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Old 05-14-2012, 05:59 AM   #5
HeidiJTP
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Location: Florida

Join Date: Nov 2011
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I realize this is an older thread, but I have a similar situation and was wondering which approach you used. I want to genotype a full gene and include 5' regulatory sequence as well for approximately 10 kb. Using long-PCR and PacBio sequencing would still require fragmentation. How can you reconstruct full alleles when genotyping large regions?

In other words, if one individual is heterozygous in both the 5' proximal promoter as well as in exon 5, but these are sequenced as separate fragments, is it possible to determine the complete allele 1 and allele 2? Would it be better to amplify shorter, overlapping fragments and hope there is enough polymorphism to allow assembly of each allele?

Thanks for any advice you can offer!
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