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Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples.

Identifieur interne : 002061 ( PubMed/Corpus ); précédent : 002060; suivant : 002062

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples.

Auteurs : Zhandong Liu ; Santosh S. Venkatesh ; Carlo C. Maley

Source :

BMC genomics [ 1471-2164 ] ; 2008.

RBID : pubmed:18973670

English descriptors

KwdEn :
- Animals, Base Composition, Computational Biology, DNA Primers (genetics), DNA Probes (genetics), Databases, Genetic, Genome, Bacterial, Genome, Human, Humans, Myxococcales (genetics), Oligonucleotides (genetics), Open Reading Frames, Sequence Analysis, DNA, Species Specificity.
MESH :
- chemical , genetics : DNA Primers, DNA Probes, Oligonucleotides.
- genetics : Myxococcales.
- Animals, Base Composition, Computational Biology, Databases, Genetic, Genome, Bacterial, Genome, Human, Humans, Open Reading Frames, Sequence Analysis, DNA, Species Specificity.

Abstract

Genomes store information for building and maintaining organisms. Complete sequencing of many genomes provides the opportunity to study and compare global information properties of those genomes.

DOI: 10.1186/1471-2164-9-509
PubMed: 18973670

Links to Exploration step

pubmed:18973670

Le document en format XML

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<author><name sortKey="Liu, Zhandong" sort="Liu, Zhandong" uniqKey="Liu Z" first="Zhandong" last="Liu">Zhandong Liu</name>
<affiliation><nlm:affiliation>Genomics and Computational Biology Graduate Group, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. zhandong@mail.med.upenn.edu</nlm:affiliation>
</affiliation>
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<author><name sortKey="Venkatesh, Santosh S" sort="Venkatesh, Santosh S" uniqKey="Venkatesh S" first="Santosh S" last="Venkatesh">Santosh S. Venkatesh</name>
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<author><name sortKey="Maley, Carlo C" sort="Maley, Carlo C" uniqKey="Maley C" first="Carlo C" last="Maley">Carlo C. Maley</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples.</title>
<author><name sortKey="Liu, Zhandong" sort="Liu, Zhandong" uniqKey="Liu Z" first="Zhandong" last="Liu">Zhandong Liu</name>
<affiliation><nlm:affiliation>Genomics and Computational Biology Graduate Group, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. zhandong@mail.med.upenn.edu</nlm:affiliation>
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<author><name sortKey="Venkatesh, Santosh S" sort="Venkatesh, Santosh S" uniqKey="Venkatesh S" first="Santosh S" last="Venkatesh">Santosh S. Venkatesh</name>
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<author><name sortKey="Maley, Carlo C" sort="Maley, Carlo C" uniqKey="Maley C" first="Carlo C" last="Maley">Carlo C. Maley</name>
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<series><title level="j">BMC genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2008" type="published">2008</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Base Composition</term>
<term>Computational Biology</term>
<term>DNA Primers (genetics)</term>
<term>DNA Probes (genetics)</term>
<term>Databases, Genetic</term>
<term>Genome, Bacterial</term>
<term>Genome, Human</term>
<term>Humans</term>
<term>Myxococcales (genetics)</term>
<term>Oligonucleotides (genetics)</term>
<term>Open Reading Frames</term>
<term>Sequence Analysis, DNA</term>
<term>Species Specificity</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA Primers</term>
<term>DNA Probes</term>
<term>Oligonucleotides</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Myxococcales</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Base Composition</term>
<term>Computational Biology</term>
<term>Databases, Genetic</term>
<term>Genome, Bacterial</term>
<term>Genome, Human</term>
<term>Humans</term>
<term>Open Reading Frames</term>
<term>Sequence Analysis, DNA</term>
<term>Species Specificity</term>
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<front><div type="abstract" xml:lang="en">Genomes store information for building and maintaining organisms. Complete sequencing of many genomes provides the opportunity to study and compare global information properties of those genomes.</div>
</front>
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<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18973670</PMID>
<DateCompleted><Year>2009</Year>
<Month>02</Month>
<Day>06</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>9</Volume>
<PubDate><Year>2008</Year>
<Month>Oct</Month>
<Day>30</Day>
</PubDate>
</JournalIssue>
<Title>BMC genomics</Title>
<ISOAbbreviation>BMC Genomics</ISOAbbreviation>
</Journal>
<ArticleTitle>Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples.</ArticleTitle>
<Pagination><MedlinePgn>509</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-9-509</ELocationID>
<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Genomes store information for building and maintaining organisms. Complete sequencing of many genomes provides the opportunity to study and compare global information properties of those genomes.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">We have analyzed aspects of the information content of Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, and Escherichia coli (K-12) genomes. Virtually all possible (> 98%) 12 bp oligomers appear in vertebrate genomes while < 2% of 19 bp oligomers are present. Other species showed different ranges of > 98% to < 2% of possible oligomers in D. melanogaster (12-17 bp), C. elegans (11-17 bp), A. thaliana (11-17 bp), S. cerevisiae (10-16 bp) and E. coli (9-15 bp). Frequencies of unique oligomers in the genomes follow similar patterns. We identified a set of 2.6 M 15-mers that are more than 1 nucleotide different from all 15-mers in the human genome and so could be used as probes to detect microbes in human samples. In a human sample, these probes would detect 100% of the 433 currently fully sequenced prokaryotes and 75% of the 3065 fully sequenced viruses. The human genome is significantly more compact in sequence space than a random genome. We identified the most frequent 5- to 20-mers in the human genome, which may prove useful as PCR primers. We also identified a bacterium, Anaeromyxobacter dehalogenans, which has an exceptionally low diversity of oligomers given the size of its genome and its GC content. The entropy of coding regions in the human genome is significantly higher than non-coding regions and chromosomes. However chromosomes 1, 2, 9, 12 and 14 have a relatively high proportion of coding DNA without high entropy, and chromosome 20 is the opposite with a low frequency of coding regions but relatively high entropy.</AbstractText>
<AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">Measures of the frequency of oligomers are useful for designing PCR assays and for identifying chromosomes and organisms with hidden structure that had not been previously recognized. This information may be used to detect novel microbes in human tissues.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName>
<ForeName>Zhandong</ForeName>
<Initials>Z</Initials>
<AffiliationInfo><Affiliation>Genomics and Computational Biology Graduate Group, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. zhandong@mail.med.upenn.edu</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Venkatesh</LastName>
<ForeName>Santosh S</ForeName>
<Initials>SS</Initials>
</Author>
<Author ValidYN="Y"><LastName>Maley</LastName>
<ForeName>Carlo C</ForeName>
<Initials>CC</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><GrantID>P30 CA010815</GrantID>
<Acronym>CA</Acronym>
<Agency>NCI NIH HHS</Agency>
<Country>United States</Country>
</Grant>
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<ArticleDate DateType="Electronic"><Year>2008</Year>
<Month>10</Month>
<Day>30</Day>
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<MedlineJournalInfo><Country>England</Country>
<MedlineTA>BMC Genomics</MedlineTA>
<NlmUniqueID>100965258</NlmUniqueID>
<ISSNLinking>1471-2164</ISSNLinking>
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</MeshHeading>
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</MeshHeading>
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</MeshHeading>
<MeshHeading><DescriptorName UI="D030541" MajorTopicYN="N">Databases, Genetic</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016680" MajorTopicYN="N">Genome, Bacterial</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D015894" MajorTopicYN="Y">Genome, Human</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D009231" MajorTopicYN="N">Myxococcales</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D009841" MajorTopicYN="N">Oligonucleotides</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016366" MajorTopicYN="N">Open Reading Frames</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
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Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples.

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples.

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