A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence.
The recent publication of the complete sequence of human chromosome 22 provides a platform from which to investigate genomic sequence variation. We report the identification and characterization of 12,267 potential variants (SNPs and other small insertions/deletions) of human chromosome 22, discovered in the overlaps of 460 clones used for the chromosome sequencing. We found, on average, 1 potential variant every 1.07 kb and approximately 18% of the potential variants involve insertions/deletions. The SNPs have been positioned both relative to each other, and to genes, predicted genes, repeat sequences, other genetic markers, and the 2730 SNPs previously identified on the chromosome. A subset of the SNPs were verified experimentally using either PCR-RFLP or genomic Invader assays. These experiments confirmed 92% of the potential variants in a panel of 92 individuals. [Details of the SNPs and RFLP assays can be found at http://www.sanger.ac.uk and in dbSNP.]
Dawson
E
E
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Chen
Y
Y
Hunt
S
S
Smink
L J
LJ
Hunt
A
A
Rice
K
K
Livingston
S
S
Bumpstead
S
S
Bruskiewich
R
R
Sham
P
P
Ganske
R
R
Adams
M
M
Kawasaki
K
K
Shimizu
N
N
Minoshima
S
S
Roe
B
B
Bentley
D
D
Dunham
I
I
D001482:Base Composition; D002872:Chromosome Deletion; D002874:Chromosome Mapping; D002892:Chromosomes, Human, Pair 22 / Q000737:chemistry / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D014644:Genetic Variation; D015894:Genome, Human; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results
D004251:DNA Transposable Elements