publication . Other literature type . Article . 2016

Indel variant analysis of short-read sequencing data with Scalpel

Han Fang; Ewa A Bergmann; Kanika Arora; Vladimir Vacic; Michael C Zody; Ivan Iossifov; Jason A O'Rawe; Yiyang Wu; Laura T Jimenez Barron; Julie Rosenbaum; ...
Open Access
  • Published: 17 Nov 2016
  • Publisher: Springer Science and Business Media LLC
Abstract
As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of indels of more than a few bases in size from short-read sequencing data remains challenging. Scalpel (http://scalpel.sourceforge.net) is an open-source software for reliable indel detection based on the microassembly technique. It has been successfully used to discover mutations in novel candidate genes for autism, and it is extensively used in other large-scale studies of human diseases. This protocol gives an overview of the algorithm and describes how to use Scalpel to perform highly accurate indel calling ...
Subjects
Medical Subject Headings: food and beverages
free text keywords: Article, General Biochemistry, Genetics and Molecular Biology
Funded by
NIH| Computational Methods for Genome Assembly, Transcript Assembly, and Variant Discovery
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 2R01HG006677-15A1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
NSF| CAREER: Algorithms for single molecule sequence analysis
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1350041
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
,
NIH| CSHL CANCER CENTER SUPPORT GRANT
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3P30CA045508-08S1
  • Funding stream: NATIONAL CANCER INSTITUTE
19 references, page 1 of 2

Collins, F.S. and H. Varmus, A new initiative on precision medicine. N Engl J Med, 2015. 372(9): p. 793-5.

James D. Watson, T.A.B., Alexander Gann, Michael Levine, Richard Losick, Molecular Biology of the Gene. Seventh Edition ed. 2013: Cold Spring Harbor Laboratory Press.

Nik-Zainal, S., et al., Mutational Processes Molding the Genomes of 21 Breast Cancers. Cell, 2012. 149(5): p. 979-993.

Zaidi, S., et al., De novo mutations in histone-modifying genes in congenital heart disease. Nature, 2013. 498(7453): p. 220-223.

Neuron, 2012. 74(2): p. 285-99.

Iossifov, I., et al., The contribution of de novo coding mutations to autism spectrum disorder. Nature, 2014. 515(7526): p. 216-21. [OpenAIRE]

Microbiol Mol Biol Rev, 1998. 62(4): p. 1435-91.

Tian, D., et al., Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature, 2008. 455(7209): p. 105-8.

MacArthur, D.G., et al., A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes. Science, 2012. 335(6070): p. 823-828.

Fukuoka, S., et al., Loss of function of a proline-containing protein confers durable disease resistance in rice. Science, 2009. 325(5943): p. 998-1001.

Denver, D.R., et al., High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature, 2004. 430(7000): p. 679-82. [OpenAIRE]

Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv e-prints, 2013. 1303, 3997.

Paila, U., et al., GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations. PLoS Comput Biol, 2013. 9(7): p. e1003153.

Genome Biol, 2014. 15(8): p. 454.

Tan, A., G.R. Abecasis, and H.M. Kang, Unified representation of genetic variants. Bioinformatics, 2015. [OpenAIRE]

19 references, page 1 of 2
Abstract
As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of indels of more than a few bases in size from short-read sequencing data remains challenging. Scalpel (http://scalpel.sourceforge.net) is an open-source software for reliable indel detection based on the microassembly technique. It has been successfully used to discover mutations in novel candidate genes for autism, and it is extensively used in other large-scale studies of human diseases. This protocol gives an overview of the algorithm and describes how to use Scalpel to perform highly accurate indel calling ...
Subjects
Medical Subject Headings: food and beverages
free text keywords: Article, General Biochemistry, Genetics and Molecular Biology
Funded by
NIH| Computational Methods for Genome Assembly, Transcript Assembly, and Variant Discovery
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 2R01HG006677-15A1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
NSF| CAREER: Algorithms for single molecule sequence analysis
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1350041
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
,
NIH| CSHL CANCER CENTER SUPPORT GRANT
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3P30CA045508-08S1
  • Funding stream: NATIONAL CANCER INSTITUTE
19 references, page 1 of 2

Collins, F.S. and H. Varmus, A new initiative on precision medicine. N Engl J Med, 2015. 372(9): p. 793-5.

James D. Watson, T.A.B., Alexander Gann, Michael Levine, Richard Losick, Molecular Biology of the Gene. Seventh Edition ed. 2013: Cold Spring Harbor Laboratory Press.

Nik-Zainal, S., et al., Mutational Processes Molding the Genomes of 21 Breast Cancers. Cell, 2012. 149(5): p. 979-993.

Zaidi, S., et al., De novo mutations in histone-modifying genes in congenital heart disease. Nature, 2013. 498(7453): p. 220-223.

Neuron, 2012. 74(2): p. 285-99.

Iossifov, I., et al., The contribution of de novo coding mutations to autism spectrum disorder. Nature, 2014. 515(7526): p. 216-21. [OpenAIRE]

Microbiol Mol Biol Rev, 1998. 62(4): p. 1435-91.

Tian, D., et al., Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature, 2008. 455(7209): p. 105-8.

MacArthur, D.G., et al., A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes. Science, 2012. 335(6070): p. 823-828.

Fukuoka, S., et al., Loss of function of a proline-containing protein confers durable disease resistance in rice. Science, 2009. 325(5943): p. 998-1001.

Denver, D.R., et al., High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature, 2004. 430(7000): p. 679-82. [OpenAIRE]

Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv e-prints, 2013. 1303, 3997.

Paila, U., et al., GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations. PLoS Comput Biol, 2013. 9(7): p. e1003153.

Genome Biol, 2014. 15(8): p. 454.

Tan, A., G.R. Abecasis, and H.M. Kang, Unified representation of genetic variants. Bioinformatics, 2015. [OpenAIRE]

19 references, page 1 of 2
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