Journal ArticleDOI
Consensus document on the implementation of next generation sequencing in the genetic diagnosis of hereditary cancer.
José Luis Soto,Ignacio Blanco,Orland Diez,Javier García Planells,Isabel Lorda,Gert Matthijs,Mercedes Robledo,Erika Souche,Conxi Lázaro +8 more
TLDR
The aim of these guidelines is to establish a framework of useful recommendations for planned and controlled implementation of NGS in the context of hereditary cancer, to consolidate the strengths and opportunities offered by this technology, and minimise the weaknesses and threats which may derive from its use.Abstract:
Genetic diagnosis of hereditary cancer syndromes offers the opportunity to establish more effective predictive and preventive measures for the patient and their families. The ultimate objective is to decrease cancer morbidity and mortality in high genetic risk families. Next Generation Sequencing (NGS) offers an important improvement in the efficiency of genetic diagnosis, allowing an increase in diagnostic yield with a substantial reduction in response times and economic costs. Consequently, the implementation of this new technology is a great opportunity for improvement in the clinical management of affected families. The aim of these guidelines is to establish a framework of useful recommendations for planned and controlled implementation of NGS in the context of hereditary cancer. These will help to consolidate the strengths and opportunities offered by this technology, and minimise the weaknesses and threats which may derive from its use. The recommendations of international societies have been adapted to our environment, taking the Spanish context into account at organisational and juridical levels. Forty-one statements are grouped under six headings: clinical and diagnostic utility, informed consent and genetic counselling pre-test and post-test, validation of analytical procedures, results report, management of information and distinction between research and clinical context. This guide has been developed by the Spanish Association of Human Genetics (AEGH), the Spanish Society of Laboratory Medicine (SEQC-ML) and the Spanish Society of Medical Oncology (SEOM).read more
Citations
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A comprehensive custom panel evaluation for routine hereditary cancer testing: improving the yield of germline mutation detection.
Carolina Velázquez,Carolina Velázquez,Enrique Lastra,Francisco Avila Cobos,Luis E. Abella,Virginia de la Cruz,Blanca Hernando,Lara Hernández,Noemí Martínez,Mar Infante,Mercedes Durán +10 more
TL;DR: The results reinforce the utility of NGS gene panels in the diagnostic routine to increase the performance of genetic testing, especially in individuals from families with overlapping cancer phenotypes.
Journal ArticleDOI
Mutational Screening of BRCA1/2 Genes as a Predictive Factor for Therapeutic Response in Epithelial Ovarian Cancer: A Consensus Guide from the Spanish Society of Pathology (SEAP-IAP) and the Spanish Society of Human Genetics (AEGH)
J Palacios,M de la Hoya,M de la Hoya,B Bellosillo,I de Juan,Xavier Matias-Guiu,Conxi Lázaro,Sarai Palanca,Ana Osorio,F Rojo,Juan Manuel Rosa-Rosa,J C Cigudosa +11 more
TL;DR: This consensus guide represents a collection of technical recommendations to address the detection of BRCA1/2 mutations in the molecular diagnostic testing strategy for OC and provides some references, quality parameters, and genomic tools aimed to standardize and facilitate the clinical genomic diagnosis of OC.
Journal ArticleDOI
Building the Framework for Standardized Clinical Laboratory Reporting of Next-generation Sequencing Data for Resistance-associated Mutations in Mycobacterium tuberculosis Complex
Jeffrey A. Tornheim,Angela M. Starks,Timothy C. Rodwell,Jennifer L. Gardy,Timothy M Walker,Daniela Maria Cirillo,Lakshmi Jayashankar,Paolo Miotto,Matteo Zignol,Marco Schito +9 more
TL;DR: This viewpoint article summarizes 2 expert workshops regarding a standardized report format, focusing on relevant variables, terminology, and required minimal elements for clinical and laboratory reports with a proposed standardized template for clinical reporting NGS results for Mycobacterium tuberculosis.
Journal ArticleDOI
Genomic profiling in oncology clinical practice
TL;DR: The clinical applications and limitations of genomic profiling in oncology clinical practice are summarized, focusing on next-generation sequencing.
Journal ArticleDOI
Improving Genetic Testing in Hereditary Cancer by RNA Analysis: Tools to Prioritize Splicing Studies and Challenges in Applying American College of Medical Genetics and Genomics Guidelines.
Paula Rofes,Mireia Menéndez,Sara González,Eva Tornero,Carolina Gómez,Gardenia Vargas-Parra,Eva Montes,Mónica Salinas,Ares Solanes,Joan Brunet,Alex Teulé,Gabriel Capellá,Lídia Feliubadaló,Jesús del Valle,Marta Pineda,Conxi Lázaro +15 more
TL;DR: This study highlights the importance of RNA studies to improve variant classification and evidences the challenge of incorporating these results into generic ACMG guidelines and the need to refine these criteria gene-specifically.
References
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Journal ArticleDOI
Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012.
Jacques Ferlay,Isabelle Soerjomataram,Rajesh Dikshit,Sultan Eser,Colin Mathers,Marise Souto Rebelo,Donald Maxwell Parkin,David Forman,Freddie Bray +8 more
TL;DR: The GLOBOCAN series of the International Agency for Research on Cancer (IARC) as mentioned in this paper provides estimates of the worldwide incidence and mortality from 27 major cancers and for all cancers combined for 2012.
Journal ArticleDOI
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.
Sue Richards,Nazneen Aziz,Nazneen Aziz,Sherri J. Bale,David P. Bick,Soma Das,Julie M. Gastier-Foster,Wayne W. Grody,Madhuri Hegde,Elaine Lyon,Elaine B. Spector,Karl V. Voelkerding,Heidi L. Rehm +12 more
TL;DR: Because of the increased complexity of analysis and interpretation of clinical genetic testing described in this report, the ACMG strongly recommends thatclinical 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.
Journal ArticleDOI
ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing
Robert C. Green,Robert C. Green,Jonathan S. Berg,Wayne W. Grody,Sarah S. Kalia,Bruce R. Korf,Christa Lese Martin,Amy L. McGuire,Robert L. Nussbaum,Julianne M. O’Daniel,Kelly E. Ormond,Heidi L. Rehm,Heidi L. Rehm,Michael S. Watson,Marc S. Williams,Leslie G. Biesecker +15 more
TL;DR: It is recommended that laboratories performing clinical sequencing seek and report mutations of the specified classes or types in the genes listed here and encourage the creation of an ongoing process for updating these recommendations at least annually as further data are collected.
Journal ArticleDOI
Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists
Marilyn M. Li,Michael B. Datto,Eric J. Duncavage,Shashikant Kulkarni,Neal I. Lindeman,Somak Roy,Apostolia Maria Tsimberidou,Cindy L. Vnencak-Jones,Daynna J. Wolff,Anas Younes,Marina N. Nikiforova +10 more
TL;DR: A four-tiered system to categorize somatic sequence variations based on their clinical significances is proposed, with variants with strong clinical significance and variants with potential clinical significance in tier I; tier III, variants of unknown clinical significance; and tier IV, variants deemed benign or likely benign.
Journal ArticleDOI
ClinGen — The Clinical Genome Resource
Heidi L. Rehm,Jonathan S. Berg,Lisa D. Brooks,Carlos Bustamante,James P. Evans,Melissa J. Landrum,David H. Ledbetter,Donna Maglott,Christa Lese Martin,Robert L. Nussbaum,Sharon E. Plon,Erin M. Ramos,Stephen T. Sherry,Michael S. Watson +13 more
TL;DR: A patient’s family pursues genetic testing that shows a “likely pathogenic” variant for the condition on the basis of a study in an original research publication, and a different variant is found that is determined to be pathogenic.