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 A.|last20=Nickerson|first20=Debbie A.|last21=Peltonen|first21=Leena|last22=Schafer|first22=Alan J.|last23=Sherry|first23=Stephen T.|last24=Wang|first24=Jun|last25=Wilson|first25=Richard K.|last26=Gibbs|first26=Richard A.|last27=Deiros|first27=David|last28=Metzker|first28=Mike|last29=Muzny|first29=Donna|last30=Reid|first30=Jeff|last31=Wheeler|first31=David|last32=Wang|first32=Jun|last33=Li|first33=Jingxiang|last34=Jian|first34=Min|last35=Li|first35=Guoqing|last36=Li|first36=Ruiqiang|last37=Liang|first37=Huiqing|last38=Tian|first38=Geng|last39=Wang|first39=Bo|last40=Wang|first40=Jian|last41=Wang|first41=Wei|last42=Yang|first42=Huanming|last43=Zhang|first43=Xiuqing|last44=Zheng|first44=Huisong|last45=Lander|first45=Eric S.|last46=Altshuler|first46=David L.|last47=Ambrogio|first47=Lauren|last48=Bloom|first48=Toby|last49=Cibulskis|first49=Kristian|last50=Fennell|first50=Tim J.|last51=Gabriel|first51=Stacey B.|last52=Jaffe|first52=David B.|last53=Shefler|first53=Erica|last54=Sougnez|first54=Carrie L.|last55=Bentley|first55=David R.|last56=Gormley|first56=Niall|last57=Humphray|first57=Sean|last58=Kingsbury|first58=Zoya|last59=Koko-Gonzales|first59=Paula|last60=Stone|first60=Jennifer|last61=McKernan|first61=Kevin J.|last62=Costa|first62=Gina L.|last63=Ichikawa|first63=Jeffry K.|last64=Lee|first64=Clarence C.|last65=Sudbrak|first65=Ralf|last66=Lehrach|first66=Hans|last67=Borodina|first67=Tatiana A.|last68=Dahl|first68=Andreas|last69=Davydov|first69=Alexey N.|last70=Marquardt|first70=Peter|last71=Mertes|first71=Florian|last72=Nietfeld|first72=Wilfiried|last73=Rosenstiel|first73=Philip|last74=Schreiber|first74=Stefan|last75=Soldatov|first75=Aleksey 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K.|last109=Dooling|first109=David|last110=Fulton|first110=Lucinda|last111=Fulton|first111=Robert|last112=Weinstock|first112=George|last113=Durbin|first113=Richard M.|last114=Burton|first114=John|last115=Carter|first115=David M.|last116=Churcher|first116=Carol|last117=Coffey|first117=Alison|last118=Cox|first118=Anthony|last119=Palotie|first119=Aarno|last120=Quail|first120=Michael|last121=Skelly|first121=Tom|last122=Stalker|first122=James|last123=Swerdlow|first123=Harold P.|last124=Turner|first124=Daniel|last125=De Witte|first125=Anniek|last126=Giles|first126=Shane|last127=Gibbs|first127=Richard 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==Principles==

The basic principles of SNP array are the same as the DNA microarray. These are the convergence of [[DNA hybridization]], [[fluorescence microscope|fluorescence microscopy]], and solid surface DNA capture. The three mandatory components of the SNP arrays are:<ref>{{cite journal|last1=LaFramboise|first1=T.|title=Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances|journal=Nucleic Acids Research|date=1 July 2009|volume=37|issue=13|pages=4181–4193|doi=10.1093/nar/gkp552|pmid=19570852|pmc=2715261}}</ref>

# An array containing immobilized [[allele-specific oligonucleotide]] (ASO) probes.

# Fragmented [[nucleic acid]] sequences of target, labelled with fluorescent dyes.

# 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=Ralph| last1=Rapley|first2=Stuart|last2=Harbron|title=Molecular analysis and genome discovery|date=2004|publisher=Wiley|___location=Chichester [u.a.]|isbn=978-0-471-49919-60}}</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|pmid=21801020}}</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|issn=1394-195X|pmc=3349395|pmid=22605952}}</ref> In research, SNP arrays are most frequently used for [[genome-wide association studies]].<ref name="GibbsBelmont2003">{{cite journal|last1=Gibbs|first1=Richard A.|last2=Belmont|first2=John W.|last3=Hardenbol|first3=Paul|last4=Willis|first4=Thomas D.|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|volume=426|issue=6968|year=2003|pages=789–796|issn=0028-0836|doi=10.1038/nature02168|pmid=14685227}}</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|pages=79|doi=10.1186/s13059-016-0948-6|pmid=27140173|pmc=4853861}}</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. A.|last59=Saunders|first59=E.|last60=Tymrakiewicz|first60=M.|last61=Mahmud|first61=N.|last62=Guy|first62=M.|last63=Govindasami|first63=K.|last64=O'Brien|first64=L. T.|last65=Wilkinson|first65=R. A.|last66=Hall|first66=A. L.|last67=Sawyer|first67=E. J.|last68=Dadaev|first68=T.|last69=Morrison|first69=J.|last70=Dearnaley|first70=D. P.|last71=Horwich|first71=A.|last72=Huddart|first72=R. A.|last73=Khoo|first73=V. S.|last74=Parker|first74=C. C.|last75=Van As|first75=N.|last76=Woodhouse|first76=C. J.|last77=Thompson|first77=A.|last78=Dudderidge|first78=T.|last79=Ogden|first79=C.|last80=Cooper|first80=C. S.|last81=Lophatonanon|first81=A.|last82=Southey|first82=M. C.|last83=Hopper|first83=J. L.|last84=English|first84=D.|last85=Virtamo|first85=J.|last86=Le Marchand|first86=L.|last87=Campa|first87=D.|last88=Kaaks|first88=R.|last89=Lindstrom|first89=S.|last90=Diver|first90=W. R.|last91=Gapstur|first91=S.|last92=Yeager|first92=M.|last93=Cox|first93=A.|last94=Stern|first94=M. 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|pmid=23065704|pmc=3526158}}</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|pmid=21091714|pmc=3057517}}</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|pmid=22289488}}</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=67406740–4|doi=10.3748/wjg.v11.i43.6740|pmid=16425377|pmc=4725022}}</ref>

Other chip-based methods such as [[comparative genomic hybridization]] can detect genomic gains or deletions leading to LOH. SNP arrays, however, have an additional advantage of being able to detect copy-neutral LOH (also called [[uniparental disomy]] or gene conversion). Copy-neutral LOH is a form of allelic imbalance. In copy-neutral LOH, one allele or whole chromosome from a parent is missing. This problem leads to duplication of the other parental allele. Copy-neutral LOH may be pathological. For example, say that the mother's allele is wild-type and fully functional, and the fathers's allele is mutated. If the mother's allele is missing and the child has two copies of the father's mutant allele, disease can occur.