Defining Human Embryo Phenotypes by Cohort-Specific Prognostic Factors
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Mendeley | Further Information

{"title"=>"Defining human embryo phenotypes by cohort-specific prognostic factors", "type"=>"journal", "authors"=>[{"first_name"=>"Sunny H.", "last_name"=>"Jun", "scopus_author_id"=>"7103305521"}, {"first_name"=>"Bokyung", "last_name"=>"Choi", "scopus_author_id"=>"24722792700"}, {"first_name"=>"Lora", "last_name"=>"Shahine", "scopus_author_id"=>"8660095100"}, {"first_name"=>"Lynn M.", "last_name"=>"Westphal", "scopus_author_id"=>"7003748779"}, {"first_name"=>"Barry", "last_name"=>"Behr", "scopus_author_id"=>"7003959268"}, {"first_name"=>"Renee A.", "last_name"=>"Reijo Pera", "scopus_author_id"=>"56777776600"}, {"first_name"=>"Wing H.", "last_name"=>"Wong", "scopus_author_id"=>"7403972659"}, {"first_name"=>"Mylene W.M.", "last_name"=>"Yao", "scopus_author_id"=>"7403318211"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"18596962", "sgr"=>"50149112645", "doi"=>"10.1371/journal.pone.0002562", "scopus"=>"2-s2.0-50149112645", "pui"=>"352212098", "isbn"=>"1932-6203 (Electronic)", "issn"=>"19326203"}, "id"=>"c7eab68d-51ec-3e3a-aef0-83e8cf112794", "abstract"=>"Hundreds of thousands of human embryos are cultured yearly at in vitro fertilization (IVF) centers worldwide, yet the vast majority fail to develop in culture or following transfer to the uterus. However, human embryo phenotypes have not been formally defined, and current criteria for embryo transfer largely focus on characteristics of individual embryos. We hypothesized that embryo cohort-specific variables describing sibling embryos as a group may predict developmental competence as measured by IVF cycle outcomes and serve to define human embryo phenotypes.", "link"=>"http://www.mendeley.com/research/defining-human-embryo-phenotypes-cohortspecific-prognostic-factors", "reader_count"=>15, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>7, "Student > Ph. D. Student"=>2, "Student > Master"=>3, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>7, "Student > Ph. D. Student"=>2, "Student > Master"=>3, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Medicine and Dentistry"=>2, "Agricultural and Biological Sciences"=>8, "Physics and Astronomy"=>1, "Psychology"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Unspecified"=>{"Unspecified"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"United States"=>1}, "group_count"=>0}

Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/927379"], "description"=>"<p>Distribution of all embryos from 665 fresh, non-donor IVF cases according to their cell number on Day 3.</p>", "links"=>[], "tags"=>["embryos", "665", "non-donor", "ivf", "cases"], "article_id"=>597814, "categories"=>["Immunology", "Medicine", "Developmental Biology", "Cell Biology", "Infectious Diseases"], "users"=>["Sunny H. Jun", "Bokyung Choi", "Lora Shahine", "Lynn M. Westphal", "Barry Behr", "Renee A. Reijo Pera", "Wing H. Wong", "Mylene W. M. Yao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002562.g002", "stats"=>{"downloads"=>4, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_all_embryos_from_665_fresh_non_donor_IVF_cases_according_to_their_cell_number_on_Day_3_/597814", "title"=>"Distribution of all embryos from 665 fresh, non-donor IVF cases according to their cell number on Day 3.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-02 02:10:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/457342", "https://ndownloader.figshare.com/files/457347", "https://ndownloader.figshare.com/files/457360"], "description"=>"<div><h3>Background</h3><p>Hundreds of thousands of human embryos are cultured yearly at <em>in vitro</em> fertilization (IVF) centers worldwide, yet the vast majority fail to develop in culture or following transfer to the uterus. However, human embryo phenotypes have not been formally defined, and current criteria for embryo transfer largely focus on characteristics of individual embryos. We hypothesized that embryo cohort-specific variables describing sibling embryos as a group may predict developmental competence as measured by IVF cycle outcomes and serve to define human embryo phenotypes.</p><h3>Methodology/Principal Findings</h3><p>We retrieved data for all 1117 IVF cycles performed in 2005 at Stanford University Medical Center, and further analyzed clinical data from the 665 fresh IVF, non-donor cycles and their associated 4144 embryos. Thirty variables representing patient characteristics, clinical diagnoses, treatment protocol, and embryo parameters were analyzed in an unbiased manner by regression tree models, based on dichotomous pregnancy outcomes defined by positive serum ß-human chorionic gonadotropin (ß-hCG). IVF cycle outcomes were most accurately predicted at ∼70% by four non-redundant, embryo cohort-specific variables that, remarkably, were more informative than any measures of individual, transferred embryos: Total number of embryos, number of 8-cell embryos, rate (percentage) of cleavage arrest in the cohort and day 3 follicle stimulating hormone (FSH) level. While three of these variables captured the effects of other significant variables, only the rate of cleavage arrest was independent of any known variables.</p><h3>Conclusions/Significance</h3><p>Our findings support defining human embryo phenotypes by non-redundant, prognostic variables that are specific to sibling embryos in a cohort.</p></div>", "links"=>[], "tags"=>["defining", "embryo", "phenotypes", "cohort-specific", "prognostic", "factors"], "article_id"=>150091, "categories"=>["Immunology", "Medicine", "Developmental Biology", "Cell Biology", "Cancer"], "users"=>["Sunny H. Jun", "Bokyung Choi", "Lora Shahine", "Lynn M. Westphal", "Barry Behr", "Renee A. Reijo Pera", "Wing H. Wong", "Mylene W. M. Yao"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0002562.s001", "https://dx.doi.org/10.1371/journal.pone.0002562.s002", "https://dx.doi.org/10.1371/journal.pone.0002562.s003"], "stats"=>{"downloads"=>6, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Defining_Human_Embryo_Phenotypes_by_Cohort_Specific_Prognostic_Factors/150091", "title"=>"Defining Human Embryo Phenotypes by Cohort-Specific Prognostic Factors", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-07-02 00:01:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/927447"], "description"=>"*<p>Positive and negative estimates indicate association with positive and negative pregnancy outcomes, respectively.</p>†<p>Clinical infertility diagnoses that were not significantly associated with pregnancy outcome (p-value >0.05) were not listed: uterine factor, polycystic ovarian syndrome, endometriosis, tubal ligation, tubal disease, hydrosalpinges, unexplained infertility, and “other diagnoses”. Each IVF case may have more than one clinical infertility diagnosis.</p>‡<p>Cleavage arrest rate is defined as the percentage of embryos with 4 or fewer cells on Day 3 of <i>in vitro</i> culture.</p>§<p>Day 5 embryo transfer is arbitrarily listed under Parameters of Transferred Embryos. It can also be considered an Embryo Cohort Parameter, as it depends on the total number of embryos and the number of 8-cell embryos.</p>", "links"=>[], "tags"=>["developmental biology", "evidence-based healthcare", "developmental biology/embryology", "developmental biology/stem cells", "evidence-based healthcare/clinical decision-making", "women's health/female subfertility and gynecological endocrinology"], "article_id"=>597894, "categories"=>["Immunology", "Medicine", "Developmental Biology", "Cell Biology", "Infectious Diseases"], "users"=>["Sunny H. Jun", "Bokyung Choi", "Lora Shahine", "Lynn M. Westphal", "Barry Behr", "Renee A. Reijo Pera", "Wing H. Wong", "Mylene W. M. Yao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002562.t001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Association_of_each_variable_with_pregnancy_outcome_/597894", "title"=>"Association of each variable with pregnancy outcome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-07-02 02:11:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/927277"], "description"=>"<p>A) IVF cycles performed in 2005. B) Utilization of oocytes and embryos in 665 fresh, non-donor IVF cycles. * All numbers in Panel A indicate the number of cycles and numbers in Panel B indicate the number of oocytes or embryos. Fresh cycles are defined by ovarian stimulation of gonadotropins and embryo transfer performed within the same cycle; cryopreserved cycles utilize embryos that were obtained and cryopreserved from a previous cycle; “freeze-all” are cycles in which ovarian stimulation was performed, but embryos were cryopreserved instead of being transferred back within the same cycle for medical or non-medical reasons. 157 cycles were removed from analysis for a variety of medical and non-medical reasons that did not result in fresh embryo transfer (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002562#pone.0002562.s001\" target=\"_blank\"><i>SI Text</i></a> for details).</p>", "links"=>[], "tags"=>["developmental biology", "evidence-based healthcare", "developmental biology/embryology", "developmental biology/stem cells", "evidence-based healthcare/clinical decision-making", "women's health/female subfertility and gynecological endocrinology"], "article_id"=>597713, "categories"=>["Immunology", "Medicine", "Developmental Biology", "Cell Biology", "Infectious Diseases"], "users"=>["Sunny H. Jun", "Bokyung Choi", "Lora Shahine", "Lynn M. Westphal", "Barry Behr", "Renee A. Reijo Pera", "Wing H. Wong", "Mylene W. M. Yao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002562.g001", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Source_of_data_/597713", "title"=>"Source of data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-02 02:08:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/927489"], "description"=>"*<p>Cohort phenotypes defined by thresholds of non-redundant prognostic variables. Each set of conditions (A–E) use “AND” as the operator where more than one condition is listed.</p>†<p>No. of cases that satisfy the threshold conditions and have pregnancy outcome. This percentage is calculated by using the No. Applicable Cases as denominator. In general, conditions that discriminate between pregnancy and no pregnancy outcomes more highly are more robust and are expected to be more useful in both clinical management and translational research.</p>‡<p>No. of cases that satisfy the threshold conditions and have no pregnancy outcome. This percentage is calculated by using the No. Applicable Cases as denominator.</p>§<p>The No. Applicable Cases is the total number of cases that satisfy the threshold conditions. This percentage is calculated by using the total number of cycles (665) as the denominator. In general, the larger the number of applicable cases, the more useful the set of conditions are for clinical management and counseling. However, for the purpose of translational research, conditions that define a smaller number of cases may have more specific correlates on a molecular level.</p>¶<p>No. Trees shows the number of CART trees that utilize each set of conditions. There are a total of 5 trees. (See Supplemental Results.) Increased utilization indicates “usefulness” or “robustness” of that particular set of conditions.</p>∥<p>Reference condition against which the Odds Ratio and 95% C.I. for having no pregnancy is calculated.</p>**<p>Conditions A–E are listed from most robust and “useful” to least “useful” based on: the number of trees that utilize each set of conditions, the number of applicable cases, and the odds ratio and 95% CI.</p>", "links"=>[], "tags"=>["thresholds", "cohort-specific"], "article_id"=>597938, "categories"=>["Immunology", "Medicine", "Developmental Biology", "Cell Biology", "Infectious Diseases"], "users"=>["Sunny H. Jun", "Bokyung Choi", "Lora Shahine", "Lynn M. Westphal", "Barry Behr", "Renee A. Reijo Pera", "Wing H. Wong", "Mylene W. M. Yao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002562.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prognostic_thresholds_defining_cohort_specific_phenotypes_/597938", "title"=>"Prognostic thresholds defining cohort-specific phenotypes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-07-02 02:12:18"}

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  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"9"}
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  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"1"}
  • {"unique-ip"=>"1", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"11"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"12"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"1"}
  • {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2015", "month"=>"11"}
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  • {"unique-ip"=>"2", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"8"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
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  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
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  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
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  • {"unique-ip"=>"13", "full-text"=>"8", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
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  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"12", "full-text"=>"12", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
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  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"11", "full-text"=>"11", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"12", "full-text"=>"13", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
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Relative Metric

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