Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels
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{"title"=>"Decoding of superimposed traces produced by direct sequencing of heterozygous indels", "type"=>"journal", "authors"=>[{"first_name"=>"Dmitry A.", "last_name"=>"Dmitriev", "scopus_author_id"=>"7005975575"}, {"first_name"=>"Roman A.", "last_name"=>"Rakitov", "scopus_author_id"=>"6603650373"}], "year"=>2008, "source"=>"PLoS Computational Biology", "identifiers"=>{"pmid"=>"18654614", "doi"=>"10.1371/journal.pcbi.1000113", "sgr"=>"48249149566", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)", "scopus"=>"2-s2.0-48249149566", "issn"=>"1553734X", "pui"=>"352076425"}, "id"=>"553e0d9e-dca1-3e17-8f65-b06866038d8c", "abstract"=>"Direct Sanger sequencing of a diploid template containing a heterozygous insertion or deletion results in a difficult-to-interpret mixed trace formed by two allelic traces superimposed onto each other. Existing computational methods for deconvolution of such traces require knowledge of a reference sequence or the availability of both direct and reverse mixed sequences of the same template. We describe a simple yet accurate method, which uses dynamic programming optimization to predict superimposed allelic sequences solely from a string of letters representing peaks within an individual mixed trace. We used the method to decode 104 human traces (mean length 294 bp) containing heterozygous indels 5 to 30 bp with a mean of 99.1% bases per allelic sequence reconstructed correctly and unambiguously. Simulations with artificial sequences have demonstrated that the method yields accurate reconstructions when (1) the allelic sequences forming the mixed trace are sufficiently similar, (2) the analyzed fragment is significantly longer than the indel, and (3) multiple indels, if present, are well-spaced. Because these conditions occur in most encountered DNA sequences, the method is widely applicable. It is available as a free Web application Indelligent at http://ctap.inhs.uiuc.edu/dmitriev/indel.asp.", "link"=>"http://www.mendeley.com/research/decoding-superimposed-traces-produced-direct-sequencing-heterozygous-indels", "reader_count"=>91, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>7, "Researcher"=>32, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>4, "Student > Master"=>4, "Other"=>2, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>7, "Researcher"=>32, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>4, "Student > Master"=>4, "Other"=>2, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>9, "Materials Science"=>1, "Agricultural and Biological Sciences"=>69, "Medicine and Dentistry"=>3, "Physics and Astronomy"=>1, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>69}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "Cuba"=>1, "United States"=>3, "Brazil"=>2, "South Africa"=>2, "Mexico"=>1, "Germany"=>2, "Spain"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/926342"], "description"=>"<p>The fragments are shown on top of each panel, with their aligned optimal solutions and consensuses of these (on a yellow background) shown below. Solid links represent matches and dashed links mismatches, letters on a grey background represent bases with no positional homologs, blue letters represent ambiguous bases, and red letters mismatching bases. Configurations yielding equal maximum scores <i>ω</i> in (B), (C), and (D) are boxed. For the meanings of the IUPAC symbols see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000113#pcbi-1000113-g001\" target=\"_blank\">Figure 1</a>. (A) A fully periodic fragment. Only three of 11 cooptimal solutions with different single phase shifts are shown. The consensus of these solutions is identical to the mixed fragment itself. (B) A fragment containing an ambiguous base (here “K”) repeated throughout the length of the fragment at regular intervals coinciding with the magnitude of the phase shift. The corresponding sites remain ambiguous in the consensus. Cooptimal solutions of this type are found mostly among fragments that are short with respect to the indel. (C) A fragment having cooptimal solutions with the same number but different locations of mismatches. Note that mismatches can either represent SNPs or result from basecalling errors. (D) A fragment containing an insertion that can be variably positioned. At one site, both alternative configurations yield maximum <i>ω</i>, each with a different phase shift.</p>", "links"=>[], "tags"=>["situations", "cooptimal"], "article_id"=>596800, "categories"=>["Medicine", "Infectious Diseases"], "users"=>["Dmitry A. Dmitriev", "Roman A. Rakitov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000113.g005", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_four_main_situations_in_which_a_mixed_sequence_fragment_can_have_multiple_cooptimal_solutions_/596800", "title"=>"Examples of four main situations in which a mixed sequence fragment can have multiple cooptimal solutions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-25 01:53:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/456434", "https://ndownloader.figshare.com/files/456485", "https://ndownloader.figshare.com/files/456555", "https://ndownloader.figshare.com/files/456603", "https://ndownloader.figshare.com/files/456721"], "description"=>"<div><p>Direct Sanger sequencing of a diploid template containing a heterozygous insertion or deletion results in a difficult-to-interpret mixed trace formed by two allelic traces superimposed onto each other. Existing computational methods for deconvolution of such traces require knowledge of a reference sequence or the availability of both direct and reverse mixed sequences of the same template. We describe a simple yet accurate method, which uses dynamic programming optimization to predict superimposed allelic sequences solely from a string of letters representing peaks within an individual mixed trace. We used the method to decode 104 human traces (mean length 294 bp) containing heterozygous indels 5 to 30 bp with a mean of 99.1% bases per allelic sequence reconstructed correctly and unambiguously. Simulations with artificial sequences have demonstrated that the method yields accurate reconstructions when (1) the allelic sequences forming the mixed trace are sufficiently similar, (2) the analyzed fragment is significantly longer than the indel, and (3) multiple indels, if present, are well-spaced. Because these conditions occur in most encountered DNA sequences, the method is widely applicable. It is available as a free Web application Indelligent at <a href=\"http://ctap.inhs.uiuc.edu/dmitriev/indel.asp\">http://ctap.inhs.uiuc.edu/dmitriev/indel.asp</a>.</p></div>", "links"=>[], "tags"=>["decoding", "superimposed", "traces", "produced", "sequencing", "heterozygous", "indels"], "article_id"=>149896, "categories"=>["Medicine", "Cancer"], "users"=>["Dmitry A. Dmitriev", "Roman A. Rakitov"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000113.s001", "https://dx.doi.org/10.1371/journal.pcbi.1000113.s002", "https://dx.doi.org/10.1371/journal.pcbi.1000113.s003", "https://dx.doi.org/10.1371/journal.pcbi.1000113.s004", "https://dx.doi.org/10.1371/journal.pcbi.1000113.s005"], "stats"=>{"downloads"=>20, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Decoding_of_Superimposed_Traces_Produced_by_Direct_Sequencing_of_Heterozygous_Indels/149896", "title"=>"Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-07-25 02:44:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/926166"], "description"=>"<p>Circles represent bases and links represent positional homologies: solid links–matches, and dashed links–mismatches. Black closed circles represent bases that have no positional homologs. In (A) vertical columns represent successive configurations of an aligned solution. The pairs of bases at sites 3, 6, and 16 are colored. Curly brackets mark segments aligned with different phase shifts. In (B) vertical columns contain pairs of positional homologs, and gaps are inserted opposite to bases having no homologs; external gaps are shown as question marks. The horizontal distances between the bases of each colored configuration (arrows) represent the corresponding phase shifts <i>k<sub>i</sub></i>.</p>", "links"=>[], "tags"=>["renderings", "illustrating"], "article_id"=>596618, "categories"=>["Medicine", "Infectious Diseases"], "users"=>["Dmitry A. Dmitriev", "Roman A. Rakitov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000113.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_renderings_of_the_same_alignment_illustrating_the_concept_of_phase_shift_/596618", "title"=>"Two renderings of the same alignment, illustrating the concept of phase shift.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-25 01:50:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/925949"], "description"=>"<p>The trace resulted from direct sequencing of the pair is shown in (D). The one-base insertion is shown in bold face. Links between the allelic strings represent positional homologies. The bases forming mixed trace are highlighted with grey. The standard IUPAC symbols for 2-fold degenerate DNA bases are enclosed in the box.</p>", "links"=>[], "tags"=>["allelic", "sequences", "aligned", "unaligned", "translated"], "article_id"=>596396, "categories"=>["Medicine", "Infectious Diseases"], "users"=>["Dmitry A. Dmitriev", "Roman A. Rakitov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000113.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_pair_of_allelic_sequences_properly_aligned_A_unaligned_B_and_translated_into_a_consensus_C_/596396", "title"=>"A pair of allelic sequences properly aligned (A), unaligned (B), and translated into a consensus (C).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-25 01:46:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/926425"], "description"=>"<p>Bases corresponding to the lower allelic string in (A) are highlighted with grey. Note that one solution can be obtained from another by swapping the parts of the allelic strings between sites 8 and 16 (orange box).</p>", "links"=>[], "tags"=>["aligned", "solutions", "shifts", "insertion"], "article_id"=>596877, "categories"=>["Medicine", "Infectious Diseases"], "users"=>["Dmitry A. Dmitriev", "Roman A. Rakitov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000113.g006", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_aligned_solutions_of_the_same_mixed_fragment_representing_the_transition_between_the_phase_shifts_k_i__2_and_k_i__3_alternatively_as_a_long_insertion_A_or_a_short_insertion_B_/596877", "title"=>"Two aligned solutions of the same mixed fragment, representing the transition between the phase shifts <i>k<sub>i</sub></i> = 2 and <i>k<sub>i</sub></i> = 3, alternatively, as a “long” insertion (A) or a “short” insertion (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-25 01:54:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/926596"], "description"=>"<p>(A) Mean percent of erroneous bases per reconstructed string. (B) Percent of fragments reconstructed with incorrect indels. Each point represents 1,000 runs. For SD and additional statistics, see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000113#pcbi.1000113.s002\" target=\"_blank\">Table S2</a>.</p>", "links"=>[], "tags"=>["decoding", "simulated", "100", "bp", "fragments", "containing", "insertion"], "article_id"=>597039, "categories"=>["Medicine", "Infectious Diseases"], "users"=>["Dmitry A. Dmitriev", "Roman A. Rakitov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000113.g008", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Accuracy_of_decoding_of_simulated_100_bp_mixed_fragments_containing_a_single_insertion_of_variable_size_in_the_middle_/597039", "title"=>"Accuracy of decoding of simulated 100 bp mixed fragments containing a single insertion of variable size in the middle.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-25 01:57:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/926518"], "description"=>"<p>The horizontal axis represents divergence between the allelic strings forming each fragment. (A) Mean percent of erroneous bases per reconstructed string. (B) Mean percent of ambiguous bases per reconstructed string. Each point represents the mean of 1,000 runs. For SD and additional statistics, see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000113#pcbi.1000113.s001\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["decoding", "simulated", "fragments", "formed", "bp", "allelic"], "article_id"=>596968, "categories"=>["Medicine", "Infectious Diseases"], "users"=>["Dmitry A. Dmitriev", "Roman A. Rakitov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000113.g007", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Accuracy_of_decoding_of_simulated_mixed_fragments_formed_by_5_bp_shift_at_the_origin_of_one_of_two_allelic_strings_/596968", "title"=>"Accuracy of decoding of simulated mixed fragments formed by 5 bp shift at the origin of one of two allelic strings.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-25 01:56:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/926050"], "description"=>"<p>Links between bases of the actual allelic strings (top) indicate positional homologies. The chosen reference sequences each differ from the top allelic string at one site (bold letters). Subtraction of Reference 1 results in one site in each reconstructed allelic string remaining unknown (red letters). Subtraction of Reference 2 results in one incorrectly reconstructed site in each allelic string (red letters). Note that, in the last case, the reconstructed fragment is heterozygous at two sites (dashed homology links). For the meanings of the IUPAC symbols see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000113#pcbi-1000113-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["situations", "reference-based", "incomplete", "incorrect", "reconstructions"], "article_id"=>596506, "categories"=>["Medicine", "Infectious Diseases"], "users"=>["Dmitry A. Dmitriev", "Roman A. Rakitov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000113.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_situations_when_the_reference_based_approach_results_in_incomplete_or_incorrect_reconstructions_of_a_mixed_sequence_/596506", "title"=>"Examples of situations when the reference-based approach results in incomplete or incorrect reconstructions of a mixed sequence.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-25 01:48:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/926229"], "description"=>"<p>For the purpose of illustration, <i>K<sub>max</sub></i> is set to 2, and the weights <i>W<sub>m</sub></i>, <i>W<sub>ms</sub></i>, <i>W<sub>in</sub></i>, and <i>W<sub>ib</sub></i> are all set to 1. Alternative configurations for each site of the input fragment F (A) are stored in the matrix (B). For each <i>k<sub>i</sub></i> considered, 0, 1, and 2, a separate matrix is computed for <i>p</i> (C) and for <i>q</i> (D). Matrices for <i>k<sub>i</sub></i>>0 are initialized with basal values at each <i>i</i>≤<i>k<sub>i</sub></i>, shown in the grey cells. The remaining cells in the <i>p</i> matrices are filled out successively left to right and in the <i>q</i> matrices right to left. Each column has to be computed in all three matrices (one for each <i>k<sub>i</sub></i>) before proceeding to the next site. For <i>i</i>><i>k<sub>i</sub></i>, computing each <i>p</i> and <i>q</i> requires first computing three <i>p</i>′ and <i>q</i>′ scores, correspondingly, one for each possible phase shift at the, respectively, preceding or following site. These calculations are omitted for space reasons, except for <i>p</i>(6, 2, 1), included as an example. The matrix of <i>ω</i>(<i>i</i>, <i>z<sub>i</sub></i>, <i>k<sub>i</sub></i>) is obtained by summation of <i>p</i> and <i>q</i> matrices; for each <i>i</i> the maximum values <i>ω</i> are highlighted (E). The configurations that received the maximum <i>ω</i>, and the corresponding <i>k<sub>i</sub></i> are selected (F) to form the aligned solution (G). The site 7 remains ambiguous because both corresponding alternative configurations have yielded equal <i>ω</i>. The post-processing algorithm determines that only one of these can be incorporated without mismatches (H). The optimal aligned solution is output in the customary form (I). Symbols and conventions are as in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000113#pcbi-1000113-g003\" target=\"_blank\">Figure 3</a>, except the bases having no homologs are shown on a black background.</p>", "links"=>[], "tags"=>["steps", "decoding"], "article_id"=>596682, "categories"=>["Medicine", "Infectious Diseases"], "users"=>["Dmitry A. Dmitriev", "Roman A. Rakitov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000113.g004", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Main_steps_in_decoding_of_a_mixed_trace_/596682", "title"=>"Main steps in decoding of a mixed trace.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-25 01:51:22"}

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Relative Metric

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