Genome-Wide Massively Parallel Sequencing of Formaldehyde Fixed-Paraffin Embedded (FFPE) Tumor Tissues for Copy-Number- and Mutation-Analysis
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{"title"=>"Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number-and mutation-analysis", "type"=>"journal", "authors"=>[{"first_name"=>"Michal R.", "last_name"=>"Schweiger", "scopus_author_id"=>"9240082000"}, {"first_name"=>"Martin", "last_name"=>"Kerick", "scopus_author_id"=>"26632263800"}, {"first_name"=>"Bernd", "last_name"=>"Timmermann", "scopus_author_id"=>"15825796600"}, {"first_name"=>"Marcus W.", "last_name"=>"Albrecht", "scopus_author_id"=>"26631770700"}, {"first_name"=>"Tatjana", "last_name"=>"Borodina", "scopus_author_id"=>"7005211553"}, {"first_name"=>"Dmitri", "last_name"=>"Parkhomchuck", "scopus_author_id"=>"26631969900"}, {"first_name"=>"Kurt", "last_name"=>"Zatloukal", "scopus_author_id"=>"23989863900"}, {"first_name"=>"Hans", "last_name"=>"Lehrach", "scopus_author_id"=>"57050399800"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-65849458558", "sgr"=>"65849458558", "pui"=>"354613566", "isbn"=>"1932-6203 (Electronic)", "pmid"=>"19440246", "doi"=>"10.1371/journal.pone.0005548"}, "id"=>"815a0bd4-92da-31c4-96b6-95591b14994a", "abstract"=>"BACKGROUND: Cancer re-sequencing programs rely on DNA isolated from fresh snap frozen tissues, the preparation of which is combined with additional preservation efforts. Tissue samples at pathology departments are routinely stored as formalin-fixed and paraffin-embedded (FFPE) samples and their use would open up access to a variety of clinical trials. However, FFPE preparation is incompatible with many down-stream molecular biology techniques such as PCR based amplification methods and gene expression studies.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: Here we investigated the sample quality requirements of FFPE tissues for massively parallel short-read sequencing approaches. We evaluated key variables of pre-fixation, fixation related and post-fixation processes that occur in routine medical service (e.g. degree of autolysis, duration of fixation and of storage). We also investigated the influence of tissue storage time on sequencing quality by using material that was up to 18 years old. Finally, we analyzed normal and tumor breast tissues using the Sequencing by Synthesis technique (Illumina Genome Analyzer, Solexa) to simultaneously localize genome-wide copy number alterations and to detect genomic variations such as substitutions and point-deletions and/or insertions in FFPE tissue samples.\\n\\nCONCLUSIONS/SIGNIFICANCE: The application of second generation sequencing techniques on small amounts of FFPE material opens up the possibility to analyze tissue samples which have been collected during routine clinical work as well as in the context of clinical trials. This is in particular important since FFPE samples are amply available from surgical tumor resections and histopathological diagnosis, and comprise tissue from precursor lesions, primary tumors, lymphogenic and/or hematogenic metastases. Large-scale studies using this tissue material will result in a better prediction of the prognosis of cancer patients and the early identification of patients which will respond to therapy.", "link"=>"http://www.mendeley.com/research/genomewide-massively-parallel-sequencing-formaldehyde-fixedparaffin-embedded-ffpe-tumor-tissues-copy", "reader_count"=>180, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>11, "Librarian"=>2, "Student > Doctoral Student"=>5, "Researcher"=>70, "Student > Ph. D. Student"=>36, "Student > Postgraduate"=>7, "Other"=>14, "Student > Master"=>17, "Student > Bachelor"=>9, "Lecturer > Senior Lecturer"=>1, "Professor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>11, "Librarian"=>2, "Student > Doctoral Student"=>5, "Researcher"=>70, "Student > Ph. D. Student"=>36, "Student > Postgraduate"=>7, "Other"=>14, "Student > Master"=>17, "Student > Bachelor"=>9, "Lecturer > Senior Lecturer"=>1, "Professor"=>6}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>13, "Nursing and Health Professions"=>1, "Mathematics"=>2, "Agricultural and Biological Sciences"=>117, "Medicine and Dentistry"=>39, "Computer Science"=>2, "Economics, Econometrics and Finance"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>39}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>117}, "Computer Science"=>{"Computer Science"=>2}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"Argentina"=>1, "United States"=>10, "United Kingdom"=>2, "Spain"=>1, "Canada"=>1, "Netherlands"=>1, "Belgium"=>1, "Taiwan"=>1, "Denmark"=>1, "Brazil"=>1, "Italy"=>2, "Australia"=>1, "Germany"=>1}, "group_count"=>13}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/444823", "https://ndownloader.figshare.com/files/444841", "https://ndownloader.figshare.com/files/444862"], "description"=>"<div><h3>Background</h3><p>Cancer re-sequencing programs rely on DNA isolated from fresh snap frozen tissues, the preparation of which is combined with additional preservation efforts. Tissue samples at pathology departments are routinely stored as formalin-fixed and paraffin-embedded (FFPE) samples and their use would open up access to a variety of clinical trials. However, FFPE preparation is incompatible with many down-stream molecular biology techniques such as PCR based amplification methods and gene expression studies.</p><h3>Methodology/Principal Findings</h3><p>Here we investigated the sample quality requirements of FFPE tissues for massively parallel short-read sequencing approaches. We evaluated key variables of pre-fixation, fixation related and post-fixation processes that occur in routine medical service (e.g. degree of autolysis, duration of fixation and of storage). We also investigated the influence of tissue storage time on sequencing quality by using material that was up to 18 years old. Finally, we analyzed normal and tumor breast tissues using the Sequencing by Synthesis technique (Illumina Genome Analyzer, Solexa) to simultaneously localize genome-wide copy number alterations and to detect genomic variations such as substitutions and point-deletions and/or insertions in FFPE tissue samples.</p><h3>Conclusions/Significance</h3><p>The application of second generation sequencing techniques on small amounts of FFPE material opens up the possibility to analyze tissue samples which have been collected during routine clinical work as well as in the context of clinical trials. This is in particular important since FFPE samples are amply available from surgical tumor resections and histopathological diagnosis, and comprise tissue from precursor lesions, primary tumors, lymphogenic and/or hematogenic metastases. Large-scale studies using this tissue material will result in a better prediction of the prognosis of cancer patients and the early identification of patients which will respond to therapy.</p></div>", "links"=>[], "tags"=>["genome-wide", "massively", "parallel", "sequencing", "formaldehyde", "fixed-paraffin", "embedded", "tissues", "copy-number-", "mutation-analysis"], "article_id"=>147644, "categories"=>["Genetics", "Cancer", "Medicine"], "users"=>["Michal R. Schweiger", "Martin Kerick", "Bernd Timmermann", "Marcus W. Albrecht", "Tatjana Borodina", "Dmitri Parkhomchuk", "Kurt Zatloukal", "Hans Lehrach"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005548.s001", "https://dx.doi.org/10.1371/journal.pone.0005548.s002", "https://dx.doi.org/10.1371/journal.pone.0005548.s003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_Massively_Parallel_Sequencing_of_Formaldehyde_Fixed_Paraffin_Embedded_FFPE_Tumor_Tissues_for_Copy_Number_and_Mutation_Analysis/147644", "title"=>"Genome-Wide Massively Parallel Sequencing of Formaldehyde Fixed-Paraffin Embedded (FFPE) Tumor Tissues for Copy-Number- and Mutation-Analysis", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-05-14 02:07:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/898311"], "description"=>"<p>(A) Shown are the distributions of sequencing fragments over chromosome 1 using three different tissue conservation techniques Left: Snap frozen tissues, middle: FFPE tissue with 20 min. ischemia, and right: FFPE tissue with 60 min. ischemia. The red line depicts median genome coverage. (B) Chromosomal coverage ratio of snap frozen versus FFPE preparations of normal tissue samples. Each chromosome has been split into equal sized bins of 50 Kb size. The log2 ratios of unique reads per bin have been plotted across all chromosomes.</p>", "links"=>[], "tags"=>["sequencing", "fragments", "dna", "extracted", "ffpe"], "article_id"=>568762, "categories"=>["Genetics", "Infectious Diseases", "Medicine"], "users"=>["Michal R. Schweiger", "Martin Kerick", "Bernd Timmermann", "Marcus W. Albrecht", "Tatjana Borodina", "Dmitri Parkhomchuk", "Kurt Zatloukal", "Hans Lehrach"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005548.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_sequencing_fragments_for_DNA_extracted_from_snap_frozen_and_FFPE_breast_tissues_/568762", "title"=>"Distribution of sequencing fragments for DNA extracted from snap frozen and FFPE breast tissues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-14 02:26:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/898429"], "description"=>"<p>(A) DNA fragment coverage ratio of tumor versus normal tissue on five chromosomes. The x-axis represents the genomic position. The y-axis represents the log2 ratio of fragments per bin of tumor versus normal tissue. The fragment numbers are calculated per 120 Kb segment. The red lines depict the local averages as calculated by DNAcopy <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005548#pone.0005548-Venkatraman1\" target=\"_blank\">[12]</a>. Local differences in copy numbers exceeding two standard deviations are highlighted. (B) Detailed view of the fragment distribution of chromosome 8 from snap frozen and FFPE breast cancer tissue samples.</p>", "links"=>[], "tags"=>["variations", "dna", "ffpe", "cancer", "tissues"], "article_id"=>568877, "categories"=>["Genetics", "Infectious Diseases", "Medicine"], "users"=>["Michal R. Schweiger", "Martin Kerick", "Bernd Timmermann", "Marcus W. Albrecht", "Tatjana Borodina", "Dmitri Parkhomchuk", "Kurt Zatloukal", "Hans Lehrach"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005548.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Copy_number_variations_in_DNA_from_snap_frozen_and_FFPE_cancer_tissues_in_relation_to_normal_tissue_/568877", "title"=>"Copy number variations in DNA from snap frozen and FFPE cancer tissues in relation to normal tissue.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-14 02:27:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/898528"], "description"=>"<p>Using the Maq 0.7.1 software nucleotide exchanges were calculated for all possible transitions (e.g. A>G, A>C) for four snap frozen (SF) and five FFPE tissue samples <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005548#pone.0005548-Li1\" target=\"_blank\">[18]</a>. Shown are boxblots with NE rates as fractions of all mutations found per patient sample.</p>", "links"=>[], "tags"=>["rates", "dna", "ffpe"], "article_id"=>568976, "categories"=>["Genetics", "Infectious Diseases", "Medicine"], "users"=>["Michal R. Schweiger", "Martin Kerick", "Bernd Timmermann", "Marcus W. Albrecht", "Tatjana Borodina", "Dmitri Parkhomchuk", "Kurt Zatloukal", "Hans Lehrach"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005548.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nucleotide_exchange_rates_in_DNA_from_snap_frozen_and_FFPE_tissues_/568976", "title"=>"Nucleotide exchange rates in DNA from snap frozen and FFPE tissues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-14 02:29:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/898596"], "description"=>"<p>For each set, ‘common SNPs’ were calculated in relation to the snap frozen samples.</p>", "links"=>[], "tags"=>["ne", "ffpe"], "article_id"=>569050, "categories"=>["Genetics", "Infectious Diseases", "Medicine"], "users"=>["Michal R. Schweiger", "Martin Kerick", "Bernd Timmermann", "Marcus W. Albrecht", "Tatjana Borodina", "Dmitri Parkhomchuk", "Kurt Zatloukal", "Hans Lehrach"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005548.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequencing_results_NE_in_snap_frozen_and_FFPE_tissues_/569050", "title"=>"Sequencing results, NE in snap frozen and FFPE tissues.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-14 02:30:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/898617"], "description"=>"<p>NE for samples ID-1.0 (snap forzen) and ID-1.1 (FFPE).</p>", "links"=>[], "tags"=>["samples"], "article_id"=>569071, "categories"=>["Genetics", "Infectious Diseases", "Medicine"], "users"=>["Michal R. Schweiger", "Martin Kerick", "Bernd Timmermann", "Marcus W. Albrecht", "Tatjana Borodina", "Dmitri Parkhomchuk", "Kurt Zatloukal", "Hans Lehrach"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005548.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_NE_for_samples_ID_1_0_snap_forzen_and_ID_1_1_FFPE_/569071", "title"=>"NE for samples ID-1.0 (snap forzen) and ID-1.1 (FFPE).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-14 02:31:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/898645"], "description"=>"<p>Snap frozen and FFPE tissue samples used for sequencing.</p>", "links"=>[], "tags"=>["ffpe", "samples"], "article_id"=>569095, "categories"=>["Genetics", "Infectious Diseases", "Medicine"], "users"=>["Michal R. Schweiger", "Martin Kerick", "Bernd Timmermann", "Marcus W. Albrecht", "Tatjana Borodina", "Dmitri Parkhomchuk", "Kurt Zatloukal", "Hans Lehrach"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005548.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Snap_frozen_and_FFPE_tissue_samples_used_for_sequencing_/569095", "title"=>"Snap frozen and FFPE tissue samples used for sequencing.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-14 02:31:35"}

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Relative Metric

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