Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data
Identifieur interne : 000429 ( Main/Exploration ); précédent : 000428; suivant : 000430Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data
Auteurs : Akio Miyao [Japon] ; Jianyu Song Kiyomiya [Japon] ; Keiko Iida [Japon] ; Koji Doi [Japon] ; Hiroshi Yasue [Japon]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2019.
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Abstract
Accurate detection of polymorphisms with a next generation sequencer data is an important element of current genetic analysis. However, there is still no detection pipeline that is completely reliable.
We demonstrate two new detection methods of polymorphisms focusing on the Polymorphic Edge (PED). In the matching between two homologous sequences, the first mismatched base to appear is the SNP, or the edge of the structural variation. The first method is based on
Using Polymorphic Edge Detection (PED), the
The PED software is available at:
The online version of this article (10.1186/s12859-019-2955-6) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12859-019-2955-6
PubMed: 31253084
PubMed Central: 6599308
Affiliations:
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sortKey="Kiyomiya, Jianyu Song" sort="Kiyomiya, Jianyu Song" uniqKey="Kiyomiya J" first="Jianyu Song" last="Kiyomiya">Jianyu Song Kiyomiya</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2222 0432</institution-id><institution-id institution-id-type="GRID">grid.416835.d</institution-id><institution>Institute of Crop Science,</institution><institution>National Agriculture and Food Research Organization,</institution></institution-wrap>2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518 Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>2-1-2, Kannondai, Tsukuba, Ibaraki</wicri:regionArea><wicri:noRegion>Ibaraki</wicri:noRegion></affiliation></author><author><name sortKey="Iida, Keiko" sort="Iida, Keiko" uniqKey="Iida K" first="Keiko" last="Iida">Keiko Iida</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2222 0432</institution-id><institution-id institution-id-type="GRID">grid.416835.d</institution-id><institution>Institute of Crop Science,</institution><institution>National Agriculture and Food Research Organization,</institution></institution-wrap>2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518 Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>2-1-2, Kannondai, Tsukuba, Ibaraki</wicri:regionArea><wicri:noRegion>Ibaraki</wicri:noRegion></affiliation></author><author><name sortKey="Doi, Koji" sort="Doi, Koji" uniqKey="Doi K" first="Koji" last="Doi">Koji Doi</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Tsukuba Gene Technology Laboratories Inc, 6-320, Arakawaoki, Tsuchiura, Ibaraki, 300-0873 Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tsukuba Gene Technology Laboratories Inc, 6-320, Arakawaoki, Tsuchiura, Ibaraki</wicri:regionArea><wicri:noRegion>Ibaraki</wicri:noRegion></affiliation></author><author><name sortKey="Yasue, Hiroshi" sort="Yasue, Hiroshi" uniqKey="Yasue H" first="Hiroshi" last="Yasue">Hiroshi Yasue</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Tsukuba Gene Technology Laboratories Inc, 6-320, Arakawaoki, Tsuchiura, Ibaraki, 300-0873 Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tsukuba Gene Technology Laboratories Inc, 6-320, Arakawaoki, Tsuchiura, Ibaraki</wicri:regionArea><wicri:noRegion>Ibaraki</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term><term>High-Throughput Nucleotide Sequencing</term><term>Polymorphism, Single Nucleotide</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Biologie informatique ()</term><term>Logiciel</term><term>Polymorphisme de nucléotide simple</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term><term>Polymorphism, Single Nucleotide</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Biologie informatique</term><term>Logiciel</term><term>Polymorphisme de nucléotide simple</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p id="Par1">Accurate detection of polymorphisms with a next generation sequencer data is an important element of current genetic analysis. However, there is still no detection pipeline that is completely reliable.</p></sec><sec><title>Result</title><p id="Par2">We demonstrate two new detection methods of polymorphisms focusing on the Polymorphic Edge (PED). In the matching between two homologous sequences, the first mismatched base to appear is the SNP, or the edge of the structural variation. The first method is based on <italic>k</italic>-mers from short reads and detects polymorphic edges with <italic>k</italic>-mers for which there is no match between target and control, making it possible to detect SNPs by direct comparison of short-reads in two datasets (target and control) without a reference genome sequence. The second method is based on bidirectional alignment to detect polymorphic edges, not only SNPs but also insertions, deletions, inversions and translocations. Using these two methods, we succeed in making a high-quality comparison map between rice cultivars showing good match to the theoretical value of introgression, and in detecting specific large deletions across cultivars.</p></sec><sec><title>Conclusions</title><p id="Par3">Using Polymorphic Edge Detection (PED), the <italic>k</italic>-mer method is able to detect SNPs by direct comparison of short-reads in two datasets without genomic alignment step, and the bidirectional alignment method is able to detect SNPs and structural variations from even single-end short-reads. The PED is an efficient tool to obtain accurate data for both SNPs and structural variations.</p></sec><sec><title>Availability</title><p id="Par4">The PED software is available at: <ext-link ext-link-type="uri" xlink:href="https://github.com/akiomiyao/ped">https://github.com/akiomiyao/ped</ext-link>.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (10.1186/s12859-019-2955-6) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author><author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Langmead, B" uniqKey="Langmead B">B Langmead</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL 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sort="Miyao, Akio" uniqKey="Miyao A" first="Akio" last="Miyao">Akio Miyao</name></noRegion><name sortKey="Doi, Koji" sort="Doi, Koji" uniqKey="Doi K" first="Koji" last="Doi">Koji Doi</name><name sortKey="Iida, Keiko" sort="Iida, Keiko" uniqKey="Iida K" first="Keiko" last="Iida">Keiko Iida</name><name sortKey="Kiyomiya, Jianyu Song" sort="Kiyomiya, Jianyu Song" uniqKey="Kiyomiya J" first="Jianyu Song" last="Kiyomiya">Jianyu Song Kiyomiya</name><name sortKey="Yasue, Hiroshi" sort="Yasue, Hiroshi" uniqKey="Yasue H" first="Hiroshi" last="Yasue">Hiroshi Yasue</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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