cFinder: definition and quantification of multiple haplotypes in a mixed sample

BMC Research Notes
Norbert NiklasChristian Gabriel

Abstract

Next-generation sequencing allows for determining the genetic composition of a mixed sample. For instance, when performing resistance testing for BCR-ABL1 it is necessary to identify clones and define compound mutations; together with an exact quantification this may complement diagnosis and therapy decisions with additional information. Moreover, that applies not only to oncological issues but also determination of viral, bacterial or fungal infection. The efforts to retrieve multiple haplotypes (more than two) and proportion information from data with conventional software are difficult, cumbersome and demand multiple manual steps. Therefore, we developed a tool called cFinder that is capable of automatic detection of haplotypes and their accurate quantification within one sample. BCR-ABL1 samples containing multiple clones were used for testing and our cFinder could identify all previously found clones together with their abundance and even refine some results. Additionally, reads were simulated using GemSIM with multiple haplotypes, the detection was very close to linear (R(2) = 0.96). Our aim is not to deduce haploblocks over statistics, but to characterize one sample's composition precisely. As a result the cFinder report...Continue Reading

References

Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Feb 18, 2012·BMC Genomics·Kerensa E McElroyTorsten Thomas
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Feb 25, 2014·Nature Biotechnology·Volodymyr KuleshovMichael Snyder

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Citations

Dec 15, 2015·Nature Biotechnology·Volodymyr KuleshovMichael Snyder
May 3, 2016·International Journal of Molecular Sciences·Sandra PreunerChristian Gabriel
Jun 30, 2016·Database : the Journal of Biological Databases and Curation·Tian TianZhen Su
May 26, 2018·Briefings in Bioinformatics·Tingting ShaoYongsheng Li
Dec 18, 2018·Frontiers in Genetics·Jiaotong YangZhen Su

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Methods Mentioned

BETA
454 profile

Software Mentioned

SAM
CLCbio
GS Amplicon Variant Analyzer (
AVA
mathop
Large Gap Mapper
cFinder
GemSIM
GemHaps
Genomics Workbench

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