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m SNP is pronounced as "snip" in the genetics community so "An SNP" was changed to "A SNP" |
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[[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)]]
A 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|author=The International HapMap Consortium|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|bibcode=2003Natur.426..789G|hdl=2027.42/62838|s2cid=4387110|url=https://deepblue.lib.umich.edu/bitstream/2027.42/62838/1/nature02168.pdf|hdl-access=free}}</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.|display-authors=etal|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|bibcode=2010NYASA1212...59B}}</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=6740–4|doi=10.3748/wjg.v11.i43.6740|pmid=16425377|pmc=4725022}}</ref>
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