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Article: A universal algorithm for de novo decrypting of heterozygous indel sequences: A tool for personalized medicine

TitleA universal algorithm for de novo decrypting of heterozygous indel sequences: A tool for personalized medicine
Authors
Issue Date2008
PublisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/cca
Citation
Clinica Chimica Acta, 2008, v. 389 n. 1-2, p. 7-13 How to Cite?
AbstractIntroduction: Indels (insertions/deletions) are important DNA sequence variations because of the high frequency in the human genome, the deleterious effects on the reading frame and protein expression, and the association with disease and disease susceptibility of common diseases. In a recent study with a human individual with the whole genome sequenced, 292,102 heterozygous indels and 559,473 homozygous indels were identified. Decrypting such a large number of heterozygous indels is computationally intensive and requires efficient algorithms. However, the current algorithms for decrypting heterozygous indel cannot be applied to unprecedented sequenced genomes and cannot be performed without reference sequences or reference sequence tracings for sequenced genomes. Methods: A new algorithm for de novo decrypting of heterozygous indels is conceptualized in the direction of isolating the indel sequence from the genotype or diploid sequence. A universal algorithm is described, here, for heterozygous indel detection, indel size determination, and de novo decrypting of the indel sequence without subtracting the diploid DNA sequence from the reference sequence or reference sequence tracing. Results: The result obtained by this algorithm is exactly the same as that obtained by PolyPhred and PolyScan. Unlike these algorithms, this new algorithm is not computationally intense for large indels, is independent of sequencing technologies and applies to genotype data derived from all existing sequencing technology platforms. A read of only 29 bases is enough to reduce the false detection rate (FDR) to 1 in a million. Conclusions: This algorithm is unique amongst all the existing algorithms in terms of performing the task of indel detection, size determination, and decrypting simultaneously. This universal approach eliminates the requirement of a reference sequence or sequence tracing and makes this algorithm unique in decrypting unprecedented sequenced genomes. Because of the high frequency of heterozygous indels in human genome, this universal algorithm will greatly reduce the time required for post-sequencing data analysis in whole genome sequencing of an individual for the practice of personalized medicine. © 2007 Elsevier B.V. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/148545
ISSN
2015 Impact Factor: 2.799
2015 SCImago Journal Rankings: 1.040
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorLam, CWen_US
dc.date.accessioned2012-05-29T06:13:38Z-
dc.date.available2012-05-29T06:13:38Z-
dc.date.issued2008en_US
dc.identifier.citationClinica Chimica Acta, 2008, v. 389 n. 1-2, p. 7-13en_US
dc.identifier.issn0009-8981en_US
dc.identifier.urihttp://hdl.handle.net/10722/148545-
dc.description.abstractIntroduction: Indels (insertions/deletions) are important DNA sequence variations because of the high frequency in the human genome, the deleterious effects on the reading frame and protein expression, and the association with disease and disease susceptibility of common diseases. In a recent study with a human individual with the whole genome sequenced, 292,102 heterozygous indels and 559,473 homozygous indels were identified. Decrypting such a large number of heterozygous indels is computationally intensive and requires efficient algorithms. However, the current algorithms for decrypting heterozygous indel cannot be applied to unprecedented sequenced genomes and cannot be performed without reference sequences or reference sequence tracings for sequenced genomes. Methods: A new algorithm for de novo decrypting of heterozygous indels is conceptualized in the direction of isolating the indel sequence from the genotype or diploid sequence. A universal algorithm is described, here, for heterozygous indel detection, indel size determination, and de novo decrypting of the indel sequence without subtracting the diploid DNA sequence from the reference sequence or reference sequence tracing. Results: The result obtained by this algorithm is exactly the same as that obtained by PolyPhred and PolyScan. Unlike these algorithms, this new algorithm is not computationally intense for large indels, is independent of sequencing technologies and applies to genotype data derived from all existing sequencing technology platforms. A read of only 29 bases is enough to reduce the false detection rate (FDR) to 1 in a million. Conclusions: This algorithm is unique amongst all the existing algorithms in terms of performing the task of indel detection, size determination, and decrypting simultaneously. This universal approach eliminates the requirement of a reference sequence or sequence tracing and makes this algorithm unique in decrypting unprecedented sequenced genomes. Because of the high frequency of heterozygous indels in human genome, this universal algorithm will greatly reduce the time required for post-sequencing data analysis in whole genome sequencing of an individual for the practice of personalized medicine. © 2007 Elsevier B.V. All rights reserved.en_US
dc.languageengen_US
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/ccaen_US
dc.relation.ispartofClinica Chimica Actaen_US
dc.subject.meshAlgorithmsen_US
dc.subject.meshBase Sequenceen_US
dc.subject.meshGenetic Diseases, Inborn - Diagnosis - Geneticsen_US
dc.subject.meshHeterozygoteen_US
dc.subject.meshIndel Mutationen_US
dc.subject.meshMolecular Sequence Dataen_US
dc.subject.meshMutationen_US
dc.titleA universal algorithm for de novo decrypting of heterozygous indel sequences: A tool for personalized medicineen_US
dc.typeArticleen_US
dc.identifier.emailLam, CW:ching-wanlam@pathology.hku.hken_US
dc.identifier.authorityLam, CW=rp00260en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1016/j.cca.2007.11.011en_US
dc.identifier.pmid18078814-
dc.identifier.scopuseid_2-s2.0-38649131448en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-38649131448&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume389en_US
dc.identifier.issue1-2en_US
dc.identifier.spage7en_US
dc.identifier.epage13en_US
dc.identifier.isiWOS:000253450300002-
dc.publisher.placeNetherlandsen_US
dc.identifier.citeulike2182193-

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