PMC:4996401 / 3721-5822 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4996401","sourcedb":"PMC","sourceid":"4996401","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4996401","text":"2. Single Nucleotide Polymorphism (SNP) Array and Its Applications\nSingle nucleotide polymorphisms (SNPs) are defined as variations of a DNA sequence at single nucleotide level which are found in a high proportion of human genome (i.e., more than 1%). SNPs might occur in any position in the genome. These polymorphisms have a wide effect on human health, ranging from disease development to response to the therapies [17]. Thus, technologies like SNP arrays were recently applied in order to screen the genome at global level allowing to better define correlations between genetic patterns and phenotypes, including diseases [17,18].\nSeveral different companies offer the related technology. However, as far as the experience in human lymphomas is concerned, two of them (i.e., Affymetrix, Santa Clara, CA, USA and Illumina, San Diego, CA, USA) demonstrated their leadership, offering arrays characterized by high reliability and reproducibility. Of note, the two technologies, albeit being based on different chemistries, show some common features [19]. Basically, a microarray/chip harboring unique probes for each SNP is prepared. The target DNA is then fragmented, labeled and hybridized to the probes present on the chip. A potential binding between the target DNA and the SNP probe is evaluated based on the intensity of the signal, which could provide the researcher with the information about the copy number state and the genotype [20,21,22,23]. As a result, genetic imbalances such as copy number variants (CNVs) and loss or gain of heterozygosity (LOH and GOH, respectively) can easily be detected [24,25,26,27,28,29]. Particularly, besides resolution, the latter cannot be identified by MC. In fact, LOH is generally caused by monoallelic deletions, the lost segment being then replaced by the same region of its homologous chromosome, resulting in a so called copy neutral loss of heterozygosity (CN-LOH) or uniparental disomy (UPD) [18,30,31,32]. The acquired homozygosity resulting from UPD could lead to development of tumors, as largely indicated by SNPs array-based studies [33,34].","divisions":[{"label":"Title","span":{"begin":0,"end":66}}],"tracks":[{"project":"2_test","denotations":[{"id":"27600240-21356189-69474261","span":{"begin":419,"end":421},"obj":"21356189"},{"id":"27600240-21356189-69474262","span":{"begin":627,"end":629},"obj":"21356189"},{"id":"27600240-22488943-69474263","span":{"begin":630,"end":632},"obj":"22488943"},{"id":"27600240-19570852-69474264","span":{"begin":1051,"end":1053},"obj":"19570852"},{"id":"27600240-19052058-69474265","span":{"begin":1442,"end":1444},"obj":"19052058"},{"id":"27600240-18057073-69474266","span":{"begin":1445,"end":1447},"obj":"18057073"},{"id":"27600240-15273396-69474267","span":{"begin":1448,"end":1450},"obj":"15273396"},{"id":"27600240-15286789-69474268","span":{"begin":1451,"end":1453},"obj":"15286789"},{"id":"27600240-16369530-69474269","span":{"begin":1611,"end":1613},"obj":"16369530"},{"id":"27600240-16909382-69474270","span":{"begin":1614,"end":1616},"obj":"16909382"},{"id":"27600240-17363630-69474271","span":{"begin":1617,"end":1619},"obj":"17363630"},{"id":"27600240-18059266-69474272","span":{"begin":1620,"end":1622},"obj":"18059266"},{"id":"27600240-18940696-69474273","span":{"begin":1623,"end":1625},"obj":"18940696"},{"id":"27600240-18369103-69474274","span":{"begin":1626,"end":1628},"obj":"18369103"},{"id":"27600240-22488943-69474275","span":{"begin":1948,"end":1950},"obj":"22488943"},{"id":"27600240-20107230-69474276","span":{"begin":1951,"end":1953},"obj":"20107230"},{"id":"27600240-16425377-69474277","span":{"begin":1954,"end":1956},"obj":"16425377"},{"id":"27600240-18505780-69474278","span":{"begin":1957,"end":1959},"obj":"18505780"},{"id":"27600240-12481003-69474279","span":{"begin":2094,"end":2096},"obj":"12481003"},{"id":"27600240-25644622-69474280","span":{"begin":2097,"end":2099},"obj":"25644622"}],"attributes":[{"subj":"27600240-21356189-69474261","pred":"source","obj":"2_test"},{"subj":"27600240-21356189-69474262","pred":"source","obj":"2_test"},{"subj":"27600240-22488943-69474263","pred":"source","obj":"2_test"},{"subj":"27600240-19570852-69474264","pred":"source","obj":"2_test"},{"subj":"27600240-19052058-69474265","pred":"source","obj":"2_test"},{"subj":"27600240-18057073-69474266","pred":"source","obj":"2_test"},{"subj":"27600240-15273396-69474267","pred":"source","obj":"2_test"},{"subj":"27600240-15286789-69474268","pred":"source","obj":"2_test"},{"subj":"27600240-16369530-69474269","pred":"source","obj":"2_test"},{"subj":"27600240-16909382-69474270","pred":"source","obj":"2_test"},{"subj":"27600240-17363630-69474271","pred":"source","obj":"2_test"},{"subj":"27600240-18059266-69474272","pred":"source","obj":"2_test"},{"subj":"27600240-18940696-69474273","pred":"source","obj":"2_test"},{"subj":"27600240-18369103-69474274","pred":"source","obj":"2_test"},{"subj":"27600240-22488943-69474275","pred":"source","obj":"2_test"},{"subj":"27600240-20107230-69474276","pred":"source","obj":"2_test"},{"subj":"27600240-16425377-69474277","pred":"source","obj":"2_test"},{"subj":"27600240-18505780-69474278","pred":"source","obj":"2_test"},{"subj":"27600240-12481003-69474279","pred":"source","obj":"2_test"},{"subj":"27600240-25644622-69474280","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ecd893","default":true}]}]}}