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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.
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.
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>{{cite journal |title=Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps | journal=Genetics |volume=157 |pages=1819–1829 |year=2001 |last1=Meuwissen |first1=T.H.E. |last2=Hayes |first2=B.J. |last3=Goddard |first3=M.E. }}</ref> This process is known as genomic selection.
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