Mammalian Genotyping Service
Genetic Research
Diallelic Insertion/Deletion Polymorphisms
The following search box permits the rapid search of our database of ~200,000 indels by chromosomal position. The chromosomal positions are taken from the human sequence assembly at the UC-Santa Cruz web site http://genome.cse.ucsc.edu, June 2002 version. Use "23" for the X chromosome and "25" for the Y chromosome. Distances should be listed in megabases.Indels are categorized as multiallelic or diallelic and confirmed or not confirmed. Searches requesting long lists of indels take many seconds to process; please be patient. Lists of indels can be sorted in various ways by clicking on the triangles under the column headings. Clicking on the marker name for a specific indel will take you to a page with detailed information about that marker.
Caution! Many of the unconfirmed diallelic indels and a small fraction of the unconfirmed multiallelic indels are not true polymorphisms. The confirmation rate for unconfirmed diallelic indels with only one base allele length difference is especially low (~25%; see Weber et al. AJHG 71, 2002).
Our best current estimate is that 20% of all human polymorphisms are of the insertion/deletion (indel) type. Indels can be broken down into a roughly 50:50 mix of multiallelic and diallelic polymorphisms. Multiallelic indels include the minisatellites (also called VNTRs) and the short tandem repeat polymorphisms STRPs) (also called microsatellites or simple sequence length polymorphisms (SSLPs)). Minisatellites are relatively rare and typically have repeat lengths of a few tens of nucleotides with tandem repeat copy numbers in the hundreds to thousands. STRPs are abundant and have repeat lengths of 1-6 nucleotides with tandem repeat copy numbers mostly <30. Diallelic indels are also common, but are only just now beginning to be studied in detail (see below). All of the diallelic indels and most of the STRPs have the nice feature of being able to be analyzed simply by PCR followed by gel electrophoresis. We believe indels are an attractive alternative to SNPs.
We have confirmed and characterized well over 2,000 human diallelic short insertion/deletion (indel)polymorphisms (Weber, et al., AJHG 71: 2002). Supporting data for the Weber et al. 2002 paper are located in the following two spreadsheets: MIDdata and MIDAlleleFreqs. The MIDAlleleFreqs table contains allele frequencies in five populations for 2000 of our Marshfield Insertion/Deletion Polymorphisms. The five populations are Europeans, Japanese, African Pygmies, Native Americans from the Amazon, and the Polymorphism Discovery Resource (PDR). Also included are average values for all populations. The MIDdata table contains in addition to the allele frequency information, other information about the markers such as chromosomal location, inserted sequence, chimp/gorilla results, and data mining sources. Still more information can be obtained by using the Search features shown above.
MIDdata
MIDAlleleFreqs