The clustering of discrepancies within families is consistent with the hypothesis that there is another SNP or insertion/deletion that obliterates an XbaI site in the vicinity of rs958883/tsc026848, thereby resulting in a fragment that is too large to amplify. The closest 5' and 3' XbaI sites are located 134 nucleotides upstream and 519 nucleotides downstream. When both of these XbaI sites are intact, the resulting fragment is within the size range (250–1,000 bp) that can be amplified using common adapters. For rs958883/tsc0260848, NCBI's dbSNP (build 123) indicates that there is, indeed, another SNP (rs17150546) in the closest upstream XbaI site that changes the wild-type sequence (TCTAGA) to TCGAGA. When this XbaI site is obliterated, the resulting fragment is 3,617 nucleotides- clearly too long to be amplified. It is perhaps of interest that the SNP that gave the second highest number of discrepancies, rs768224/tsc0075731, also has a SNP (rs10977965) in its neighboring XbaI site. When the minor allele is present at this SNP, the resulting fragment is 2,978 nucleotides in length- again, too long to be amplified. Accordingly, these two known
