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Conbase :
Conbase : a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
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- Hard, Joanna (author)
- Karolinska Institutet
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- Al Hakim, Ezeddin (author)
- Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden.
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- Kindblom, Marie (author)
- Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden.
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- Björklund, Åsa K. (author)
- Uppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab
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- Sennblad, Bengt (author)
- Uppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab
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- Demirci, Ilke (author)
- Karolinska Institutet
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- Paterlini, Marta (author)
- Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden.
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- Reu, Pedro (author)
- Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden.
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- Borgström, Erik (author)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi,KTH Royal Inst Technol, Div Gene Technol, Scilifelab, Solna, Sweden
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- Stahl, Patrik L. (author)
- Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden.
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- Michaelsson, Jakob (author)
- Karolinska Institutet
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- Mold, Jeff E. (author)
- Karolinska Institutet
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- Frisen, Jonas (author)
- Karolinska Institutet
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Karolinska Institutet Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden (creator_code:org_t)
- 2019-04-01
- 2019
- English.
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In: Genome Biology. - : BMC. - 1465-6906 .- 1474-760X. ; 20
- Related links:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
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- Accurate variant calling and genotyping represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase for the identification of somatic mutations in single-cell DNA sequencing data. Conbase leverages phased read data from multiple samples in a dataset to achieve increased confidence in somatic variant calls and genotype predictions. Comparing the performance of Conbase to three other methods, we find that Conbase performs best in terms of false discovery rate and specificity and provides superior robustness on simulated data, in vitro expanded fibroblasts and clonal lymphocyte populations isolated directly from a healthy human donor.
Subject headings
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Keyword
- Single-cell DNA sequencing
- Single-cell variant calling
- Somatic variation
Publication and Content Type
- ref (subject category)
- art (subject category)
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To the university's database
- By the author/editor
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Hard, Joanna
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Al Hakim, Ezeddi ...
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Kindblom, Marie
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Björklund, Åsa K ...
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Sennblad, Bengt
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Demirci, Ilke
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show more...
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Paterlini, Marta
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Reu, Pedro
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Borgström, Erik
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Stahl, Patrik L.
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Michaelsson, Jak ...
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Mold, Jeff E.
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Frisen, Jonas
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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
- Articles in the publication
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Genome Biology
- By the university
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Royal Institute of Technology
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Uppsala University
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Karolinska Institutet