Publications by authors named "Michael Segal"

53 Publications

User testing of a diagnostic decision support system with machine-assisted chart review to facilitate clinical genomic diagnosis.

BMJ Health Care Inform 2021 May;28(1)

SimulConsult, Inc, Chestnut Hill, Massachusetts, USA.

Objectives: There is a need in clinical genomics for systems that assist in clinical diagnosis, analysis of genomic information and periodic reanalysis of results, and can use information from the electronic health record to do so. Such systems should be built using the concepts of human-centred design, fit within clinical workflows and provide solutions to priority problems.

Methods: We adapted a commercially available diagnostic decision support system (DDSS) to use extracted findings from a patient record and combine them with genomic variant information in the DDSS interface. Three representative patient cases were created in a simulated clinical environment for user testing. A semistructured interview guide was created to illuminate factors relevant to human factors in CDS design and organisational implementation.

Results: Six individuals completed the user testing process. Tester responses were positive and noted good fit with real-world clinical genetics workflow. Technical issues related to interface, interaction and design were minor and fixable. Testers suggested solving issues related to terminology and usability through training and infobuttons. Time savings was estimated at 30%-50% and additional uses such as in-house clinical variant analysis were suggested for increase fit with workflow and to further address priority problems.

Conclusion: This study provides preliminary evidence for usability, workflow fit, acceptability and implementation potential of a modified DDSS that includes machine-assisted chart review. Continued development and testing using principles from human-centred design and implementation science are necessary to improve technical functionality and acceptability for multiple stakeholders and organisational implementation potential to improve the genomic diagnosis process.
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http://dx.doi.org/10.1136/bmjhci-2021-100331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8108675PMC
May 2021

The Human Phenotype Ontology in 2021.

Nucleic Acids Res 2021 01;49(D1):D1207-D1217

Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg.

The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.
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http://dx.doi.org/10.1093/nar/gkaa1043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778952PMC
January 2021

Clinician-centric diagnosis of rare genetic diseases: performance of a gene pertinence metric in decision support for clinicians.

Orphanet J Rare Dis 2020 07 22;15(1):191. Epub 2020 Jul 22.

Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.

Background: In diagnosis of rare genetic diseases we face a decision as to the degree to which the sequencing lab offers one or more diagnoses based on clinical input provided by the clinician, or the clinician reaches a diagnosis based on the complete set of variants provided by the lab. We tested a software approach to assist the clinician in making the diagnosis based on clinical findings and an annotated genomic variant table, using cases already solved using less automated processes.

Results: For the 81 cases studied (involving 216 individuals), 70 had genetic abnormalities with phenotypes previously described in the literature, and 11 were not described in the literature at the time of analysis ("discovery genes"). These included cases beyond a trio, including ones with different variants in the same gene. In 100% of cases the abnormality was recognized. Of the 70, the abnormality was ranked #1 in 94% of cases, with an average rank 1.1 for all cases. Large CNVs could be analyzed in an integrated analysis, performed in 24 of the cases. The process is rapid enough to allow for periodic reanalysis of unsolved cases.

Conclusions: A clinician-friendly environment for clinical correlation can be provided to clinicians who are best positioned to have the clinical information needed for this interpretation.
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http://dx.doi.org/10.1186/s13023-020-01461-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7374885PMC
July 2020

A rare complication of testicular infarction after femorofemoral bypass highlighting the importance of surgical technique.

J Surg Case Rep 2019 Nov 11;2019(11):rjz271. Epub 2019 Nov 11.

Division of Vascular Surgery, Department of Surgery, Northwell Health, New Hyde Park, NY, USA.

We present an interesting case of a 66-year-old male who had acute testicular infarction following a right common femoral artery to left profunda femoris artery bypass with advanced symptoms of claudication. Angiography in the preoperative period demonstrated the extent of peripheral arterial disease present, revealing a calcified aorta, partially occluded left hypogastric artery, occluded left external iliac, common femoral and superficial femoral arteries and an occluded right hypogastric artery. A bypass was performed without any initial complications and subsequent relief of symptoms of claudication and rest pain. Postoperative scrotal pain and follow-up duplex demonstrated lack of perfusion of the testicle necessitating orchiectomy. This case serves to illustrate the importance of preserving collateral vessels as a technical consideration, as well as presenting a rare potential complication.
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http://dx.doi.org/10.1093/jscr/rjz271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6847100PMC
November 2019

An operating system for the biology lab.

Authors:
Michael Segal

Nature 2019 09;573(7775):S112-S113

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http://dx.doi.org/10.1038/d41586-019-02875-zDOI Listing
September 2019

How automation is changing work.

Authors:
Michael Segal

Nature 2018 11;563(7733):S132-S135

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http://dx.doi.org/10.1038/d41586-018-07501-yDOI Listing
November 2018

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.

Nucleic Acids Res 2019 01;47(D1):D1018-D1027

The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.

The Human Phenotype Ontology (HPO)-a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases-is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO's interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.
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http://dx.doi.org/10.1093/nar/gky1105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324074PMC
January 2019

Retrograde embolization of anterior tibial artery for an iatrogenic arterio-venous fistula causing left lower extremity claudication.

J Surg Case Rep 2018 Aug 27;2018(8):rjy219. Epub 2018 Aug 27.

Department of Vascular Surgery, Wyckoff Heights Medical Center, 374 Stockholm St., Brooklyn, NY, USA.

Lower extremity angiogram is generally a safe and effective procedure with a low rate of vascular complications. We report here a unique case of a 33-year-old female with anterior tibial artery (ATA) to anterior tibial vein fistula formation after lower extremity endovascular intervention. This was initially treated with open repair of the fistula and ligation of ATA. However, patient continued to complain of claudication like symptoms. Patient subsequently had an endovascular embolization of ATA in a retrograde fashion. Recovery was unremarkable; patient was discharged home same day. Three months postoperatively patient denies leg pain, a follow-up arterial duplex failed to show presence of arterio-venous fistula. This case illustrates the effectiveness of an endovascular approach as a minimally invasive treatment for this uncommon complication that occurs after lower extremity endovascular intervention.
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http://dx.doi.org/10.1093/jscr/rjy219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6109892PMC
August 2018

Experience with Integrating Diagnostic Decision Support Software with Electronic Health Records: Benefits versus Risks of Information Sharing.

EGEMS (Wash DC) 2017 Dec 6;5(1):23. Epub 2017 Dec 6.

Geisinger Health System.

Introduction: Reducing misdiagnosis has long been a goal of medical informatics. Current thinking has focused on achieving this goal by integrating diagnostic decision support into electronic health records.

Methods: A diagnostic decision support system already in clinical use was integrated into electronic health record systems at two large health systems, after clinician input on desired capabilities. The decision support provided three outputs: editable text for use in a clinical note, a summary including the suggested differential diagnosis with a graphical representation of probability, and a list of pertinent positive and pertinent negative findings (with onsets).

Results: Structured interviews showed widespread agreement that the tool was useful and that the integration improved workflow. There was disagreement among various specialties over the risks versus benefits of documenting intermediate diagnostic thinking. Benefits were most valued by specialists involved in diagnostic testing, who were able to use the additional clinical context for richer interpretation of test results. Risks were most cited by physicians making clinical diagnoses, who expressed concern that a process that generated diagnostic possibilities exposed them to legal liability.

Discussion And Conclusion: Reconciling the preferences of the various groups could include saving only the finding list as a patient-wide resource, saving intermediate diagnostic thinking only temporarily, or adoption of professional guidelines to clarify the role of decision support in diagnosis.
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http://dx.doi.org/10.5334/egems.244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5994959PMC
December 2017

Endovascular retrieval of foreign body in persistent left-sided superior vena cava.

Radiol Case Rep 2017 Dec 5;12(4):768-771. Epub 2017 Sep 5.

Department of Surgery, Wyckoff Heights Medical Center, Brooklyn, USA.

Endovascular retrieval of a foreign body is becoming an increasingly common procedure in the management of complications resulting from more frequent endovascular procedures. Many procedures are performed on a regular basis in assessment of vascular anatomy, endovascular-guided therapy, and catheter placement. This case report depicts a complication of a chemoport placement resulting in a foreign body. Evaluation of the foreign body raised attention to aberrant anatomy, a persistent left-sided superior vena cava. We further discuss briefly the embryology behind a persistent left-sided superior vena cava, technical errors leading to the foreign body, and assessing the nature of the foreign body through different imaging modalities. This is followed by the subsequent endovascular retrieval by Interventional Radiology and a literature review and individual case assessment of endovascular foreign body retrieval. We discuss considerations for practice based upon our literature review.
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http://dx.doi.org/10.1016/j.radcr.2017.07.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5823482PMC
December 2017

Impact of a Patient-Facing Enhanced Genomic Results Report to Improve Understanding, Engagement, and Communication.

J Genet Couns 2018 04 4;27(2):358-369. Epub 2017 Dec 4.

Geisinger Genomic Medicine Institute, 26-20, 100 N. Academy Ave., Danville, PA, 17822, USA.

"The objective of this study was to" test the effectiveness of an enhanced genomic report on patient-centered outcome domains including communication, engagement and satisfaction. "Study design utilized" a prospective, randomized, mixed-methods desctiptive study of a whole genome sequencing results report, GenomeCOMPASS™, that was accessed by providers through the electronic health record and by patients through the associated patient portal. "The study was set in" an integrated healthcare delivery system in central Pennsylvania. "Eighty-four" parents of 46 children with undiagnosed Intellectual Disability, Autism Spectrum Disorder and/or multiple congenital anomalies who had participated in a previous study offering whole genome sequencing for their affected child were invited to enroll. Fifty-two parents enrolled. Following a traditional genetics results informing visit, the study coordinator stratified families by diagnostic result and uninformative result and then randomized families within each group to an intervention arm to receive the GenomeCOMPASS™ report or to the usual care arm to receive a summary letter from the medical geneticist. A letter inviting enrollment included a baseline survey, which once returned, constituted enrollment. Surveys were administered at 3 months post-genetics visit. At 6 months, the usual care arm crossed over to receive the intervention and were administered an additional survey at 3 months. Qualitative interviews were conducted following survey completion to augment the survey data regarding the patient centered outcomes of interest. Patient reported outcomes including communication, engagement, empowerment and satisfaction. In the intervention arm, GenomeCOMPASS™ reports were released to 14 families (N = 28 parents) and of those 21 (75%) returned 3 month surveys. In the usual care arm, 12 families (N = 24 parents) received usual care summary letters and of those 20 (83%) returned 3 month surveys. At crossover, GenomeCOMPASS™ reports were released to 20 individuals and 15 (75%) returned 3 month surveys. Qualitative interviews were conducted with 5 individuals. Use of the GenomeCOMPASS™ report was reported by this small group of parents to improve communication with providers and non-health professionals such as educators and therapists and led to increased engagement and high satisfaction. Providers and others involved in the children's care also endorsed the report's effectiveness. Reports that addressed negative findings, i.e. uninformative results, were not found to be useful. Although the number of users was small, this study supports that customizable template reports may provide a useful and durable source of information that can support and enhance the information provided by genetics professionals in traditional face-to-face encounters.

Trial Registration: Clinicaltrials.gov (Record 2013-0594).
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http://dx.doi.org/10.1007/s10897-017-0176-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859697PMC
April 2018

Case Report: Modified Laparoscopic Subtotal Cholecystectomy: An Alternative Approach to the "Difficult Gallbladder".

Am J Case Rep 2017 Feb 21;18:186-189. Epub 2017 Feb 21.

Department of Surgery, Wyckoff Heights Medical Center, Brooklyn, NY, USA.

BACKGROUND Laparoscopic cholecystectomy is a commonly performed surgical procedure. In certain situations visualization of the Callot triangle can become difficult due to inflammation, adhesions, and sclerosing of the anatomy. Without being able to obtain the "critical view of safety" (CVS), there is increased risk of damage to vital structures. An alternative approach to the conventional conversion to an open cholecystectomy (OC) would be a laparoscopic subtotal cholecystectomy (LSC). CASE REPORT We present a case of a 56-year-old male patient with acute cholecystitis with a "difficult gallbladder" managed with LSC. Due to poor visualization of the Callot triangle due to adhesions, safe dissection was not feasible. In an effort to avoid injury to the common bile duct (CBD), dissection began at the dome of the gallbladder allowing an alternative view while ensuring safety of critical structures. CONCLUSIONS We discuss the potential benefits and risks of LSC versus conversion to OC. Our discussion incorporates the pathophysiology that allows LSC in this particular circumstance to be successful, and the considerations a surgeon faces in making a decision in management.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5331888PMC
http://dx.doi.org/10.12659/ajcr.900646DOI Listing
February 2017

Meta-analysis of open and endovascular repair of popliteal artery aneurysms.

J Vasc Surg 2017 Jan;65(1):246-256.e2

Department of Surgery, Division of Vascular Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pa.

Objective: Endovascular popliteal artery aneurysm repair (EPAR) is increasingly used over open surgical repair (OPAR). The purpose of this study was to analyze the available literature on their comparative outcomes.

Methods: The PubMed and Embase databases were searched to identify studies comparing OPAR and EPAR. Studies with only one treatment and fewer than five patients were excluded. Demographics and outcomes were collected. Bias risk was assessed using a modified version of the Newcastle-Ottawa Scale. Results were computed from random-effects meta-analyses using the DerSimonian-Laird algorithm.

Results: A total of 14 studies were identified encompassing 4880 popliteal artery aneurysm repairs (OPAR, 3915; EPAR, 1210) during the last decade. OPAR patients were younger (standard mean difference, -0.798 [-0.798 to -1.108]; P < .001) and more likely to have worse tibial runoff (odds ratio [OR], 1.949 (1.15-3.31); P = .013) than EPAR patients. OPAR had higher odds of wound complications (OR, 5.182 [2.191-12.256]; P < .001) and lower odds of thrombotic complications (OR, 0.362 [0.155-0.848]; P < .001). OPAR had longer length of stay (standardized mean difference, 2.158 [1.225-3.090]; P < .001) and fewer reinterventions (OR, 0.275 [0.166-0.454]; P < .001). Primary patency was better for OPAR at 1 year and 3 years (relative risk, 0.607 [P = .01] and 0.580 [P = .006], respectively). There was no difference in secondary patency at 1 year and 3 years (0.770 [P = .458] and 0.642 [P = .073], respectively).

Conclusions: EPAR has a lower wound complication rate and shorter length of hospital stay compared with OPAR. This comes at the cost of inferior primary patency but not secondary patency out to 3 years. Studies reporting long-term outcomes are lacking and necessary.
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http://dx.doi.org/10.1016/j.jvs.2016.09.029DOI Listing
January 2017

Evidence-based decision support for pediatric rheumatology reduces diagnostic errors.

Pediatr Rheumatol Online J 2016 Dec 13;14(1):67. Epub 2016 Dec 13.

Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA.

Background: The number of trained specialists world-wide is insufficient to serve all children with pediatric rheumatologic disorders, even in the countries with robust medical resources. We evaluated the potential of diagnostic decision support software (DDSS) to alleviate this shortage by assessing the ability of such software to improve the diagnostic accuracy of non-specialists.

Methods: Using vignettes of actual clinical cases, clinician testers generated a differential diagnosis before and after using diagnostic decision support software. The evaluation used the SimulConsult® DDSS tool, based on Bayesian pattern matching with temporal onset of each finding in each disease. The tool covered 5405 diseases (averaging 22 findings per disease). Rheumatology content in the database was developed using both primary references and textbooks. The frequency, timing, age of onset and age of disappearance of findings, as well as their incidence, treatability, and heritability were taken into account in order to guide diagnostic decision making. These capabilities allowed key information such as pertinent negatives and evolution over time to be used in the computations. Efficacy was measured by comparing whether the correct condition was included in the differential diagnosis generated by clinicians before using the software ("unaided"), versus after use of the DDSS ("aided").

Results: The 26 clinicians demonstrated a significant reduction in diagnostic errors following introduction of the software, from 28% errors while unaided to 15% using decision support (p < 0.0001). Improvement was greatest for emergency medicine physicians (p = 0.013) and clinicians in practice for less than 10 years (p = 0.012). This error reduction occurred despite the fact that testers employed an "open book" approach to generate their initial lists of potential diagnoses, spending an average of 8.6 min using printed and electronic sources of medical information before using the diagnostic software.

Conclusions: These findings suggest that decision support can reduce diagnostic errors and improve use of relevant information by generalists. Such assistance could potentially help relieve the shortage of experts in pediatric rheumatology and similarly underserved specialties by improving generalists' ability to evaluate and diagnose patients presenting with musculoskeletal complaints.

Trial Registration: ClinicalTrials.gov ID: NCT02205086.
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http://dx.doi.org/10.1186/s12969-016-0127-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5155385PMC
December 2016

The Human Phenotype Ontology in 2017.

Nucleic Acids Res 2017 01 28;45(D1):D865-D876. Epub 2016 Nov 28.

John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
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http://dx.doi.org/10.1093/nar/gkw1039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210535PMC
January 2017

From damage to discovery via virtual unwrapping: Reading the scroll from En-Gedi.

Sci Adv 2016 Sep 21;2(9):e1601247. Epub 2016 Sep 21.

Israel Antiquities Authority, Jerusalem, Israel.

Computer imaging techniques are commonly used to preserve and share readable manuscripts, but capturing writing locked away in ancient, deteriorated documents poses an entirely different challenge. This software pipeline-referred to as "virtual unwrapping"-allows textual artifacts to be read completely and noninvasively. The systematic digital analysis of the extremely fragile En-Gedi scroll (the oldest Pentateuchal scroll in Hebrew outside of the Dead Sea Scrolls) reveals the writing hidden on its untouchable, disintegrating sheets. Our approach for recovering substantial ink-based text from a damaged object results in readable columns at such high quality that serious critical textual analysis can occur. Hence, this work creates a new pathway for subsequent textual discoveries buried within the confines of damaged materials.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5031465PMC
http://dx.doi.org/10.1126/sciadv.1601247DOI Listing
September 2016

Genome interpretation: Clinical correlation is recommended.

Authors:
Michael M Segal

Appl Transl Genom 2015 Sep 22;6:26-7. Epub 2015 Jul 22.

27 Crafts Road, Brookline, MA 02467, USA.

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http://dx.doi.org/10.1016/j.atg.2015.07.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4803777PMC
September 2015

Enhancing genomic laboratory reports: A qualitative analysis of provider review.

Am J Med Genet A 2016 May 3;170A(5):1134-41. Epub 2016 Feb 3.

Geisinger Genomic Medicine, Danville, Pennsylvania.

This study reports on the responses of physicians who reviewed provider and patient versions of a genomic laboratory report designed to communicate results of whole genome sequencing. Semi-structured interviews addressed concept communication, elements, and format of example genome reports. Analysis of the coded transcripts resulted in recognition of three constructs around communication of genome sequencing results: (1) Providers agreed that whole genomic sequencing results are complex and they welcomed a report that provided supportive interpretation information to accompany sequencing results; (2) Providers strongly endorsed a report that included active clinical guidance, such as reference to practice guidelines, if available; and (3) Providers valued the genomic report as a resource that would serve as the basis to facilitate communication of genome sequencing results with their patients and families. Providers valued both versions of the report, though they affirmed the need for a provider-oriented report. Critical elements of the report included clear language to explain the result, as well as consolidated yet comprehensive prognostic information with clear guidance over time for the clinical care of the patient. Most importantly, it appears a report with this design has the potential not only to return results but also serves as a communication tool to help providers and patients discuss and coordinate care over time.
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http://dx.doi.org/10.1002/ajmg.a.37573DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5067598PMC
May 2016

Enhancing genomic laboratory reports from the patients' view: A qualitative analysis.

Am J Med Genet A 2015 Oct 18;167A(10):2238-43. Epub 2015 Jun 18.

Geisinger Genomic Medicine, Danville, Pennsylvania.

The purpose of this study was to develop a family genomic laboratory report designed to communicate genome sequencing results to parents of children who were participating in a whole genome sequencing clinical research study. Semi-structured interviews were conducted with parents of children who participated in a whole genome sequencing clinical research study to address the elements, language and format of a sample family-directed genome laboratory report. The qualitative interviews were followed by two focus groups aimed at evaluating example presentations of information about prognosis and next steps related to the whole genome sequencing result. Three themes emerged from the qualitative data: (i) Parents described a continual search for valid information and resources regarding their child's condition, a need that prior reports did not meet for parents; (ii) Parents believed that the Family Report would help facilitate communication with physicians and family members; and (iii) Parents identified specific items they appreciated in a genomics Family Report: simplicity of language, logical flow, visual appeal, information on what to expect in the future and recommended next steps. Parents affirmed their desire for a family genomic results report designed for their use and reference. They articulated the need for clear, easy to understand language that provided information with temporal detail and specific recommendations regarding relevant findings consistent with that available to clinicians.
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http://dx.doi.org/10.1002/ajmg.a.37174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744953PMC
October 2015

The attitudes of psychiatric hospital staff toward hospitalization and treatment of patients with borderline personality disorder.

BMC Psychiatry 2015 Jan 22;15. Epub 2015 Jan 22.

Tel Aviv University, The Beer Yaakov Mental Health Center, Yavne, Israel.

Background: Negative attitudes towards patients with borderline personality disorder (BPD) may affect their treatment. We aimed to identify attitudes toward patients with BPD.

Methods: Clinicians in four psychiatric hospitals in Israel (n = 710; psychiatrists, psychologists, social workers and nurses) were approached and completed questionnaires on attitudes toward these patients.

Results: Nurses and psychiatrists reported encountering a higher number of patients with BPD during the last month, and exhibited more negative attitudes and less empathy toward these patients than the other two professions. The whole sample evaluated the decision to hospitalize such a patient as less justified than the decision to hospitalize a patient with Major Depressive Disorder. Negative attitudes were positively correlated with caring for greater numbers of patients with BPD in the past month and in the past 12 months. Nurses expressed the highest interest in studying short-term methods for treating patients with BPD and a lower percentage of psychiatrists expressed an interest in improving their professional skills in treating these patients.

Conclusions: The findings show that nurses and psychiatrists differ from the other professions in their experience and attitudes toward patients with BPD. We conclude that nurses and psychiatrists may be the target of future studies on their attitudes toward provocative behavioral patterns (e.g., suicide attempts) characterizing these patients. We also recommend implementing workshops for improving staff attitudes toward patients with BPD.
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http://dx.doi.org/10.1186/s12888-014-0380-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4307152PMC
January 2015

Clinical pertinence metric enables hypothesis-independent genome-phenome analysis for neurologic diagnosis.

J Child Neurol 2015 Jun 24;30(7):881-8. Epub 2014 Aug 24.

Center for Brain Development, University of California, San Diego, La Jolla, CA, USA.

We describe an "integrated genome-phenome analysis" that combines both genomic sequence data and clinical information for genomic diagnosis. It is novel in that it uses robust diagnostic decision support and combines the clinical differential diagnosis and the genomic variants using a "pertinence" metric. This allows the analysis to be hypothesis-independent, not requiring assumptions about mode of inheritance, number of genes involved, or which clinical findings are most relevant. Using 20 genomic trios with neurologic disease, we find that pertinence scores averaging 99.9% identify the causative variant under conditions in which a genomic trio is analyzed and family-aware variant calling is done. The analysis takes seconds, and pertinence scores can be improved by clinicians adding more findings. The core conclusion is that automated genome-phenome analysis can be accurate, rapid, and efficient. We also conclude that an automated process offers a methodology for quality improvement of many components of genomic analysis.
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http://dx.doi.org/10.1177/0883073814545884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339658PMC
June 2015

Intrusive trauma recollections is associated with impairment of interference inhibition and psychomotor speed in PTSD.

Compr Psychiatry 2014 Oct 17;55(7):1587-94. Epub 2014 May 17.

Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel; Flügelman's (Mazra) Mental Health Medical Center, Acre, Israel; Sha'ar Menashe Mental Health Center, Sha'ar Menashe, Israel. Electronic address:

Background: Intrusive cognitions that enter consciousness involuntarily are prominent symptoms of posttraumatic stress disorder (PTSD). The present study aimed to identify neuropsychological mechanisms involved.

Method: Fifty PTSD outpatients and 50 healthy controls were tested using Finger Tapping, Simple and Choice Reaction Times and Stroop Tasks, to measure motor, psychomotor speed, response selection, and interference inhibition ability respectively.

Results: PTSD patients performed poorly in all tests, presumably owing to their generalized slowness of information processing and motor reaction. Psychomotor speed was a predictor of slowness and high error rate during the Stroop. Impaired inhibition, as measured by the interference index of the Stroop task, explained 9.7% of the predicated variance in frequency of re-experiencing PTSD symptoms and 23.5% of the predicated variance in augmentation of the interference response time.

Conclusion: Impaired interference control may be related to internal (re-experiencing) and external (sensory) stimuli that leads to cognitive deficits in PTSD patients.
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http://dx.doi.org/10.1016/j.comppsych.2014.05.004DOI Listing
October 2014

We cannot say whether attention deficit hyperactivity disorder exists, but we can find its molecular mechanisms.

Authors:
Michael M Segal

Pediatr Neurol 2014 Jul 18;51(1):15-6. Epub 2014 Apr 18.

SimulConsult, Inc., Brookline, Massachusetts. Electronic address:

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http://dx.doi.org/10.1016/j.pediatrneurol.2014.04.014DOI Listing
July 2014

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

Genome Biol 2014 Mar 25;15(3):R53. Epub 2014 Mar 25.

Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance.

Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization.

Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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http://dx.doi.org/10.1186/gb-2014-15-3-r53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073084PMC
March 2014

Evidence-based decision support for neurological diagnosis reduces errors and unnecessary workup.

J Child Neurol 2014 Apr 10;29(4):487-92. Epub 2013 Apr 10.

1SimulConsult, Chestnut Hill, MA, USA.

Using vignettes of real cases and the SimulConsult diagnostic decision support software, neurologists listed a differential diagnosis and workup before and after using the decision support. Using the software, there was a significant reduction in error, up to 75% for diagnosis and 56% for workup. This error reduction occurred despite the baseline being one in which testers were allowed to use narrative resources and Web searching. A key factor that improved performance was taking enough time (>2 minutes) to enter clinical findings into the software accurately. Under these conditions and for instances in which the diagnoses changed based on using the software, diagnostic accuracy improved in 96% of instances. There was a 6% decrease in the number of workup items accompanied by a 34% increase in relevance. The authors conclude that decision support for a neurological diagnosis can reduce errors and save on unnecessary testing.
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http://dx.doi.org/10.1177/0883073813483365DOI Listing
April 2014

[Periodic breathing Cheyne-Stokes type, predict excessively reduced exercise tolerance in patients with chronic heart failure].

Harefuah 2012 Feb;151(2):86-9, 128, 127

The Pulmonary Institute, The Chaim Sheba Medical Center, Tel-Aviv University, Sackler Faculty of Medicine Tel-Aviv University, Israel.

Introduction: Periodic breathing (PB) is evident during exercise in some patients with chronic heart failure (CHF) and is accompanied by hyperventilation.

Aim: To determine whether the presence of PB predicts excessive reduced exercise capacity in patients with severe CHF relative to patient with CHF of similar severity but with no PB.

Methods: Sixty-one CHF patients underwent cardiopulmonary exercise from 2009 to 2011 as part of their evaluation for cardiac transplantation. From this data, we selected patients in which the term "periodic breathing" appeared in their report. Matching patients with CHF without PB were identified from the same pool.

Results: Fifteen CHF patients with PB and 18 patients with CHF with similar ejection fraction but without PB (control) were identified from the pool of 61 patients. The PB group had a lower peak oxygen uptake related to body weight (VO2/ kg] and anaerobic threshold [AT) than the control group, by 30 +/- 11 and 39 +/- 4%, respectively (p < 0.05). The ventilatory equivalent for CO2 production (VE/VCO2) at the AT was higher and the end tidal pressure of CO2 (PETCO2) was lower in the control group as compared with the PB group (p < 0.05]. VE/ VCO2 at the AT was inversely correlated with peak VO2/kg [r = -0.45, p < 0.05].

Discussion: PB in patients with severe CHF is associated with excessively reduced exercise capacity. Increased ventilatory requirement may enhance dyspnea and may add to exercise limitation in these patients.

Conclusion: Periodic breathing reflects the severity of CHF and is associated with excessively reduced exercise tolerance in patients with CHF.
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February 2012

Material history: Learning from silicon.

Authors:
Michael Segal

Nature 2012 Mar 14;483(7389):S43-4. Epub 2012 Mar 14.

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http://dx.doi.org/10.1038/483S43aDOI Listing
March 2012
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