the gene gets damaged, they may become more likely to develop cancer.<ref>{{cite journal|last1=Zheng|first1=Hai-Tao|title=Loss of heterozygosity analyzed by single nucleotide polymorphism array in cancer|journal=World Journal of Gastroenterology|date=2005|volume=11|issue=43|pages=6740|doi=10.3748/wjg.v11.i43.6740}}</ref>

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High density SNP arrays help scientists identify patterns of allelic imbalance. These studies have potential prognostic and diagnostic uses. Because LOH is so common in many human cancers, SNP arrays have great potential in cancer diagnostics. For example, recent SNP array studies have shown that solid [[tumor]]s such as [[gastric cancer]] and [[hepatocellular carcinoma|liver cancer]] show LOH, as do non-solid malignancies such as [[leukemia|hematologic malignancies]], [[leukemia#acute lymphocytic leukemia (ALL)|ALL]], [[myelodysplastic syndrome|MDS]], [[Leukemia#Chronic myelogenous|CML]] and others. These studies may provide insights into how these diseases develop, as well as information about how to create therapies for them.<ref>{{cite journal|last1=Mao|first1=Xueying|last2=Young|first2=Bryan D|last3=Lu|first3=Yong-Jie|title=The Application of Single Nucleotide Polymorphism Microarrays in Cancer Research|journal=Current Genomics|date=2007|volume=8|issue=4|pages=219–228|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430687/|issn=1389-2029}}</ref>

Breeding in a number of animal and plant species has been revolutionized by the emergence of SNP arrays. The method is based on the prediction of genetic merit by incorporating relationships among individuals based on SNP array data.<ref name="pmid11290733">{{cite journal |vauthors = Meuwissen TH, Hayes BJ, Goddard ME |title = Prediction of Totaltotal Geneticgenetic Valuevalue Usingusing Genomegenome-Widewide Densedense Markermarker Mapsmaps | journal = Genetics |volume = 157 |issue = 4 |pages =1819–1829 1819–29 |year = 2001 |last1=Meuwissenpmid |first1=T.H.E. |last2=Hayes11290733 |first2=B.J.pmc |last3=Goddard |first3=M.E.1461589 }}</ref> This process is known as genomic selection.

==References==