SNP array: Difference between revisions

Revision as of 16:37, 10 June 2020

Revision as of 18:42, 8 September 2020

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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>

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 fathersfather'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.

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|issn=1389-2029|doi=10.2174/138920207781386924|pmc=2430687|pmid=18645599}}</ref>