Document Detail


Characterization of frequencies and distribution of single nucleotide insertions/deletions in the human genome.
MedLine Citation:
PMID:  16781088     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Most of the studies on single nucleotide variations are on substitutions rather than insertions/deletions. In this study, we examined the distribution and characteristics of single nucleotide insertions/deletions (SNindels), using data available from dbSNP for all the human chromosomes. There are almost 300,000 SNindels in the database, of which only 0.8% are validated. They occur at the frequency of 0.887 per 10 kb on average for the whole genome, or approximately 1 for every 11,274 bp. More than half occur in regions with mononucleotide repeats the longest of which is 47 bases. Overall the mononucleotide repeats involving C and G are much shorter than those for A and T. About 12% are surrounded by palindromes. There is general correlation between chromosome size and total number for each chromosome. Inter-chromosomal variation in density ranges from 0.6 to 21.7 per kilobase. The overall spectrum shows very high proportion of SNindel of types -/A and -/T at over 81%. The proportion of -/A and -/T SNindels for each chromosome is correlated to its AT content. Less than half of the SNindels are within or near known genes and even fewer (<0.183%) in coding regions, and more than 1.4% of -/C and -/G are in coding compared to 0.2% for -/A and -/T types. SNindels of -/A and -/T types make up 80% of those found within untranslated regions but less than 40% of those within coding regions. A separate analysis using the subset of 2324 validated SNindels showed slightly less AT bias of 74%, SNindels not within mononucleotide repeats showed even less AT bias at 58%. Density of validated SNindels is 0.007/10 kb overall and 90% are found within or near genes. Among all chromosomes, Y has the lowest numbers and densities for all SNindels, validated SNindels, and SNindels not within repeats.
Authors:
Ene-Choo Tan; Haixia Li
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Publication Detail:
Type:  Comparative Study; Journal Article     Date:  2006-05-03
Journal Detail:
Title:  Gene     Volume:  376     ISSN:  0378-1119     ISO Abbreviation:  Gene     Publication Date:  2006 Jul 
Date Detail:
Created Date:  2006-07-10     Completed Date:  2006-08-31     Revised Date:  2008-11-21    
Medline Journal Info:
Nlm Unique ID:  7706761     Medline TA:  Gene     Country:  Netherlands    
Other Details:
Languages:  eng     Pagination:  268-80     Citation Subset:  IM    
Affiliation:
KK Research Centre, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore. tenec@bigfoot.com
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MeSH Terms
Descriptor/Qualifier:
Base Pairing / genetics
Base Sequence / genetics
Chromosomes, Human
DNA, Intergenic
Exons
Gene Frequency*
Genetic Variation
Genome, Human*
Humans
Introns
Mutagenesis, Insertional*
Nucleotides / genetics*
Polymorphism, Single Nucleotide
Reproducibility of Results
Sequence Deletion*
Chemical
Reg. No./Substance:
0/DNA, Intergenic; 0/Nucleotides

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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