Indels polymorphisms

Jing R, Bolshakov V, Flavell AJ. The tagged microatray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms. Nat. Rotoc. 2007 2 168-177. 

When the sequence polymorphisms in ACE are resolved into haplotypes and a gene tree constructed [52], the pattern of variation in ACE reveals the presence of two major dades that are detected by the Alu indel (Figure 3.3). Because the deletion dade has been consistently associated with cardiovascular disease pathology including myocardial infarction, arterial hyper-... 

The NCBI established the dbSNP database in September 1998 as a central repository for both SNPs and short INDEL polymorphisms. In June 2004 (Build 121) dbSNP contained 19.9 million SNPs. These SNPs collapse into a nonredundant set of 9.9 million SNPs, known as Reference SNPs (RefSNPs). Further information exists on a subset of the 9.9 million RefSNPs 4.5 million are validated, at least in as much as they have been observed more than once, which is a fairly reliable indicator that the SNPs are likely to be real and of relatively high frequency. There are 840,038 that have a know frequency in at least one population. These quantities of SNPs give a very high level of coverage across the genome, with most known exons now within 1 to 2 kb of at least one SNP in the dbSNP database. 

Any primer design software, freely available or custom purchased may be used to design PCR primers for Pyrosequencing. The polymorphism may be in any position of the PCR amplicon from 1 base in from the 3 end of the PCR primer sequence to centered between the primers. SNPs, indels, repeats, etc., do not require specific PCR primer design modifications. 

Fig. 2. Examples of probe and primer designs for genotyping indel polymorphisms of different size. (A) The example discussed in this article is shown with a small insert that requires only one primer pair and two probes for genotyping. (B) The design for larger inserts is shown. There are still two probes, one specific for insert sequences and the other specific for the immediate 3 and 5 sequences, flanking the insert. However, for larger inserts there is an additional insert-specific primer pair (ins fwd and ins rev) that amplify the portion of the insert recognized by the ins probe. In both designs the probes can be designed to hybridize to either strand, but the reporter fluorophores (Rf and RJ must be on the 5 end with the quencher (Q) on the 3 end.

Being able to sequence all or part of the genome for a number of individuals allows their sequences to be lined up for comparison so that sites where nucleotides vary called SNPs (single nucleotide polymorphism) can be found. SNPs are referred to as common if a particular variant is found in more than 1% of the population. Such SNPs represent most of the 0.5% of the genetic differences that occur between different people. " They aren t the only way that genomes vary. Non-SNP mutations include insertions and deletions of nucleotides (collectively known as indels) which can have profound effects if they occur within coding sequences. This is especially true when they don t occur in multiples of three base... 

Polymorphisms are related to the insertion, deletion, and substitution of one or more nucleotides in a DNA strand (Bell, 2002 Bentley, 2000), events that can occur during the duplication process of these strands. Two important and common types of polymorphism are the so called SNP - Single Nucleotide Polymorphism, which is related to only one nucleotide, and the InDels, when there are insertions and deletions of more than one nucleotide. 

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