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Diagnostic gene sequencing panels: from design to report—a technical standard of the American College of Medical Genetics and Genomics (ACMG)
Gene sequencing panels are a powerful diagnostic tool for many clinical presentations associated with genetic disorders. Advances in DNA sequencing technology have made gene panels more economical, flexible, and efficient. Because the genes included on gene panels vary widely between laboratories in gene content (e.g., number, reason for inclusion, evidence level for gene–disease association) and technical completeness (e.g., depth of coverage), standards that address technical and clinical aspects of gene panels are needed. This document serves as a technical standard for laboratories designing, offering, and reporting gene panel testing. Although these principles can apply to multiple indications for genetic testing, the primary focus is on diagnostic gene panels (as opposed to carrier screening or predictive testing) with emphasis on technical considerations for the specific genes being tested. This technical standard specifically addresses the impact of gene panel content on clinical sensitivity, specificity, and validity—in the context of gene evidence for contribution to and strength of evidence for gene–disease association—as well as technical considerations such as sequencing limitations, presence of pseudogenes/gene families, mosaicism, transcript choice, detection of copy-number variants, reporting, and disclosure of assay limitations.
Journal Article
Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen)
Copy-number analysis to detect disease-causing losses and gains across the genome is recommended for the evaluation of individuals with neurodevelopmental disorders and/or multiple congenital anomalies, as well as for fetuses with ultrasound abnormalities. In the decade that this analysis has been in widespread clinical use, tremendous strides have been made in understanding the effects of copy-number variants (CNVs) in both affected individuals and the general population. However, continued broad implementation of array and next-generation sequencing–based technologies will expand the types of CNVs encountered in the clinical setting, as well as our understanding of their impact on human health.
This Article was originally published without the accompanying supplementary file “All evaluated CNVs”. This file is now available in the HTML version of the Article; the PDF was correct from the time of publication.
A Correction to this paper has been published: https://doi.org/10.1038/s41436-021-01150-9
To assist clinical laboratories in the classification and reporting of CNVs, irrespective of the technology used to identify them, the American College of Medical Genetics and Genomics has developed the following professional standards in collaboration with the National Institutes of Health (NIH)–funded Clinical Genome Resource (ClinGen) project.
This update introduces a quantitative, evidence-based scoring framework; encourages the implementation of the five-tier classification system widely used in sequence variant classification; and recommends “uncoupling” the evidence-based classification of a variant from its potential implications for a particular individual.
These professional standards will guide the evaluation of constitutional CNVs and encourage consistency and transparency across clinical laboratories.
Journal Article
Laboratory analysis of organic acids, 2018 update: a technical standard of the American College of Medical Genetics and Genomics (ACMG)
Organic acid analysis detects accumulation of organic acids in urine and other body fluids and is a crucial first-tier laboratory test for a broad spectrum of inborn errors of metabolism. It is also frequently ordered as follow-up for a positive newborn screen result, as recommended by American College of Medical Genetics and Genomics newborn screening ACTion sheets and algorithms. The typical assay is performed by gas chromatography–mass spectrometry. These technical standards were developed to provide guidance for laboratory practices in organic acid analysis, interpretation, and reporting. In addition, new diagnostic biomarkers for recently discovered organic acidurias have been added.
Journal Article
Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG)
Next-generation sequencing (NGS) technologies are now established in clinical laboratories as a primary testing modality in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude. It is now cost-effective to analyze an individual with disease-targeted gene panels, exome sequencing, or genome sequencing to assist in the diagnosis of a wide array of clinical scenarios. While clinical validation and use of NGS in many settings is established, there are continuing challenges as technologies and the associated informatics evolve. To assist clinical laboratories with the validation of NGS methods and platforms, the ongoing monitoring of NGS testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics (ACMG) has developed the following technical standards.
Journal Article
Technical laboratory standards for interpretation and reporting of acquired copy-number abnormalities and copy-neutral loss of heterozygosity in neoplastic disorders: a joint consensus recommendation from the American College of Medical Genetics and Genomics (ACMG) and the Cancer Genomics Consortium (CGC)
The detection of acquired copy-number abnormalities (CNAs) and copy-neutral loss of heterozygosity (CN-LOH) in neoplastic disorders by chromosomal microarray analysis (CMA) has significantly increased over the past few years with respect to both the number of laboratories utilizing this technology and the broader number of tumor types being assayed. This highlights the importance of standardizing the interpretation and reporting of acquired variants among laboratories. To address this need, a clinical laboratory-focused workgroup was established to draft recommendations for the interpretation and reporting of acquired CNAs and CN-LOH in neoplastic disorders. This project is a collaboration between the American College of Medical Genetics and Genomics (ACMG) and the Cancer Genomics Consortium (CGC). The recommendations put forth by the workgroup are based on literature review, empirical data, and expert consensus of the workgroup members. A four-tier evidence-based categorization system for acquired CNAs and CN-LOH was developed, which is based on the level of available evidence regarding their diagnostic, prognostic, and therapeutic relevance: tier 1, variants with strong clinical significance; tier 2, variants with some clinical significance; tier 3, clonal variants with no documented neoplastic disease association; and tier 4, benign or likely benign variants. These recommendations also provide a list of standardized definitions of terms used in the reporting of CMA findings, as well as a framework for the clinical reporting of acquired CNAs and CN-LOH, and recommendations for how to deal with suspected clinically significant germline variants.
Journal Article
Laboratory screening and diagnosis of open neural tube defects, 2019 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG)
Open neural tube defects (ONTDs) include open spina bifida (OSB) and anencephaly. These defects are caused by incomplete closure of the neural tube at about 4 weeks of pregnancy. Levels of early second-trimester maternal serum (ms) alpha-fetoprotein (AFP) are sufficiently elevated in affected pregnancies to be used as a population-based screening test. The basic screening methodology was described in the late 1970s and screening programs were active a few years later. By identifying pregnancies with the highest msAFP levels, about 80% of OSB and 95% of anencephaly can be identified as early as 16 weeks gestation. The interpretation of msAFP levels is complicated by the need to consider multiple factors such as gestational age, maternal weight, maternal race, multiple gestations, and more. Testing for AFP and acetylcholinesterase in amniotic fluid and/or identification of the lesion by targeted ultrasound is considered diagnostic of ONTD. When a diagnosis is made, options include termination, surgery after delivery, or in utero surgery, depending on factors such as location and size of the defect, and the presence of any additional anomalies. Screening for ONTD should be performed as part of a comprehensive program linking primary obstetrical care providers, laboratorians, and high-risk clinicians.
Journal Article
Teaching and Collecting Technical Standards
Technical standards are a vital source of information for providing guidelines during the design, manufacture, testing, and use of whole products, materials, and components. To prepare students—especially engineering students—for the workforce, universities are increasing the use of standards within the curriculum. Employers believe it is important for recent university graduates to be familiar with standards. Despite the critical role standards play within academia and the workforce, little information is available on the development of standards information literacy, which includes the ability to understand the standardization process; identify types of standards; and locate, evaluate, and use standards effectively. Libraries and librarians are a critical part of standards education, and much of the discussion has been focused on the curation of standards within libraries. However, librarians also have substantial experience in developing and teaching standards information literacy curriculum. With the need for universities to develop a workforce that is well-educated on the use of standards, librarians and course instructors can apply their experiences in information literacy toward teaching students the knowledge and skills regarding standards that they will need to be successful in their field. This title provides background information for librarians on technical standards as well as collection development best practices. It also creates a model for librarians and course instructors to use when building a standards information literacy curriculum.
eBook
Teaching and Collecting Technical Standards
Technical standards are a vital source of information for providing guidelines during the design, manufacture, testing, and use of whole products, materials, and components. To prepare students—especially engineering students—for the workforce, universities are increasing the use of standards within the curriculum. Employers believe it is important for recent university graduates to be familiar with standards. Despite the critical role standards play within academia and the workforce, little information is available on the development of standards information literacy, which includes the ability to understand the standardization process; identify types of standards; and locate, evaluate, and use standards effectively. Libraries and librarians are a critical part of standards education, and much of the discussion has been focused on the curation of standards within libraries. However, librarians also have substantial experience in developing and teaching standards information literacy curriculum. With the need for universities to develop a workforce that is well-educated on the use of standards, librarians and course instructors can apply their experiences in information literacy toward teaching students the knowledge and skills regarding standards that they will need to be successful in their field. This title provides background information for librarians on technical standards as well as collection development best practices. It also creates a model for librarians and course instructors to use when building a standards information literacy curriculum.
eBook
Laboratory analysis of amino acids, 2018 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG)
Amino acid abnormalities are observed in a broad spectrum of inheritedmetabolic diseases, such as disorders of amino acid metabolism and transport,organic acidemias, and ureagenesis defects. Comprehensive analysis of physiologicamino acids in blood, urine, and cerebrospinal fluid is typically performed in thefollowing clinical settings: evaluation of symptomatic patients in whom a diagnosisis not known; evaluation of previously diagnosed patients to monitor treatmentefficacy; evaluation of asymptomatic or presymptomatic (at-risk) relatives of knownpatients; follow-up testing for an abnormal newborn screen; and assessment ofdietary protein adequacy or renal function in general patient populations.Currently, the most common analytical method to quantify amino acids is based on ionexchange chromatography using post-column derivatization with ninhydrin andspectrophotometric detection. Newer methodologies are based on liquidchromatographic separation with detection by mass spectrometry or spectrophotometry.Amino acid analysis by nonseparation methods, such as the flow injection–tandem massspectrometric (MS/MS) method used for newborn screening, is considered inadequatefor the diagnosis of at-risk patients. The purpose of this document is to provide atechnical standard for amino acid analysis as applied to the diagnosis andmanagement of inborn errors of metabolism.
Journal Article