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IsoCon: Deciphering highly similar multigene family transcripts from Iso-Seq data

View ORCID ProfileKristoffer Sahlin, Marta Tomaszkiewicz, View ORCID ProfileKateryna D. Makova, Paul Medvedev
doi: https://doi.org/10.1101/246066
Kristoffer Sahlin
1Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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Marta Tomaszkiewicz
2Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
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Kateryna D. Makova
2Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
3Center for Medical Genomics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
4Center for Computational Biology and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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Paul Medvedev
1Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA.
3Center for Medical Genomics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
4Center for Computational Biology and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
5Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
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Abstract

A significant portion of genes in vertebrate genomes belongs to multigene families, with each family containing several gene copies whose presence/absence can be highly variable across individuals. For example, each Y chromosome ampliconic gene family harbors several nearly identical (up to 99.99%) gene copies. Existing de novo techniques for assaying the sequences of such highly-similar gene families fall short of reconstructing end to end transcripts with nucleotide-level precision or assigning them to their respective gene copies. We present IsoCon, a novel approach that combines experimental and computational techniques that leverage the power of long PacBio Iso-Seq reads to determine the full-length transcripts of highly similar multicopy gene families. IsoCon uses a cautiously iterative process to correct errors, followed by a statistical framework that allows it to distinguish errors from true variants with high precision. IsoCon outperforms existing methods for transcriptome analysis of Y ampliconic gene families in both simulated and real human data and is able to detect rare transcripts that differ by as little as one base pair from much more abundant transcripts. IsoCon has allowed us to detect an unprecedented number of novel isoforms, as well as to derive estimates on the number of gene copies in human Y ampliconic gene families.

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Posted January 10, 2018.
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IsoCon: Deciphering highly similar multigene family transcripts from Iso-Seq data
Kristoffer Sahlin, Marta Tomaszkiewicz, Kateryna D. Makova, Paul Medvedev
bioRxiv 246066; doi: https://doi.org/10.1101/246066
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IsoCon: Deciphering highly similar multigene family transcripts from Iso-Seq data
Kristoffer Sahlin, Marta Tomaszkiewicz, Kateryna D. Makova, Paul Medvedev
bioRxiv 246066; doi: https://doi.org/10.1101/246066

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