scholarly journals A literature review at genome scale: improving clinical variant assessment

2017 ◽  
Author(s):  
Christopher A. Cassa ◽  
Daniel M. Jordan ◽  
Ivan Adzhubei ◽  
Shamil Sunyaev

AbstractIntroduction: Over 150,000 variants have been reported to cause Mendelian disease in the medical literature. It is still difficult to leverage this knowledge base in clinical practice as many reports lack strong statistical evidence or may include false associations. Clinical laboratories assess whether these variants (along with newly observed variants that are adjacent to these published ones) underlie clinical disorders.Materials and Methods: We measured whether citation data—including journal impact factor and the number of cited variants (NCV) in each gene with published disease associations—can be used to improve variant assessment.Results: Surprisingly, we find that impact factor is not predictive of pathogenicity, but the NCV score for each gene can provide statistical support of pathogenicity. When combining this gene-level citation metric with variant-level evolutionary conservation and structural features, classification accuracy reaches 89.5%. Further, variants identified in clinical exome sequencing cases have higher NCV scores than simulated rare variants from ExAC in matched genes and consequences (p<2.22x10-16).Discussion: Aggregate citation data can complement existing variant-based predictive algorithms, and can boost their performance without accessing and reviewing large numbers of manuscripts. The NCV is a slow-growing metric of scientific knowledge about each gene’s association with disease.Funding: This research was supported by NIH NHGRI grant HG007229 (C.C.) and NIGMS grant GM078598 (I.A., D.J., and S.S.).

Science ◽  
2021 ◽  
pp. eabi8870
Author(s):  
Saba Parvez ◽  
Chelsea Herdman ◽  
Manu Beerens ◽  
Korak Chakraborti ◽  
Zachary P. Harmer ◽  
...  

CRISPR-Cas9 can be scaled up for large-scale screens in cultured cells, but CRISPR screens in animals have been challenging because generating, validating, and keeping track of large numbers of mutant animals is prohibitive. Here, we report Multiplexed Intermixed CRISPR Droplets (MIC-Drop), a platform combining droplet microfluidics, single-needle en masse CRISPR ribonucleoprotein injections, and DNA barcoding to enable large-scale functional genetic screens in zebrafish. The platform can efficiently identify genes responsible for morphological or behavioral phenotypes. In one application, we show MIC-Drop can identify small molecule targets. Furthermore, in a MIC-Drop screen of 188 poorly characterized genes, we discover several genes important for cardiac development and function. With the potential to scale to thousands of genes, MIC-Drop enables genome-scale reverse-genetic screens in model organisms.


Light and electronmicroscopic observations of changes throughout the small intestine of foetal, and both suckled and unsuckled newborn pigs are reported. Foetal animals between 73 days gestation and term showed vacuolation in the terminal ileum. This was most extensive between 90 and 100 days when the terminal 30% of the small intestine contained vacuolated cells. The apical region of such cells contained a system of smooth tubes and vesicles, some of which showed evidence of a characteristic surface pattern. The vacuoles contained material of variable electron density and were sometimes seen apparently discharging their contents into the dilated intercellular spaces. Unsuckled newborn animals showed most of the features described above, but, in addition, the vacuolated cells contained large numbers of electron dense inclusions. In suckled animals from birth to 70 h of age there were considerable variations in cellular structure, which could be related to the position in the small intestine, the position on the villus and the age of the animal. The structural features described are discussed in relation to the transfer of colostrum immunoglobulins into the circulation. Keywords: swine, foetus, newborn, small intestine, structure.


2018 ◽  
Vol 24 (3) ◽  
pp. 471-481 ◽  
Author(s):  
Lichy Han ◽  
Mateusz Maciejewski ◽  
Christoph Brockel ◽  
Lovisa Afzelius ◽  
Russ B Altman

2019 ◽  
Vol 26 (5) ◽  
pp. 734-742
Author(s):  
Rob Law ◽  
Daniel Leung

As the citation frequency of a journal is a representation of how many people have read and acknowledged their works, academia generally shares the notion that impact factor and citation data signify the quality and importance of a journal to the discipline. Although this notion is well-entrenched, is it reasonable to deduce that a journal is not of good quality due to its lower impact factor? Do journal impact factors truly symbolize the quality of a journal? What must be noted when we interpret journal impact factors? This commentary article discusses these questions and their answers thoroughly.


1997 ◽  
Vol 170 (2) ◽  
pp. 109-112 ◽  
Author(s):  
Louise Howard ◽  
Greg Wilkinson

BackgroundWe examined citation data for the British Journal of Psychiatry (BJP) and four other general psychiatry journals to assess their impact on the scientific community.MethodData on three measures of citations (total number of citations, impact factor and ranking by impact factor) were obtained from Journal Citation Reports for 1985–1994. Rank correlations from year to year were calculated.ResultsThe BJP currently ranks sixth of all psychiatry journals when journals are ranked by impact factor. The journal's impact factor fell between 1985 and 1990 and this was followed by a rise in impact factor after 1991. The BJP did not rank in the top 10 psychiatry journals between 1991 and 1993. Archives of General Psychiatry is cited more frequently than any other psychiatry journal, with the American Journal of Psychiatry usually ranking second. Psychopharmacology journals are replacing more general journals in the top rankings. Rankings of most journals have become less stable in recent years.ConclusionsThe BJP would have to change the nature and number of papers published to improve its impact factor. There are a number of limitations to citation data and such data are only one of several factors useful in evaluating the importance of a journal's contribution to scientific and clinical communities.Conflict of interestThese condauthor is Editor of the British Journal of Psychiatry.


2007 ◽  
Vol 1 (1) ◽  
pp. 144-167 ◽  
Author(s):  
Marianne Mithun

AbstractA continuing issue in work on language contact has been determining the relative borrowability of various structural features. It is easy to imagine, for example, how a tendency to use particular word order patterns in one language might be replicated by bilinguals in another, but difficult to understand how abstract morphological structures could be transferred. When we look at linguistic areas, however, we often find grammatical features shared by genetically unrelated languages that seem unborrowable. Here we consider the importance of adding the dimension of time to investigations into the potential effects of contact. As a point of departure we examine a relatively straightforward example from western North America, a striking parallelism in verbal structure among large numbers of languages indigenous to California. The example illustrates the fact that parallel grammatical structures in neighboring languages need not have been borrowed in their current form. They might instead be the result of an earlier transfer of patterns of expression that set the stage for subsequent parallel developments.


2008 ◽  
Vol 40 (1) ◽  
pp. 1
Author(s):  
Evan Simpson ◽  
Anna Spada

Dear Readers, Having served as Editor-in-Chief of Journal of Molecular Endocrinology for seven years, I would like to take this opportunity to thank all those who have contributed to the journal's success – the Editorial Board, authors and referees.Following a great increase in the journal's impact factor in the early part of my term of office, submissions to the journal began to increase significantly, approaching a remarkable 250% of what they had been previously. This gave us the opportunity to build upon the journal's established reputation by improving its high quality standards even further. One of the ways of achieving this was to increase the rejection rate. Prior to 2000, the acceptance rate of the journal had typically been around 60% for many years. In recent years, this percentage has often been in the thirties. Despite this, the number of papers published in a year has frequently been more than it was historically, and rapid growth from one year to the next has sometimes had the effect of temporarily decreasing the journal's impact factor compared with the heights we had previously achieved, because of the way it is calculated. We have also increased the journal's online frequency to monthly, ensuring that the journal is poised ready for the rapid publication of greater numbers of higher quality papers.With this legacy, I am pleased to hand over the reins of the journal to Professor Anna Spada, and I wish her well in taking the journal to new heights.As the incoming Editor-in-Chief of the Journal of Molecular Endocrinology, I feel proud to be associated with a major international journal dedicated to publishing excellent science in the field of molecular endocrinology. Together with the new members of the Editorial Board, we are committed to continue the tradition of excellence established by our predecessors. We would like to take this opportunity to thank the outgoing Editor-in-Chief, Professor Evan Simpson, who contributed greatly to the development and prestige of the journal during his tenure. We would also like to acknowledge with gratitude the efforts of all the other members of the Editorial Board who are retiring.As we enter the year 2008, the journal begins its 20th year of serving the global endocrine community as a vital forum for research on molecular endocrinology. Moreover, the journal recently became an official journal of the European Society of Endocrinology, a fact that confirms its increasing significance and importance. The journal has an active Editorial Board who represent both the global reach of the journal and the breadth of expertise needed to build upon its current subject coverage.Journal of Molecular Endocrinology has undergone substantial developments recently, including full migration to an electronic manuscript handling system and monthly online publication, together with immediate publication of authors' accepted manuscripts. These changes, together with the hard work of the staff of the Society for Endocrinology, the journal's publisher, have had a major impact on the efficiency of manuscript handling, with rapid and careful decisions on submitted manuscripts. High-profile review articles are freely available to all on the web and the improved features of the new platform, including toll-free reference linking and ‘This article has been cited by…’ links to and from other major journals, have increased JME's online visibility.We are committed to publishing the best endocrine research at the molecular level, and we believe that the journal has a particular role in integrating basic molecular mechanisms towards understanding the physiological and pathological processes of the endocrine system. We want to encourage the submission of manuscripts that expand our knowledge of the molecular mechanisms underlying hormone action; examples of potential topics include proteomics, structural features of RNA and the impact on mRNA regulation and processing, DNA repair mechanisms underlying endocrine disorders and cancers, DNA–protein complexes and chromatin structures and the accessibility of promoter–regulatory regions, molecular chaperones, etc. Articles on molecular endocrinology with potential translational/clinical significance, methodology and bioinformatics tools are especially welcome. We also want to attract papers from leaders in other fields who are investigating endocrine-related aspects but do not traditionally publish in our journal. A series of mini-reviews will address a wide range of provocative and updated topics that we believe will extend our range of interest and will aim to anticipate the future direction of many specific research areas. As many of the mini-reviews will be invited, we welcome suggestions of topics and authors as well as outlines of potential mini-reviews from interested authors.It is with a good deal of humility that I take over the reins of the journal. It is my intention to ensure that it remains at the forefront of endocrine research and, along with the Editorial Board, we are hopeful that we can raise JME's standards even higher.


2019 ◽  
Author(s):  
Brett M. Kroncke ◽  
Derek K. Smith ◽  
Andrew M. Glazer ◽  
Dan M. Roden ◽  
Jeffrey D. Blume

AbstractPurposeA major challenge in genomic medicine is how to best predict risk of disease from rare variants discovered in Mendelian disease genes but with limited phenotypic data. We have recently used Bayesian methods to show that in vitro functional measurements and computational pathogenicity classification of variants in the cardiac gene SCN5A correlate with rare arrhythmia penetrance. We hypothesized that similar predictors could be used to impute variant-specific penetrance prior probabilities.MethodsFrom a review of 756 publications, we developed a pattern mixture algorithm, based on a Bayesian Beta-Binomial model, to generate SCN5A variant-specific penetrance priors for the heart arrhythmia Brugada syndrome (BrS).ResultsThe resulting priors correlate with mean BrS penetrance posteriors (cross validated R2= 0.41). SCN5A variant function and structural context provide the most information predictive of BrS penetrance. The resulting priors are interpretable as equivalent to the observation of affected and unaffected carriers.ConclusionsBayesian estimates of penetrance can efficiently integrate variant-specific data (e.g. functional, structural, and sequence) to accurately estimate disease risk attributable to individual variants. We suggest this formulation of penetrance is quantitative, probabilistic, and more precise than, but consistent with, discrete pathogenicity classification approaches.


2021 ◽  
Vol 22 (19) ◽  
pp. 10401
Author(s):  
Jiri Bonaventura ◽  
Eva Polakova ◽  
Veronika Vejtasova ◽  
Josef Veselka

Hypertrophic cardiomyopathy (HCM) is a common inherited heart disease with an estimated prevalence of up to 1 in 200 individuals. In the majority of cases, HCM is considered a Mendelian disease, with mainly autosomal dominant inheritance. Most pathogenic variants are usually detected in genes for sarcomeric proteins. Nowadays, the genetic basis of HCM is believed to be rather complex. Thousands of mutations in more than 60 genes have been described in association with HCM. Nevertheless, screening large numbers of genes results in the identification of many genetic variants of uncertain significance and makes the interpretation of the results difficult. Patients lacking a pathogenic variant are now believed to have non-Mendelian HCM and probably have a better prognosis than patients with sarcomeric pathogenic mutations. Identifying the genetic basis of HCM creates remarkable opportunities to understand how the disease develops, and by extension, how to disrupt the disease progression in the future. The aim of this review is to discuss the brief history and recent advances in the genetics of HCM and the application of molecular genetic testing into common clinical practice.


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