The Experts below are selected from a list of 324 Experts worldwide ranked by ideXlab platform
Erica K Barnell - One of the best experts on this subject based on the ideXlab platform.
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Standard Operating Procedure for curation and clinical interpretation of variants in cancer
Genome Medicine, 2019Co-Authors: Arpad M. Danos, Erica K Barnell, Kilannin Krysiak, Lana M Sheta, Adam C. Coffman, Joshua F. Mcmichael, Susanna Kiwala, Nicholas C. Spies, Shahil P. Pema, Lynzey KujanAbstract:Manually curated variant knowledgebases and their associated knowledge models are serving an increasingly important role in distributing and interpreting variants in cancer. These knowledgebases vary in their level of public accessibility, and the complexity of the models used to capture clinical knowledge. CIViC (Clinical Interpretation of Variants in Cancer - www.civicdb.org ) is a fully open, free-to-use cancer variant interpretation knowledgebase that incorporates highly detailed curation of evidence obtained from peer-reviewed publications and meeting abstracts, and currently holds over 6300 Evidence Items for over 2300 variants derived from over 400 genes. CIViC has seen increased adoption by, and also undertaken collaboration with, a wide range of users and organizations involved in research. To enhance CIViC’s clinical value, regular submission to the ClinVar database and pursuit of other regulatory approvals is necessary. For this reason, a formal peer reviewed curation guideline and discussion of the underlying principles of curation is needed. We present here the CIViC knowledge model, standard Operating Procedures (SOP) for variant curation, and detailed examples to support community-driven curation of cancer variants.
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standard Operating Procedure for somatic variant refinement of sequencing data with paired tumor and normal samples
Genetics in Medicine, 2019Co-Authors: Erica K Barnell, Peter Ronning, Katie M Campbell, Kilannin Krysiak, Benjamin J Ainscough, Lana M Sheta, Shahil Pema, Alina Schmidt, Megan Richters, Kelsy C CottoAbstract:Following automated variant calling, manual review of aligned read sequences is required to identify a high-quality list of somatic variants. Despite widespread use in analyzing sequence data, methods to standardize manual review have not been described, resulting in high inter- and intralab variability. This manual review standard Operating Procedure (SOP) consists of methods to annotate variants with four different calls and 19 tags. The calls indicate a reviewer’s confidence in each variant and the tags indicate commonly observed sequencing patterns and artifacts that inform the manual review call. Four individuals were asked to classify variants prior to, and after, reading the SOP and accuracy was assessed by comparing reviewer calls with orthogonal validation sequencing. After reading the SOP, average accuracy in somatic variant identification increased by 16.7% (p value = 0.0298) and average interreviewer agreement increased by 12.7% (p value < 0.001). Manual review conducted after reading the SOP did not significantly increase reviewer time. This SOP supports and enhances manual somatic variant detection by improving reviewer accuracy while reducing the interreviewer variability for variant calling and annotation.
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standard Operating Procedure for somatic variant refinement of tumor sequencing data
bioRxiv, 2018Co-Authors: Erica K Barnell, Peter Ronning, Katie M Campbell, Kilannin Krysiak, Benjamin J Ainscough, Cody Ramirez, Zachary L Skidmore, Felicia Gomez, Lee Trani, Matthew K MatlockAbstract:Purpose: Manual review of aligned sequencing reads is required to develop a high-quality list of somatic variants from massively parallel sequencing data (MPS). Despite widespread use in analyzing MPS data, there has been little attempt to describe methods for manual review, resulting in high inter- and intra-lab variability in somatic variant detection and characterization of tumors. Methods: Open source software was used to develop an optimal method for manual review setup. We also developed a systemic approach to visually inspect each variant during manual review. Results: We present a standard Operating Procedures for somatic variant refinement for use by manual reviewers. The approach is enhanced through representative examples of 4 different manual review categories that indicate a reviewer's confidence in the somatic variant call and 19 annotation tags that contextualize commonly observed sequencing patterns during manual review. Representative examples provide detailed instructions on how to classify variants during manual review to rectify lack of confidence in automated somatic variant detection. Conclusion: Standardization of somatic variant refinement through systematization of manual review will improve the consistency and reproducibility of identifying true somatic variants after automated variant calling.
James G Pfaus - One of the best experts on this subject based on the ideXlab platform.
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a standardized diagnostic interview for hypoactive sexual desire disorder in women standard Operating Procedure sop part 2
The Journal of Sexual Medicine, 2013Co-Authors: Johannes Bitzer, Annamaria Giraldi, James G PfausAbstract:ABSTRACT Introduction Taking into account that Hypoactive Sexual Desire Disorder (HSDD) is a patient-reported symptom and that the disorder is in general the result of the interaction of biological and psychosocial factors (see part 1), it is necessary to provide healthcare professionals with an Operating Procedure that is patient centered and multidimensional. Aim Describing a patient-centered and multidimensional standard Procedure to diagnose and manage HSDD on a primary care level. Methods Review of the literature. Semistructured interview and description of process. Result The interactive process with the patient follows several steps: initiation, narrative of the patient to understand the individual profile of the disorder, differentiating questions, descriptive diagnosis, exploration of conditioning biomedical, individual psychological, interpersonal, and sociocultural factors (including biomedical examinations), establishment of a biopsychosocial comprehensive explanatory diagnosis, which can be summarized in a nine-field matrix. This matrix will serve as orientation for therapeutic interventions adapted to the individual person. These interventions should always be based on basic counseling as a basis of treatment. Then adapted to the individual condition specific hormonal treatments (mainly estrogen and testosterone alone or combined) can be used after exclusion of contraindications. In patients with predominant psychosocial factors contributing to HSDD individual or couple psychotherapy is indicated. Psychopharmacological drugs are in development and partially investigated and will add to the therapeutic possibilities in the future. Conclusion. This model can serve as an ideal basis for the approach to the female patient with HSDD. It can be adapted to the individual clinical setting. Bitzer J, Giraldi A, and Pfaus J. A standardized diagnostic interview for Hypoactive Sexual Desire Disorder in women: standard Operating Procedure (SOP part 2). J Sex Med **;**:**–**.
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sexual desire and hypoactive sexual desire disorder in women introduction and overview standard Operating Procedure sop part 1
The Journal of Sexual Medicine, 2013Co-Authors: Johannes Bitzer, Annamaria Giraldi, James G PfausAbstract:ABSTRACT Introduction Hypoactive sexual desire disorder (HSDD) is defined in Diagnostic and Statistical Manual of Mental Disorders Fourth Edition as persistent or recurrent deficiency (or absence) of sexual fantasies/thoughts, and/or desire for or receptivity to sexual activity, which causes personal distress. As a largely subjective experience, sexual desire may or may not be accompanied by externally observable changes in sexual behavior. Aim Describe the models of understanding HSDD and the contributing factors to provide the basis for a diagnostic interview and guidance for care for healthcare professionals as a standard Operating Procedure method. Review of the literature. Results There are several models which have been developed to describe sexual desire, although there is still no universally accepted definition or description of it. The models are generally divided into more general twofactor models (e.g., excitation–inhibition, appetitive–consummatory) or more specific multifactorial models (in which the differentcomponents of sexual activity and their interaction are delineated). The etiology of the disorder is generally considered as multifactorial. Biomedical factors like diseases, drugs, and hormones, and psychological factors like life events, sexual biography, affective state, etc., as well as interpersonal factors like partner satisfaction, communication, duration of the relationship, and sociocultural factors interact with each other and contribute to the individualexperience of desire or lack or absence of desire. In analogy to the multifactorial pathogenesis the therapeutic approach is usually multidimensional and includes basic counseling, individual and couple psychotherapy, hormonal and psychopharmacological treatment. Conclusion The standard operation Procedure for HSDD in women must be based on a biopsychosocial, multidimensional, and integrative perspective. Bitzer J, Giraldi A, and Pfaus J. Sexual desire and hypoactive sexual desire disorder in women. Introduction and overview. Standard Operating Procedure (SOP part 1). J Sex Med **;**:**–**.
Kilannin Krysiak - One of the best experts on this subject based on the ideXlab platform.
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Standard Operating Procedure for curation and clinical interpretation of variants in cancer
Genome Medicine, 2019Co-Authors: Arpad M. Danos, Erica K Barnell, Kilannin Krysiak, Lana M Sheta, Adam C. Coffman, Joshua F. Mcmichael, Susanna Kiwala, Nicholas C. Spies, Shahil P. Pema, Lynzey KujanAbstract:Manually curated variant knowledgebases and their associated knowledge models are serving an increasingly important role in distributing and interpreting variants in cancer. These knowledgebases vary in their level of public accessibility, and the complexity of the models used to capture clinical knowledge. CIViC (Clinical Interpretation of Variants in Cancer - www.civicdb.org ) is a fully open, free-to-use cancer variant interpretation knowledgebase that incorporates highly detailed curation of evidence obtained from peer-reviewed publications and meeting abstracts, and currently holds over 6300 Evidence Items for over 2300 variants derived from over 400 genes. CIViC has seen increased adoption by, and also undertaken collaboration with, a wide range of users and organizations involved in research. To enhance CIViC’s clinical value, regular submission to the ClinVar database and pursuit of other regulatory approvals is necessary. For this reason, a formal peer reviewed curation guideline and discussion of the underlying principles of curation is needed. We present here the CIViC knowledge model, standard Operating Procedures (SOP) for variant curation, and detailed examples to support community-driven curation of cancer variants.
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standard Operating Procedure for somatic variant refinement of sequencing data with paired tumor and normal samples
Genetics in Medicine, 2019Co-Authors: Erica K Barnell, Peter Ronning, Katie M Campbell, Kilannin Krysiak, Benjamin J Ainscough, Lana M Sheta, Shahil Pema, Alina Schmidt, Megan Richters, Kelsy C CottoAbstract:Following automated variant calling, manual review of aligned read sequences is required to identify a high-quality list of somatic variants. Despite widespread use in analyzing sequence data, methods to standardize manual review have not been described, resulting in high inter- and intralab variability. This manual review standard Operating Procedure (SOP) consists of methods to annotate variants with four different calls and 19 tags. The calls indicate a reviewer’s confidence in each variant and the tags indicate commonly observed sequencing patterns and artifacts that inform the manual review call. Four individuals were asked to classify variants prior to, and after, reading the SOP and accuracy was assessed by comparing reviewer calls with orthogonal validation sequencing. After reading the SOP, average accuracy in somatic variant identification increased by 16.7% (p value = 0.0298) and average interreviewer agreement increased by 12.7% (p value < 0.001). Manual review conducted after reading the SOP did not significantly increase reviewer time. This SOP supports and enhances manual somatic variant detection by improving reviewer accuracy while reducing the interreviewer variability for variant calling and annotation.
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standard Operating Procedure for somatic variant refinement of tumor sequencing data
bioRxiv, 2018Co-Authors: Erica K Barnell, Peter Ronning, Katie M Campbell, Kilannin Krysiak, Benjamin J Ainscough, Cody Ramirez, Zachary L Skidmore, Felicia Gomez, Lee Trani, Matthew K MatlockAbstract:Purpose: Manual review of aligned sequencing reads is required to develop a high-quality list of somatic variants from massively parallel sequencing data (MPS). Despite widespread use in analyzing MPS data, there has been little attempt to describe methods for manual review, resulting in high inter- and intra-lab variability in somatic variant detection and characterization of tumors. Methods: Open source software was used to develop an optimal method for manual review setup. We also developed a systemic approach to visually inspect each variant during manual review. Results: We present a standard Operating Procedures for somatic variant refinement for use by manual reviewers. The approach is enhanced through representative examples of 4 different manual review categories that indicate a reviewer's confidence in the somatic variant call and 19 annotation tags that contextualize commonly observed sequencing patterns during manual review. Representative examples provide detailed instructions on how to classify variants during manual review to rectify lack of confidence in automated somatic variant detection. Conclusion: Standardization of somatic variant refinement through systematization of manual review will improve the consistency and reproducibility of identifying true somatic variants after automated variant calling.
Kelsy C Cotto - One of the best experts on this subject based on the ideXlab platform.
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standard Operating Procedure for somatic variant refinement of sequencing data with paired tumor and normal samples
Genetics in Medicine, 2019Co-Authors: Erica K Barnell, Peter Ronning, Katie M Campbell, Kilannin Krysiak, Benjamin J Ainscough, Lana M Sheta, Shahil Pema, Alina Schmidt, Megan Richters, Kelsy C CottoAbstract:Following automated variant calling, manual review of aligned read sequences is required to identify a high-quality list of somatic variants. Despite widespread use in analyzing sequence data, methods to standardize manual review have not been described, resulting in high inter- and intralab variability. This manual review standard Operating Procedure (SOP) consists of methods to annotate variants with four different calls and 19 tags. The calls indicate a reviewer’s confidence in each variant and the tags indicate commonly observed sequencing patterns and artifacts that inform the manual review call. Four individuals were asked to classify variants prior to, and after, reading the SOP and accuracy was assessed by comparing reviewer calls with orthogonal validation sequencing. After reading the SOP, average accuracy in somatic variant identification increased by 16.7% (p value = 0.0298) and average interreviewer agreement increased by 12.7% (p value < 0.001). Manual review conducted after reading the SOP did not significantly increase reviewer time. This SOP supports and enhances manual somatic variant detection by improving reviewer accuracy while reducing the interreviewer variability for variant calling and annotation.
Johannes Bitzer - One of the best experts on this subject based on the ideXlab platform.
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a standardized diagnostic interview for hypoactive sexual desire disorder in women standard Operating Procedure sop part 2
The Journal of Sexual Medicine, 2013Co-Authors: Johannes Bitzer, Annamaria Giraldi, James G PfausAbstract:ABSTRACT Introduction Taking into account that Hypoactive Sexual Desire Disorder (HSDD) is a patient-reported symptom and that the disorder is in general the result of the interaction of biological and psychosocial factors (see part 1), it is necessary to provide healthcare professionals with an Operating Procedure that is patient centered and multidimensional. Aim Describing a patient-centered and multidimensional standard Procedure to diagnose and manage HSDD on a primary care level. Methods Review of the literature. Semistructured interview and description of process. Result The interactive process with the patient follows several steps: initiation, narrative of the patient to understand the individual profile of the disorder, differentiating questions, descriptive diagnosis, exploration of conditioning biomedical, individual psychological, interpersonal, and sociocultural factors (including biomedical examinations), establishment of a biopsychosocial comprehensive explanatory diagnosis, which can be summarized in a nine-field matrix. This matrix will serve as orientation for therapeutic interventions adapted to the individual person. These interventions should always be based on basic counseling as a basis of treatment. Then adapted to the individual condition specific hormonal treatments (mainly estrogen and testosterone alone or combined) can be used after exclusion of contraindications. In patients with predominant psychosocial factors contributing to HSDD individual or couple psychotherapy is indicated. Psychopharmacological drugs are in development and partially investigated and will add to the therapeutic possibilities in the future. Conclusion. This model can serve as an ideal basis for the approach to the female patient with HSDD. It can be adapted to the individual clinical setting. Bitzer J, Giraldi A, and Pfaus J. A standardized diagnostic interview for Hypoactive Sexual Desire Disorder in women: standard Operating Procedure (SOP part 2). J Sex Med **;**:**–**.
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sexual desire and hypoactive sexual desire disorder in women introduction and overview standard Operating Procedure sop part 1
The Journal of Sexual Medicine, 2013Co-Authors: Johannes Bitzer, Annamaria Giraldi, James G PfausAbstract:ABSTRACT Introduction Hypoactive sexual desire disorder (HSDD) is defined in Diagnostic and Statistical Manual of Mental Disorders Fourth Edition as persistent or recurrent deficiency (or absence) of sexual fantasies/thoughts, and/or desire for or receptivity to sexual activity, which causes personal distress. As a largely subjective experience, sexual desire may or may not be accompanied by externally observable changes in sexual behavior. Aim Describe the models of understanding HSDD and the contributing factors to provide the basis for a diagnostic interview and guidance for care for healthcare professionals as a standard Operating Procedure method. Review of the literature. Results There are several models which have been developed to describe sexual desire, although there is still no universally accepted definition or description of it. The models are generally divided into more general twofactor models (e.g., excitation–inhibition, appetitive–consummatory) or more specific multifactorial models (in which the differentcomponents of sexual activity and their interaction are delineated). The etiology of the disorder is generally considered as multifactorial. Biomedical factors like diseases, drugs, and hormones, and psychological factors like life events, sexual biography, affective state, etc., as well as interpersonal factors like partner satisfaction, communication, duration of the relationship, and sociocultural factors interact with each other and contribute to the individualexperience of desire or lack or absence of desire. In analogy to the multifactorial pathogenesis the therapeutic approach is usually multidimensional and includes basic counseling, individual and couple psychotherapy, hormonal and psychopharmacological treatment. Conclusion The standard operation Procedure for HSDD in women must be based on a biopsychosocial, multidimensional, and integrative perspective. Bitzer J, Giraldi A, and Pfaus J. Sexual desire and hypoactive sexual desire disorder in women. Introduction and overview. Standard Operating Procedure (SOP part 1). J Sex Med **;**:**–**.