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"text/html" } }, "meta": { "createdByUser": { "id": 1672898, "username": "aledj2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/aledj2", "type": "text/html" } } }, "creatorSummary": "Richards et al.", "parsedDate": "2015-05", "numChildren": 2 }, "data": { "key": "Z53M5KR4", "version": 52, "itemType": "journalArticle", "title": "Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology", "creators": [ { "creatorType": "author", "firstName": "Sue", "lastName": "Richards" }, { "creatorType": "author", "firstName": "Nazneen", "lastName": "Aziz" }, { "creatorType": "author", "firstName": "Sherri", "lastName": "Bale" }, { "creatorType": "author", "firstName": "David", "lastName": "Bick" }, { "creatorType": "author", "firstName": "Soma", "lastName": "Das" }, { "creatorType": "author", "firstName": "Julie", "lastName": "Gastier-Foster" }, { "creatorType": "author", "firstName": "Wayne W.", "lastName": "Grody" }, { "creatorType": "author", "firstName": "Madhuri", "lastName": "Hegde" }, { "creatorType": "author", "firstName": "Elaine", "lastName": "Lyon" }, { "creatorType": "author", "firstName": "Elaine", "lastName": "Spector" }, { "creatorType": "author", "firstName": "Karl", "lastName": "Voelkerding" }, { "creatorType": "author", "firstName": "Heidi L.", "lastName": "Rehm" }, { "creatorType": "author", "firstName": "on behalf of the ACMG Laboratory Quality Assurance", "lastName": "Committee" } ], "abstractNote": "Disclaimer: These ACMG Standards and Guidelines were developed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory services. Adherence to these standards and guidelines is voluntary and does not necessarily assure a successful medical outcome. These Standards and Guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the clinical laboratory geneticist should apply his or her own professional judgment to the specific circumstances presented by the individual patient or specimen. Clinical laboratory geneticists are encouraged to document in the patient’s record the rationale for the use of a particular procedure or test, whether or not it is in conformance with these Standards and Guidelines. They also are advised to take notice of the date any particular guideline was adopted and to consider other relevant medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures.\nThe American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants. In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic testing spanning genotyping, single genes, gene panels, exomes, genomes, transcriptomes, and epigenetic assays for genetic disorders. By virtue of increased complexity, this shift in genetic testing has been accompanied by new challenges in sequence interpretation. In this context the ACMG convened a workgroup in 2013 comprising representatives from the ACMG, the Association for Molecular Pathology (AMP), and the College of American Pathologists to revisit and revise the standards and guidelines for the interpretation of sequence variants. The group consisted of clinical laboratory directors and clinicians. This report represents expert opinion of the workgroup with input from ACMG, AMP, and College of American Pathologists stakeholders. These recommendations primarily apply to the breadth of genetic tests used in clinical laboratories, including genotyping, single genes, panels, exomes, and genomes. This report recommends the use of specific standard terminology—“pathogenic,” “likely pathogenic,” “uncertain significance,” “likely benign,” and “benign”—to describe variants identified in genes that cause Mendelian disorders. Moreover, this recommendation describes a process for classifying variants into these five categories based on criteria using typical types of variant evidence (e.g., population data, computational data, functional data, segregation data). Because of the increased complexity of analysis and interpretation of clinical genetic testing described in this report, the ACMG strongly recommends that clinical molecular genetic testing should be performed in a Clinical Laboratory Improvement Amendments–approved laboratory, with results interpreted by a board-certified clinical molecular geneticist or molecular genetic pathologist or the equivalent.\nGenet Med 17 5, 405–423.", "publicationTitle": "Genetics in Medicine", "publisher": "", "place": "", "date": "May 2015", "volume": "17", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "405-423", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Genet Med", "DOI": "10.1038/gim.2015.30", "citationKey": "", "url": "http://www.nature.com/gim/journal/v17/n5/full/gim201530a.html", "accessDate": "2015-10-01T14:39:05Z", "PMID": "", "PMCID": "", "ISSN": "1098-3600", "archive": "", "archiveLocation": "", "shortTitle": "Standards and guidelines for the interpretation of sequence variants", "language": "en", "libraryCatalog": "www.nature.com", "callNumber": "", "rights": "© 2015 American College of Medical Genetics and Genomics", "extra": "", "tags": [ { "tag": "ACMG laboratory guideline", "type": 1 }, { "tag": "clinical genetic testing", "type": 1 }, { "tag": "interpretation", "type": 1 }, { "tag": "reporting", "type": 1 }, { "tag": "sequence", "type": 1 }, { "tag": "variant reporting", "type": 1 }, { "tag": "variant terminology", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2015-10-01T14:39:05Z", "dateModified": "2015-10-01T14:39:05Z" } }, { "key": "UTXXA8RB", "version": 50, "library": { "type": "group", "id": 334539, "name": "STP Clinical Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/stp_clinical_bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/334539/items/UTXXA8RB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stp_clinical_bioinformatics/items/UTXXA8RB", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/334539/items/R4GIGG2Z", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1672898, "username": "aledj2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/aledj2", "type": "text/html" } } }, "lastModifiedByUser": { "id": 2217264, "username": "ryys1122", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/ryys1122", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "UTXXA8RB", "version": 50, "parentItem": "R4GIGG2Z", "itemType": "note", "note": "

\"Updated for 3.3 and 2.7\"--Cover Includes index

", "tags": [], "relations": {}, "dateAdded": "2015-03-06T09:50:01Z", "dateModified": "2015-07-10T03:23:55Z" } }, { "key": "UAHZHDD5", "version": 48, "library": { "type": "group", "id": 334539, "name": "STP Clinical Bioinformatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/stp_clinical_bioinformatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/334539/items/UAHZHDD5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stp_clinical_bioinformatics/items/UAHZHDD5", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1672898, "username": "aledj2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/aledj2", "type": "text/html" } } }, "creatorSummary": "The 1000 Genomes Project Consortium", "parsedDate": "2012-11-01", "numChildren": 2 }, "data": { "key": "UAHZHDD5", "version": 48, "itemType": "journalArticle", "title": "An integrated map of genetic variation from 1,092 human genomes", "creators": [ { "creatorType": "author", "name": "The 1000 Genomes Project Consortium" } ], "abstractNote": "By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations.", "publicationTitle": "Nature", "publisher": "", "place": "", "date": "November 1, 2012", "volume": "491", "issue": "7422", "section": "", "partNumber": "", "partTitle": "", "pages": "56-65", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nature", "DOI": "10.1038/nature11632", "citationKey": "", "url": "http://www.nature.com/nature/journal/v491/n7422/full/nature11632.html", "accessDate": "2015-03-27T13:16:34Z", "PMID": "", "PMCID": "", "ISSN": "0028-0836", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.nature.com", "callNumber": "", "rights": "© 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. 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It is clinically and genetically heterogeneous with three distinctive clinical types (I–III) and nine Usher genes identified. This study is a comprehensive clinical and genetic analysis of 172 Usher patients and evaluates the contribution of digenic inheritance.\n\nMethods\nThe genes MYO7A, USH1C, CDH23, PCDH15, USH1G, USH2A, GPR98, WHRN, CLRN1 and the candidate gene SLC4A7 were sequenced in 172 UK Usher patients, regardless of clinical type.\n\nResults\nNo subject had definite mutations (nonsense, frameshift or consensus splice site mutations) in two different USH genes. Novel missense variants were classified UV1-4 (unclassified variant): UV4 is ‘probably pathogenic’, based on control frequency <0.23%, identification in trans to a pathogenic/probably pathogenic mutation and segregation with USH in only one family; and UV3 (‘likely pathogenic’) as above, but no information on phase. Overall 79% of identified pathogenic/UV4/UV3 variants were truncating and 21% were missense changes. MYO7A accounted for 53.2%, and USH1C for 14.9% of USH1 families (USH1C:c.496+1G>A being the most common USH1 mutation in the cohort). USH2A was responsible for 79.3% of USH2 families and GPR98 for only 6.6%. No mutations were found in USH1G, WHRN or SLC4A7.\n\nConclusions\nOne or two pathogenic/likely pathogenic variants were identified in 86% of cases. No convincing cases of digenic inheritance were found. 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