Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation

Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient s...

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Published inHuman mutation Vol. 41; no. 12; pp. 2028 - 2057
Main Authors McCormick, Elizabeth M., Lott, Marie T., Dulik, Matthew C., Shen, Lishuang, Attimonelli, Marcella, Vitale, Ornella, Karaa, Amel, Bai, Renkui, Pineda‐Alvarez, Daniel E., Singh, Larry N., Stanley, Christine M., Wong, Stacey, Bhardwaj, Anshu, Merkurjev, Daria, Mao, Rong, Sondheimer, Neal, Zhang, Shiping, Procaccio, Vincent, Wallace, Douglas C., Gai, Xiaowu, Falk, Marni J.
Format Journal Article
LanguageEnglish
Published United States John Wiley & Sons, Inc 01.12.2020
Subjects
Computer applications
criteria
Databases, Genetic
Decision Trees
Deoxyribonucleic acid
DNA
DNA, Mitochondrial - genetics
Genetic Variation
Genomes
Guidelines as Topic
Haplotypes - genetics
Heteroplasmy
Humans
Maternal inheritance
mitochondria
Mitochondrial DNA
mtDNA
Nucleotide sequence
Pathogenicity
Phenotype
Phylogeny
Reference Standards
Societies, Scientific
variant interpretation
heteroplasmy
pathogenicity
mtDNA
criteria
mitochondria
variant interpretation
Online AccessGet full text
ISSN1059-7794
1098-1004
1098-1004
DOI10.1002/humu.24107

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Abstract Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.
AbstractList Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.
Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics (ACMG) and Association of Molecular Pathology (AMP) standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel based consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well specifications for utilization of mtDNA genomic databases and computational algorithms.
Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.
Author Merkurjev, Daria
Stanley, Christine M.
Dulik, Matthew C.
Bai, Renkui
Falk, Marni J.
Shen, Lishuang
Bhardwaj, Anshu
Gai, Xiaowu
Pineda‐Alvarez, Daniel E.
Karaa, Amel
Zhang, Shiping
Wong, Stacey
Procaccio, Vincent
Vitale, Ornella
Attimonelli, Marcella
Singh, Larry N.
Lott, Marie T.
Sondheimer, Neal
Wallace, Douglas C.
McCormick, Elizabeth M.
Mao, Rong
AuthorAffiliation 6 Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Bari, Italy
17 Biochemistry and Genetics Department, MitoVasc Institute, UMR CNRS 6015– INSERM U1083, CHU Angers, 49933 Angers, France
18 Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
7 Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
16 Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
2 Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
3 Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
11 QNA Diagnostics, Cambridge, MA 02139, USA
10 Variantyx, Inc, Framingham, MA 01701, USA
4 Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
13 ARUP Institute for Clinical and
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Issue 12
Keywords heteroplasmy
pathogenicity
mtDNA
criteria
mitochondria
variant interpretation
Language English
License 2020 Wiley Periodicals LLC.
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Notes Elizabeth M. McCormick, Marie T. Lott, and Matthew C. Dulik equally contributed as first authors. Douglas C. Wallace, Xiaowu Gai, and Marni J. Falk equally contributed as senior authors.
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These authors contributed equally to this work.
MJF conceived of the project. EMM, MTL, MCD, LS, MA, OV, AK, RB, DEPA, LNS, CMS, SW, RM, and NS met regularly to specify guidelines with oversight by VP, DCW, XG, and MJF. SZ, DM, LS, and AB provided bioinformatics support. The manuscript was written by EMM, MTL, MCD, LS, MA, OV, NS, XG, and MJF with all authors reviewing and agreeing with final submission.
Author contributions
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Snippet Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal...
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pubmed
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wiley
SourceType Open Access Repository
Aggregation Database
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StartPage 2028
SubjectTerms Computer applications
criteria
Databases, Genetic
Decision Trees
Deoxyribonucleic acid
DNA
DNA, Mitochondrial - genetics
Genetic Variation
Genomes
Guidelines as Topic
Haplotypes - genetics
Heteroplasmy
Humans
Maternal inheritance
mitochondria
Mitochondrial DNA
mtDNA
Nucleotide sequence
Pathogenicity
Phenotype
Phylogeny
Reference Standards
Societies, Scientific
variant interpretation
Title Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation
URI https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fhumu.24107
https://www.ncbi.nlm.nih.gov/pubmed/32906214
https://www.proquest.com/docview/2464539889
https://www.proquest.com/docview/2441603539
https://pubmed.ncbi.nlm.nih.gov/PMC7717623
Volume 41
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