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Cold Spring Harbor Molecular Case Studies -- Author Information Details
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RSS"><span>ALERTS / RSS</span></a></li> <li><a href="/feedback" title="CONTACT"><span>CONTACT</span></a></li> <li class="last"><a href="/help/" title="HELP"><span>HELP</span></a></li> </ul> <div class="header-qs"> <form class="searchbox" action="/search" method="get"> <div><label for="header-qs-input" id="header-qs-search-label">Search for Keyword:</label><input value="" title="Search Cold Spring Harbor Molecular Case Studies" type="text" name="fulltext" id="header-qs-input" /><input type="hidden" name="submit" value="yes" /><label for="header-qs-search" id="header-qs-search-label">GO</label><input value="GO" alt="Link: Go" type="image" id="header-qs-search-go" src="/shared/img/standard-design/design2/go.gif" /></div> <div class="adv-search-link"><a href="/search">Advanced Search</a></div> </form> </div> <div class="header-ac-elements"> <div id="authstring" class="suppress-header-login"></div> <div id="hdr-login" class="suppress-header-login"></div> </div> <div class="bar"> <div class="bar-inner"></div> </div> </div> <div id="content-block"> <div id="proxied-contents"> <div class="misc-body"> <table> <tbody> <tr> <td><br /><dl> <dt></dt> </dl> <h2>Information for Authors</h2> <dl> <dd><a href="#fees">APC Open Access publication fees</a></dd> <dd><a href="#turnaround">Average Turnaround Times</a></dd> <dd><a href="#intro">Introduction</a></dd> <dd><a href="#cover">Cover letter</a></dd> <dd><a href="#types">Article type</a></dd> <dd><a href="#minimum">Guidelines for reported data</a></dd> <dd><a href="#setup">Manuscript setup (Research Reports and Research Articles)</a></dd> <dd><a href="#setup_rapid">Manuscript setup (Rapid Communications, Rapid Cancer Communications, and Variant Discrepancy Resolutions)</a></dd> <dd><a href="#setup_followup">Manuscript setup (Follow-up Reports)</a></dd> <dd><a href="#at_acceptance">Additional information required</a></dd> <dd><a href="#nom">Nomenclature</a></dd> <dd><a href="#cite_ref">Citations and references</a></dd> <dd><a href="#math">Math objects</a></dd> <dd><a href="#perm">Permissions</a></dd> <dd><a href="#supp">Supplemental material</a></dd> <dd><a href="#art">Art guidelines</a></dd> <dd><a href="#referee">Referee process</a></dd> </dl> <p>----------</p> <p><em>Cold Spring Harbor Molecular Case Studies</em> publishes genomic and molecular analyses of individuals or cohorts alongside their clinical presentations and phenotypic information. The aim is to rapidly share insights into disease development and treatment gained by application of genomics, proteomics, metabolomics, biomarker analysis, and other approaches. For Research Reports, the minimal requirements for publication are typically a clinical description of an individual alongside a genomic analysis* or an equivalent detailed molecular profile (e.g., pathogen analysis for infectious disease or metabolomic profiling for metabolic disease**). Research Articles describe more extensive work using larger cohorts and/or functional analyses. </p> <p>*<em>For genomic analyses, whole-genome sequencing, exome sequencing, cytogenetic arrays, or targeted panels may be presented. Cytogenetic arrays or targeted panels alone are usually only appropriate if the phenotype/response is novel.</em></p> <p>**<em>For metabolomic analyses, the data presented must go beyond the typical clinical metabolic workup if no genomic analysis is supplied.</em></p> <p>----------</p><a name="fees" id="fees"></a><h3>APC OPEN ACCESS PUBLICATION FEES </h3> <p>All articles in the journal are Open Access. An Article Processing Charge (APC) is based on the number of papers accepted for publication by the same corresponding author in a calendar year. As of March 1, 2023, the fee schedule for publication is $3000 for the first article and $2550 for all subsequent articles. Variant Discrepancy Resolution articles are billed at $500 each. </p> <p>----------</p><a name="turnaround" id="turnaround"></a><h3>AVERAGE TURNAROUND TIMES</h3> <p>Initial decision to review: 5-7 days after submission</p> <p>Submission to first decision: 6 weeks after submission</p> <p>Submission to acceptance: 3-4 months</p> <p>Publication of accepted manuscripts: 5-7 days after acceptance</p> <p>----------</p><a name="intro" id="intro"></a><h3>INTRODUCTION</h3> <p>Papers should be submitted via our online manuscript submission system at <a href="http://submit.molecularcasestudies.org">http://submit.molecularcasestudies.org</a>. </p> <p>As an online journal, we do not impose arbitrary restrictions on manuscript length. However, authors are asked to consider readers and make papers as concise as possible (as a guide, articles should normally not exceed 30 double-spaced pages). </p> <p>At initial submission, manuscripts should be in PDF format (<a href="#setup">order of elements noted below</a>) and include both text and artwork. Manuscripts must include a statement that all authors have approved the current version of the manuscript and its submission to <em>CSH Molecular Case Studies</em>. </p> <p>At manuscript revision and all later stages, manuscripts should be in Microsoft Word format, with equations in MathType or Word Equation Editor, and should include text, tables, and figure legends. Tables should also be in Word Table format, not embedded as an Excel file or as an object file. Figures must be supplied as individual figure files (see <a href="#art">Art Guidelines</a>, below). </p> <p>To facilitate searching and ontology-based indexing of articles with specific phenotypic features, all published manuscripts are accompanied by Human Phenotype Ontology (HPO) terms. Authors must select these terms during the submission process. The HPO terms should represent a precise and comprehensive clinical description of the reported phenotypic abnormalities (for more information, see <a href="http://molecularcasestudies.cshlp.org/content/1/1/a000372.full">Robinson et al. 2015, 10.1101/mcs.a000372</a>). </p> <p>----------</p><a name="cover" id="cover"></a><h3>COVER LETTER</h3> <p>Must include:</p> <p>(1) a paragraph highlighting the main points of the work and its suitability for the journal’s readership;
</p> <p>
(2) the status of any statements of personal communication or other permissions needed (any data presented as unpublished results from individuals other than the authors require permission for use). All related manuscripts in press, submitted, or in preparation must be disclosed. </p> <p>(3) the availability of data generated in the course of the work, including the repositories in which the data are deposited and relevant accession numbers (see <a href="/site/misc/ifora_policies.xhtml"><strong>Editorial Policies</strong></a> for more information). If genomic sequence data cannot be deposited due to restrictions imposed by the IRB or lack of patient consent, this limitation must be acknowledged. </p> <p>----------</p><a name="types" id="types"></a><h3>ARTICLE TYPE</h3> <p>The selection of type is based on the content of the manuscript, and will ultimately be decided by the Editor.</p> <p><strong>Research Report:</strong> presents detailed case studies of individuals and small cohorts </p> <p><strong>Research Article:</strong> describes more extensive work using larger cohorts and/or functional analyses </p> <p><strong>Rapid Communication:</strong> streamlined format for presenting the discovery of a novel variant and/or novel phenotype associated with a known disease gene in an individual </p> <p><strong>Rapid Cancer Communication:</strong> streamlined format for presenting the discovery of a novel variant or combination of variants in a cancer type </p> <p><strong>Variant Discrepancy Resolution:</strong> description of efforts to resolve differences or update variant classifications in ClinVar through case-level or functional data sharing </p> <p><strong>Follow-up Report:</strong> presents new data that follow up on previous observations published in the journal as a Research Report or Research Article (e.g., new data obtained following responses to therapy, data from additional individuals or a larger cohort, new data from a longitudinal study, or new data from cell lines or PDXs) </p> <p>We also publish a variety of other article types, including Precision Medicine in Practice, Reviews, Mini-Reviews, Commentaries, Perspectives, and Position Statements. If you are interested in submitting an article in one of these categories and would like additional information, please contact us at <span class="em-link"><span class="em-addr">mcs{at}cshl.edu</span></span>. </p> <p>----------</p><a name="minimum" id="minimum"></a><h3>GUIDELINES FOR REPORTED DATA</h3> <p>For all types of data, details regarding instrumentation, analysis pipeline, and the algorithms employed should be provided. Additionally, manuscripts should meet technology-specific criteria outlined below. </p> <p><strong>Whole-genome sequencing:</strong> For blood-based/constitutional genetics studies, a minimum average coverage of 30-fold is usually recommended. For somatic tissues, a minimum average coverage of 50-fold is usually recommended. Sequence read lengths and read type (single- or paired-end) should be reported. Coverage at reported germline variants should be at least 20-fold and we strongly suggest an orthogonal validation method (e.g., Sanger sequencing or another NGS platform) be used to verify the variant. </p> <p><strong>Exome sequencing:</strong> A minimum average coverage of 100-fold is usually recommended. Sequence read lengths and read type (single- or paired-end) should be reported. Coverage at reported germline variants should be at least 20-fold and we strongly suggest an orthogonal validation method (e.g., Sanger sequencing or another NGS platform) be used to verify the variant. </p> <p><strong>Targeted panels:</strong> Specify whether the panel is offered as a commercial service through a pathology service provider, by your institution as an insurance-reimbursable CLIA assay, etc. Note that targeted panels are usually only acceptable as a minimal form of genomic analysis for papers if the phenotype or response described is novel. </p> <p><strong>Cytogenetic microarrays:</strong> Cytogenetic microarrays are usually only acceptable as a minimal form of genomic analysis for papers if the phenotype/response described is novel. </p> <p>For cancer genomic studies, information regarding the estimated tumor cellularity/percent tumor nuclei, from pathologic examination of tissue slices, should be provided. For reported somatic variants, the read depth at each reported site from the tumor and normal sample is required. If no normal matched tissue is available, the criteria used to ascertain the somatic status of the variant must be included. </p> <p>For germline variants being reported with clinical significance, variants should be evaluated according to the ACMG/AMP 2015 guidelines (PMID: 25741868) with additional guidance provided by (<a href="https://clinicalgenome.org/working-groups/sequence-variant-interpretation/">ClinGen</a>). </p> <p><strong>Metabolomics:</strong> Metabolomic data sets that go substantially beyond the typical clinical metabolic workup of patients with a suspected inborn error of metabolism (i.e., urine organic acids, plasma acylcarnitines, and amino acids) may be supplied as an alternative to a genomic analysis. Note that standard metabolic workups are of course acceptable if provided in addition to a genomic analysis as part of the phenotypic description. </p> <p>----------</p><a name="setup" id="setup"></a><h3>MANUSCRIPT SETUP (Research Reports and Research Articles)</h3> <p><strong>TITLE PAGE</strong> including article title, all authors’ names and affiliations, corresponding author’s e-mail, and a short running title (50 characters or less, including spaces). Please do NOT include keywords. (This will not affect PubMed indexing as keywords are auto-generated.) </p> <p><strong>ABSTRACT</strong> (250 words max.) </p> <p><strong>INTRODUCTION</strong></p> <p><strong>RESULTS</strong> (subheadings may include the following) </p> <ul> <li> <p><strong>Clinical presentation and family history</strong></p> </li> <li> <p><strong>Genomic analyses</strong></p> </li> </ul> <dl> <dt>—Variant tables</dt> <dd><em>For all genomics papers, please include a <a href="/misc/variant_table.docx"><strong>Variant Table</strong></a> showing the variants you wish to highlight. This should include the following columns: Gene, Chromosome, HGVS DNA Reference, HGVS Protein Reference, Variant Type (substitution, deletion, etc.), Predicted Effect, dbSNP/dbVar ID, Genotype (heterozygous/ homozygous). Optional additional columns include ClinVar ID, Parent of Origin, Observed Effect (if shown to be different from Predicted Effect), Comments.</em></dd> </dl> <ul> <li> <p><strong>Phenotypic analyses*</strong> (e.g., FMRI, metabolomics, behavioral studies) </p> </li> <li> <p><strong>Functional analyses*</strong> (in vitro or culture-based assays; model organisms) </p> </li> <li> <p><strong>Treatment outcomes*</strong></p> </li> </ul> <p>*<em>These items are usually only in Research Articles but can also appear in Research Reports.</em></p> <p><strong>DISCUSSION</strong></p> <p><strong>METHODS</strong> (including tables for sequencing coverage) </p> <p><strong>ADDITIONAL INFORMATION</strong></p> <ul> <li> <p><strong>Data Deposition and Access</strong>—should provide details of databases where data has been deposited and relevant accession numbers. For any data that are not publicly available (e.g., because consent could not be obtained), a statement to this effect must be included. </p> </li> <li> <p><strong>Ethics Statement</strong>—details of patient consent (written and/or oral) obtained and IRB(s) under which the work was performed must be included in the manuscript. </p> </li> <li> <p><strong>Acknowledgments</strong></p> </li> <li> <p><strong>Author Contributions</strong>—should provide a statement detailing the contributions of authors to the manuscript. </p> </li> <li> <p><strong>Funding</strong></p> </li> </ul> <p><strong>REFERENCES</strong></p> <p><strong>FIGURE LEGENDS</strong></p> <p><strong>FIGURES</strong> (Note: At manuscript revision and later stages, each figure must be captured in a separate figure file; see Art Guidelines, below) </p> <p>----------</p><a name="setup_rapid" id="setup_rapid"></a><h3>MANUSCRIPT SETUP (Rapid Communications, Rapid Cancer Communications, and Variant Discrepancy Resolutions)</h3> <p>Please see template for formatting <a href="/site/misc/rapid_comm_template.pdf">Rapid Communications</a></p> <p>Please see template for formatting <a href="/site/misc/rapid_cancer_comm_template.pdf">Rapid Cancer Communications</a></p> <p>Please see template for formatting <a href="/site/misc/variant_discrep_res_template.pdf">Variant Discrepancy Resolutions</a></p> <p>----------</p><a name="setup_followup" id="setup_followup"></a><h3>MANUSCRIPT SETUP (Follow-up Reports)</h3> <p>Follow-up Reports should be arranged as above but should feature only a brief introduction referencing the original paper, the results obtained since the original paper, and a discussion of the significance of the new findings in the context of the original paper. Only new methods not used in the original paper need to be described. </p> <p>----------</p><a name="at_acceptance" id="at_acceptance"></a><h3>ADDITIONAL INFORMATION REQUIRED</h3> <p><strong>1. Competing Interests Statement</strong>—you will be required to provide a statement disclosing potential conflicts of interest when a manuscript is submitted. </p> <p><strong>2. Ethics Statement</strong>—you will be required to supply a signed version of the Cold Spring Harbor Molecular Case Studies Ethics form when a manuscript is accepted. </p> <p>----------</p><a name="nom" id="nom"></a><h3>NOMENCLATURE</h3> <p>You must use current and approved nomenclature for gene and protein names and symbols, including appropriate use of italics and capitalization in text, tables, and figures. </p> <p>For human nomenclature, please follow the guidelines from the <a href="http://www.genenames.org/about/guidelines">Human Genome Organisation (HUGO) Gene Nomenclature Committee</a>. Human gene symbols should be in capitals and italicized. Human protein symbols are shown in capitals and non-italicized. For sequence variants, please follow <a href="http://www.hgvs.org/mutnomen/recs.html#general">Human Genome Variation Society (HGVS) guidelines</a>—for example, NM_004006.1:c.3G>T (see also <a href="/misc/ifora_policies.xhtml">Data Deposition</a>). </p> <p>Where articles present work from model organisms, please follow the appropriate guidelines for gene and protein names: <a href="http://www.informatics.jax.org/mgihome/nomen/">mouse</a><a></a>, <a href="http://rgd.mcw.edu/nomen/nomen.shtml">rat</a>, <a href="http://birdbase.arizona.edu/birdbase">avian</a>, <a href="https://wiki.zfin.org/display/general/ZFIN+Zebrafish+Nomenclature+Guidelines">zebrafish</a>, <a href="http://flybase.org/static_pages/docs/nomenclature/nomenclature3.html"><em>Drosophila</em></a>, <a href="http://www.wormbase.org/about/userguide/nomenclature#b21je0a37dig4lc9fk68h5--10"><em>C. elegans</em></a>, <a href="http://www.yeastgenome.org/help/community/gene-registry"><em>S. cerevisiae</em></a>. For bacterial nomenclature, follow the guidelines established by <a href="http://www.genetics.org/content/54/1/61.long">Demerec et al. (1966), <em>Genetics</em><strong>54:</strong> 61–76</a>. For viruses and other pathogens, please use appropriate gene/protein nomenclature defined by the relevant committee. </p> <p>----------</p><a name="cite_ref" id="cite_ref"></a><h3>CITATIONS AND REFERENCES</h3> <p>Authors must ensure that all relevant previously published work is properly acknowledged and cited at the appropriate point in the main text, with the correct bibliographic information given in the Reference list. Quotation marks (“ ”), with the appropriate citation and Reference, should be used where statements made in a previously published work are reproduced verbatim. The journal reserves the right to employ automated tools to identify any instances of plagiarism and to withdraw the article if detected. </p> <p>Authors are also responsible for obtaining permission from the rights holder to adapt or reproduce material previously published elsewhere and for including any required permission statement alongside the citation. </p> <p><strong>Citations</strong></p> <p>References cited in text should be in name/year format, not in numbered format. Cite “both names” if there are only two authors and cite “First author et al.” for more than two authors (examples: Smith 1992; Smith and Jones 1998; Jones et al. 2005). </p> <p>Undated citations (unpubl., in prep. [in lieu of “submitted”], pers. comm.) should include first initials and last names of all authors up to three before et al.—e.g., (F Smith, C Graves, A Hershey, pers. comm.). </p> <p>Software URLs should be included in text (not in the Reference list) next to the mention of where material was obtained for performing the work. </p> <p><strong>Reference list</strong></p> <p>Reference lists should be alphabetized, not numbered. Each reference should include all authors’ names up to 10 authors before et al. </p> <p>Journals: Include all authors’ names (surname and initials) up to 10 authors before et al. followed by publication year, journal article title, journal name or abbreviation, volume: page range OR, if none, then doi number or other article identifier (e.g., online article number). </p> <p><em>Example</em>: Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, et al. 2012. Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. <em>Mol Cell </em><strong>47:</strong> 203–214. </p> <p>Books: Include all authors’ names (surname and initials) up to 10 authors before et al. followed by publication year, book title, editors, chapter and page range, publisher and publisher location. </p> <p><em>Example</em>: Jenks WP, Regenstein J. 1975. Ionization constants of acids and bases. In <em>Handbook of biochemistry and molecular biology</em> (ed. Fasman GD), Vol. 1, pp. 305–351. CRC Press, OH. </p> <p>----------</p><a name="math" id="math"></a><h3>MATH OBJECTS </h3> <p>Please be sure to update any MathType objects in the file; otherwise, italics and other font specifications might be lost. Greek symbols should be inserted directly from Word’s “symbol insert” pulldown menu; equations/schemes should be inserted using MathType or Word's Equation Editor. (Note: Authors who use Word 2007 also are requested to create equations using MathType or Word’s original Equation Editor. Equations that are created in Word 2007’s Equation Builder are converted to picture format, which should be avoided.) Please double-check your Word file printout visually to ensure the accuracy of fonts. </p> <p>----------</p><a name="perm" id="perm"></a><h3>PERMISSIONS</h3> <p>It is the author’s responsibility to obtain permission from the rights holder to reproduce/modify/adapt any previously published figure or table for use online in <em>CSH Molecular Case Studies</em>. Authors must include the permissions letter at the time of manuscript submission (as Supplemental Material). The complete reference must be included in the Reference list. </p> <p>----------</p><a name="supp" id="supp"></a><h3>SUPPLEMENTAL MATERIAL </h3> <p><strong>For review purposes</strong></p> <p>All related manuscripts in press, or submitted, must be uploaded as supplemental material. Additional material for the Editors or reviewers should be included and marked as such (e.g., source code for software, permission letters, etc.). </p> <p><strong>For publication</strong></p> <p>Supplemental Material is peer-reviewed and must be directly relevant to the conclusions offered in the main text but not essential for reader understanding. It should be succinct, organized carefully, and labeled appropriately. File sizes should be as small as possible. Tables providing information (such as primer sequences) that are essential for reproducing the work but not essential for understanding the content of the paper should be included only as supplemental material. </p> <p>Each Supplemental figure, table, movie, or data file must be cited in the main text (Supplemental Fig. S1).</p> <p>Authors submitting papers for which in-house software is presented or necessary to reproduce the work should be prepared to make a downloadable program freely available and are encouraged to upload the source code as Supplemental Material for posterity, in addition to depositing in an appropriate repository (e.g., SourceForge, GitHub, etc.) </p> <p>----------</p><a name="art" id="art"></a><h3>ART GUIDELINES (excludes initial manuscript submission)</h3> <p>Authors are required to mask identifying information—such as patients’ eyes, names, initials, or hospital numbers—from view, as required by the patient (or parent or guardian) unless written informed consent prior to publication has been secured by the author (see <a href="/site/misc/ifora_policies.xhtml"><strong>Editorial Policies</strong></a>). </p> <p>The journal will not accept artwork that is manipulated to hide, add, remove, merge, or otherwise change any of the original data. Adjustments to the brightness or contrast of artwork are acceptable, providing they are applied to the entire image and do not obscure any feature of the original. </p> <p>Each file must be provided in its own appropriately named figure file, (101834_Smith_Fig1, e.g.). However, tables must be included directly in the source file, Word or LaTex (see Manuscript Setup/Section Order, above). Multi-paneled figures must be presented on single pages. Cover art proposals must include an electronic version in any of the formats and specifications outlined below. </p> <p><strong>OVERALL:</strong></p> <p>—Use the highest possible resolution setting. (Adequate figure resolution is essential for good online rendering of your paper. It should be at minimum 300 dpi for both line art and halftones.) </p> <p>—All fonts <strong>MUST</strong> be embedded. </p> <p>—PDF-quality settings must always be set to Press Quality.</p> <p>—Disable any image compression or down-sampling.</p> <p><strong>File formats:</strong></p> <p>Acceptable figure file formats: GIF, TIFF, EPS, PDF, JPEG, PPT, and PSD. Recommended file formats are EPS, PDF, TIFF or JPEG.</p> <p><strong>Fonts:</strong></p> <p>Recommended fonts are Helvetica and Arial for regular text, Courier font for genetic code, and Symbol font for special characters in artwork. If the manuscript is accepted for publication, the size of the figures might be adjusted to fit the journal format. </p> <p>Please make sure that text point size is no smaller than 8 pt. and no larger than 10 pt. Do not allow font sizes to vary more than 2 points within any figure or across panels within a given figure. In general, it is best to avoid heavy lettering, which does not display well at a reduced size. </p> <p><strong>Color mode:</strong></p> <p>All figures should be submitted in grayscale or RGB (not CMYK).</p> <p><strong>Color selection:</strong></p> <p>Color choices should be universally accessible. Color keys should be included in the body of the figure rather than in the figure legend. </p> <p><strong>Figure filenames, panels, labels:</strong></p> <p>Properly label figure files by first author’s name/article number/figure number (e.g., Smith1234_Fig1, Smith1234_Fig2, etc.).</p> <p>Do not include panel headings or titles directly in the figure files; instead, include headings directly in the figure legend itself. </p> <p>All panel labels (A, B, C) must be identified in the figure legend. All panel labels representing the parts should be presented as <strong>bold</strong> capital letters (<strong>A, B, C</strong>) in 12-pt Helvetica or Arial. </p> <p><strong>Lines/rules: </strong></p> <p>The weight of all rules used in artwork must be 0.25 point or heavier.</p> <p>----------</p><a name="referee" id="referee"></a><h3>REFEREE PROCESS </h3> <p>Referees are asked to provide a technical evaluation of the work that offers a clear path to publication. They assess the validity of the methods and results presented and provide guidance on revisions necessary to ensure their utility as a publication to other researchers/physicians. Their role is to identify any areas where conclusions are not supported by the data, claims are made without appropriate caveats, or experiments are incomplete. 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