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  Integrated sequence analysis pipeline provides one-stop solution for identifying disease-causing mutations

Hu, H., Wienker, T. F., Musante, L., Kalscheuer, V. M., Kahrizi, K., Najmabadi, H., et al. (2014). Integrated sequence analysis pipeline provides one-stop solution for identifying disease-causing mutations. Human Mutation, 35(12), 1427-1435. doi:10.1002/humu.22695.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0025-C2FA-E Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0025-C301-5
Genre: Journal Article

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© 2014 Wiley Periodicals, Inc.
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 Creators:
Hu, H.1, Author              
Wienker, T. F.2, Author              
Musante, L.3, Author              
Kalscheuer, V. M.4, Author              
Kahrizi, K., Author
Najmabadi, H., Author
Ropers, H. H.1, Author              
Affiliations:
1Dept. of Human Molecular Genetics (Head: Hans-Hilger Ropers), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433549              
2Clinical Genetics (Thomas F. Wienker), Dept. of Human Molecular Genetics (Head: Hans-Hilger Ropers), Max Planck Institute for Molecular Genetics, Max Planck Society, 1479643              
3Familial Cognitive Disorders (Luciana Musante), Dept. of Human Molecular Genetics (Head: Hans-Hilger Ropers), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479644              
4Chromosome Rearrangements and Disease (Vera Kalscheuer), Dept. of Human Molecular Genetics (Head: Hans-Hilger Ropers), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479642              

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 Abstract: Next-generation sequencing has greatly accelerated the search for disease-causing defects, but even for experts the data analysis can be a major challenge. To facilitate the data processing in a clinical setting, we have developed a novel medical resequencing analysis pipeline (MERAP). MERAP assesses the quality of sequencing, and has optimized capacity for calling variants, including single-nucleotide variants, insertions and deletions, copy-number variation, and other structural variants. MERAP identifies polymorphic and known causal variants by filtering against public domain databases, and flags nonsynonymous and splice-site changes. MERAP uses a logistic model to estimate the causal likelihood of a given missense variant. MERAP considers the relevant information such as phenotype and interaction with known disease-causing genes. MERAP compares favorably with GATK, one of the widely used tools, because of its higher sensitivity for detecting indels, its easy installation, and its economical use of computational resources. Upon testing more than 1,200 individuals with mutations in known and novel disease genes, MERAP proved highly reliable, as illustrated here for five families with disease-causing variants. We believe that the clinical implementation of MERAP will expedite the diagnostic process of many disease-causing defects.

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Language(s): eng - English
 Dates: 2014-11-242014-12
 Publication Status: Published in print
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 Rev. Type: Peer
 Identifiers: DOI: 10.1002/humu.22695
ISSN: 1098-1004 (Electronic)1059-7794 (Print)
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Title: Human Mutation
  Other : Hum Mut
Source Genre: Journal
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Publ. Info: New York, N.Y. : Wiley-Liss
Pages: - Volume / Issue: 35 (12) Sequence Number: - Start / End Page: 1427 - 1435 Identifier: ISSN: 1059-7794
CoNE: https://pure.mpg.de/cone/journals/resource/954925597586