Loss of imprinting in human cancer

AP Feinberg, LM Kalikin, LA Johnson… - Cold Spring Harbor …, 1994 - symposium.cshlp.org
AP Feinberg, LM Kalikin, LA Johnson, JS Thompson
Cold Spring Harbor symposia on quantitative biology, 1994symposium.cshlp.org
METHODS To assay for genomic imprinting, it was necessary to determine not just which
patients were heterozygous for a given polymorphism, but also which alleles were
transcribed into RNA. For IGF2, there was already a known transcribed ApaI polymorphism
(Tadokoro et al. 1991), but the fraction of informative individuals is relatively small. To
examine a relatively large number of tumors, polymerase chain reaction (PCR) primers were
designed to amplify a dinucleotide repeat (DR), but initially we saw no variation in length …
METHODS
To assay for genomic imprinting, it was necessary to determine not just which patients were heterozygous for a given polymorphism, but also which alleles were transcribed into RNA. For IGF2, there was already a known transcribed ApaI polymorphism (Tadokoro et al. 1991), but the fraction of informative individuals is relatively small. To examine a relatively large number of tumors, polymerase chain reaction (PCR) primers were designed to amplify a dinucleotide repeat (DR), but initially we saw no variation in length among normal individuals. However, the DR is unusually large (800 bp), and most polymorphic DRs show length differences of only a few nucleotides, which would likely be unresolvable with this size fragment. Because of the repetitive nature of the sequence, it was not possible to design PCR primers that would amplify only a portion of the DR. However, there is a unique MvnI site in the approximate middle of the DR, allowing digestion of the PCR product into two segments of
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