Exploring concordance and discordance for return of incidental findings from clinical sequencing
Purpose: The aim of this study was to explore specific conditions and types of genetic variants that specialists in genetics recommend should be returned as incidental findings in clinical sequencing. Methods: Sixteen specialists in clinical genetics and/or molecular medicine selected variants in 99...
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| Published in | Genetics in medicine Vol. 14; no. 4; pp. 405 - 410 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Nature Publishing Group US
01.04.2012
Elsevier Limited |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Purpose:
The aim of this study was to explore specific conditions and types of genetic variants that specialists in genetics recommend should be returned as incidental findings in clinical sequencing.
Methods:
Sixteen specialists in clinical genetics and/or molecular medicine selected variants in 99 common conditions to return to the ordering physician if discovered incidentally through whole-genome sequencing. For most conditions, the specialists independently considered three molecular scenarios for both adults and minor children: a known pathogenic mutation, a truncating variant presumed pathogenic (where other truncating variants are known to be pathogenic), and a missense variant predicted
in silico
to be pathogenic.
Results:
On average, for adults and children, respectively, each specialist selected 83.5 and 79.0 conditions or genes of 99 in the known pathogenic mutation categories, 57.0 and 53.5 of 72 in the truncating variant categories, and 33.4 and 29.7 of 72 in the missense variant categories. Concordance in favor of disclosure within the adult/known pathogenic mutation category was 100% for 21 conditions or genes and 80% or higher for 64 conditions or genes.
Conclusion:
Specialists were highly concordant for the return of findings for 64 conditions or genes if discovered incidentally during whole-exome sequencing or whole-genome sequencing.
Genet Med
2012:14(4):405–410 |
|---|---|
| AbstractList | Purpose:
The aim of this study was to explore specific conditions and types of genetic variants that specialists in genetics recommend should be returned as incidental findings in clinical sequencing.
Methods:
Sixteen specialists in clinical genetics and/or molecular medicine selected variants in 99 common conditions to return to the ordering physician if discovered incidentally through whole-genome sequencing. For most conditions, the specialists independently considered three molecular scenarios for both adults and minor children: a known pathogenic mutation, a truncating variant presumed pathogenic (where other truncating variants are known to be pathogenic), and a missense variant predicted
in silico
to be pathogenic.
Results:
On average, for adults and children, respectively, each specialist selected 83.5 and 79.0 conditions or genes of 99 in the known pathogenic mutation categories, 57.0 and 53.5 of 72 in the truncating variant categories, and 33.4 and 29.7 of 72 in the missense variant categories. Concordance in favor of disclosure within the adult/known pathogenic mutation category was 100% for 21 conditions or genes and 80% or higher for 64 conditions or genes.
Conclusion:
Specialists were highly concordant for the return of findings for 64 conditions or genes if discovered incidentally during whole-exome sequencing or whole-genome sequencing.
Genet Med
2012:14(4):405–410 The aim of this study was to explore specific conditions and types of genetic variants that specialists in genetics recommend should be returned as incidental findings in clinical sequencing. Sixteen specialists in clinical genetics and/or molecular medicine selected variants in 99 common conditions to return to the ordering physician if discovered incidentally through whole-genome sequencing. For most conditions, the specialists independently considered three molecular scenarios for both adults and minor children: a known pathogenic mutation, a truncating variant presumed pathogenic (where other truncating variants are known to be pathogenic), and a missense variant predicted in silico to be pathogenic. On average, for adults and children, respectively, each specialist selected 83.5 and 79.0 conditions or genes of 99 in the known pathogenic mutation categories, 57.0 and 53.5 of 72 in the truncating variant categories, and 33.4 and 29.7 of 72 in the missense variant categories. Concordance in favor of disclosure within the adult/known pathogenic mutation category was 100% for 21 conditions or genes and 80% or higher for 64 conditions or genes. Specialists were highly concordant for the return of findings for 64 conditions or genes if discovered incidentally during whole-exome sequencing or whole-genome sequencing.Genet Med 2012:14(4):405-410. The aim of this study was to explore specific conditions and types of genetic variants that specialists in genetics recommend should be returned as incidental findings in clinical sequencing.PURPOSEThe aim of this study was to explore specific conditions and types of genetic variants that specialists in genetics recommend should be returned as incidental findings in clinical sequencing.Sixteen specialists in clinical genetics and/or molecular medicine selected variants in 99 common conditions to return to the ordering physician if discovered incidentally through whole-genome sequencing. For most conditions, the specialists independently considered three molecular scenarios for both adults and minor children: a known pathogenic mutation, a truncating variant presumed pathogenic (where other truncating variants are known to be pathogenic), and a missense variant predicted in silico to be pathogenic.METHODSSixteen specialists in clinical genetics and/or molecular medicine selected variants in 99 common conditions to return to the ordering physician if discovered incidentally through whole-genome sequencing. For most conditions, the specialists independently considered three molecular scenarios for both adults and minor children: a known pathogenic mutation, a truncating variant presumed pathogenic (where other truncating variants are known to be pathogenic), and a missense variant predicted in silico to be pathogenic.On average, for adults and children, respectively, each specialist selected 83.5 and 79.0 conditions or genes of 99 in the known pathogenic mutation categories, 57.0 and 53.5 of 72 in the truncating variant categories, and 33.4 and 29.7 of 72 in the missense variant categories. Concordance in favor of disclosure within the adult/known pathogenic mutation category was 100% for 21 conditions or genes and 80% or higher for 64 conditions or genes.RESULTSOn average, for adults and children, respectively, each specialist selected 83.5 and 79.0 conditions or genes of 99 in the known pathogenic mutation categories, 57.0 and 53.5 of 72 in the truncating variant categories, and 33.4 and 29.7 of 72 in the missense variant categories. Concordance in favor of disclosure within the adult/known pathogenic mutation category was 100% for 21 conditions or genes and 80% or higher for 64 conditions or genes.Specialists were highly concordant for the return of findings for 64 conditions or genes if discovered incidentally during whole-exome sequencing or whole-genome sequencing.Genet Med 2012:14(4):405-410.CONCLUSIONSpecialists were highly concordant for the return of findings for 64 conditions or genes if discovered incidentally during whole-exome sequencing or whole-genome sequencing.Genet Med 2012:14(4):405-410. Purpose:The aim of this study was to explore specific conditions and types of genetic variants that specialists in genetics recommend should be returned as incidental findings in clinical sequencing.Methods:Sixteen specialists in clinical genetics and/or molecular medicine selected variants in 99 common conditions to return to the ordering physician if discovered incidentally through whole-genome sequencing. For most conditions, the specialists independently considered three molecular scenarios for both adults and minor children: a known pathogenic mutation, a truncating variant presumed pathogenic (where other truncating variants are known to be pathogenic), and a missense variant predicted in silico to be pathogenic.Results:On average, for adults and children, respectively, each specialist selected 83.5 and 79.0 conditions or genes of 99 in the known pathogenic mutation categories, 57.0 and 53.5 of 72 in the truncating variant categories, and 33.4 and 29.7 of 72 in the missense variant categories. Concordance in favor of disclosure within the adult/known pathogenic mutation category was 100% for 21 conditions or genes and 80% or higher for 64 conditions or genes.Conclusion:Specialists were highly concordant for the return of findings for 64 conditions or genes if discovered incidentally during whole-exome sequencing or whole-genome sequencing.Genet Med 2012:14(4):405–410 Purpose: The aim of this study was to explore specific conditions and types of genetic variants that specialists in genetics recommend should be returned as incidental findings in clinical sequencing. Methods: Sixteen specialists in clinical genetics and/or molecular medicine selected variants in 99 common conditions to return to the ordering physician if discovered incidentally through whole-genome sequencing. For most conditions, the specialists independently considered three molecular scenarios for both adults and minor children: a known pathogenic mutation, a truncating variant presumed pathogenic (where other truncating variants are known to be pathogenic), and a missense variant predicted in silico to be pathogenic. Results: On average, for adults and children, respectively, each specialist selected 83.5 and 79.0 conditions or genes of 99 in the known pathogenic mutation categories, 57.0 and 53.5 of 72 in the truncating variant categories, and 33.4 and 29.7 of 72 in the missense variant categories. Concordance in favor of disclosure within the adult/known pathogenic mutation category was 100% for 21 conditions or genes and 80% or higher for 64 conditions or genes. Conclusion: Specialists were highly concordant for the return of findings for 64 conditions or genes if discovered incidentally during whole-exome sequencing or whole-genome sequencing. |
| Author | Rehm, Heidi L. Green, Robert C. Dimmock, David P. Hegde, Madhuri R. Krantz, Ian McGuire, Amy L. Grody, Wayne W. Miller, David T. Jacob, Howard J. Korf, Bruce R. Biesecker, Leslie G. Berg, Jonathan S. Plon, Sharon E. Nussbaum, Robert L. Kalia, Sarah Evans, James P. Murray, Michael F. Berry, Gerard T. |
| AuthorAffiliation | 3 Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina 15 Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 7 Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 6 National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 1 Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 9 Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 12 Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas 14 Division of Medical Genetics, Department of Medicine, UCSF, San Francisco, California 16 Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 4 Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, Massachusetts 5 Department of Medicine, Chil |
| AuthorAffiliation_xml | – name: 14 Division of Medical Genetics, Department of Medicine, UCSF, San Francisco, California – name: 15 Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – name: 1 Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts – name: 6 National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland – name: 11 Division of Human Genetics and Molecular Biology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania – name: 13 Department of Laboratory Medicine, Children’s Hospital Boston and Harvard Medical School, Boston, Massachusetts – name: 8 Divisions of Medical Genetics and Molecular Pathology, Departments of Pathology & Laboratory Medicine, Pediatrics, and Human Genetics, UCLA School of Medicine, Los Angeles, California – name: 12 Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas – name: 4 Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, Massachusetts – name: 5 Department of Medicine, Children’s Hospital Boston and Harvard Medical School, Boston, Massachusetts – name: 10 Department of Genetics, University of Alabama, Birmingham, Alabama – name: 2 Partners Center for Personalized Genetic Medicine, Boston, Massachusetts – name: 9 Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia – name: 3 Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina – name: 7 Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin – name: 16 Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts |
| Author_xml | – sequence: 1 givenname: Robert C. surname: Green fullname: Green, Robert C. email: rcgreen@genetics.med.harvard.edu organization: Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Partners Center for Personalized Genetic Medicine – sequence: 2 givenname: Jonathan S. surname: Berg fullname: Berg, Jonathan S. organization: Department of Genetics, University of North Carolina at Chapel Hill School of Medicine – sequence: 3 givenname: Gerard T. surname: Berry fullname: Berry, Gerard T. organization: Division of Genetics, Children’s Hospital Boston and Harvard Medical School, The Manton Center for Orphan Disease Research, Children’s Hospital Boston – sequence: 4 givenname: Leslie G. surname: Biesecker fullname: Biesecker, Leslie G. organization: National Human Genome Research Institute, National Institutes of Health – sequence: 5 givenname: David P. surname: Dimmock fullname: Dimmock, David P. organization: Division of Genetics, Department of Pediatrics, Medical College of Wisconsin – sequence: 6 givenname: James P. surname: Evans fullname: Evans, James P. organization: Department of Genetics, University of North Carolina at Chapel Hill School of Medicine – sequence: 7 givenname: Wayne W. surname: Grody fullname: Grody, Wayne W. organization: Division of Medical Genetics, Department of Human Genetics, UCLA School of Medicine, Division of Molecular Pathology, Department of Pathology & Laboratory Medicine, UCLA School of Medicine, Division of Pediatric Genetics, Department of Pediatrics, UCLA School of Medicine – sequence: 8 givenname: Madhuri R. surname: Hegde fullname: Hegde, Madhuri R. organization: Department of Human Genetics, Emory University School of Medicine – sequence: 9 givenname: Sarah surname: Kalia fullname: Kalia, Sarah organization: Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School – sequence: 10 givenname: Bruce R. surname: Korf fullname: Korf, Bruce R. organization: Department of Genetics, University of Alabama – sequence: 11 givenname: Ian surname: Krantz fullname: Krantz, Ian organization: Division of Human Genetics and Molecular Biology, The Children’s Hospital of Philadelphia – sequence: 12 givenname: Amy L. surname: McGuire fullname: McGuire, Amy L. organization: Center for Medical Ethics and Health Policy, Baylor College of Medicine – sequence: 13 givenname: David T. surname: Miller fullname: Miller, David T. organization: Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Department of Laboratory Medicine, Children’s Hospital Boston and Harvard Medical School – sequence: 14 givenname: Michael F. surname: Murray fullname: Murray, Michael F. organization: Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Partners Center for Personalized Genetic Medicine – sequence: 15 givenname: Robert L. surname: Nussbaum fullname: Nussbaum, Robert L. organization: Division of Medical Genetics, Department of Medicine, and Institute for Human Genetics, University of California, San Francisco – sequence: 16 givenname: Sharon E. surname: Plon fullname: Plon, Sharon E. organization: Department of Pediatrics, Baylor College of Medicine, Department of Molecular and Human Genetics, Baylor College of Medicine – sequence: 17 givenname: Heidi L. surname: Rehm fullname: Rehm, Heidi L. organization: Partners Center for Personalized Genetic Medicine, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School – sequence: 18 givenname: Howard J. surname: Jacob fullname: Jacob, Howard J. organization: Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Department of Physiology, Medical College of Wisconsin |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/22422049$$D View this record in MEDLINE/PubMed |
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| References | Ginsburg, Willard (CR3) 2009; 154 Mayer, Dimmock, Arca (CR7) 2011; 13 Link, Schuettpelz, Shen (CR10) 2011; 305 Lupski, Reid, Gonzaga-Jauregui (CR8) 2010; 362 Berg, Evans, Leigh (CR12) 2011; 13 Khoury (CR5) 2011; 13 Feero, Guttmacher, Collins (CR2) 2010; 362 CR18 Korf (CR4) 2011; 13 Worthey, Mayer, Syverson (CR9) 2011; 13 CR15 CR14 CR13 Berg, Khoury, Evans (CR17) 2011; 13 Green, Guyer (CR6) 2011; 470 Bainbridge, Wiszniewski, Murdock (CR11) 2011; 3 Guttmacher, McGuire, Ponder, Stefánsson (CR1) 2010; 11 Kohane, Masys, Altman (CR16) 2006; 296 10.1038/gim.2012.21_bb0095 10.1038/gim.2012.21_bb0075 10.1038/gim.2012.21_bb0080 Green (10.1038/gim.2012.21_bb0035) Berg (10.1038/gim.2012.21_bb0065) 10.1038/gim.2012.21_bb0070 Lupski (10.1038/gim.2012.21_bb0045) Mayer (10.1038/gim.2012.21_bb0040) Link (10.1038/gim.2012.21_bb0055) Kohane (10.1038/gim.2012.21_bb0085) Khoury (10.1038/gim.2012.21_bb0030) Worthey (10.1038/gim.2012.21_bb0050) Bainbridge (10.1038/gim.2012.21_bb0060) Ginsburg (10.1038/gim.2012.21_bb0020) Feero (10.1038/gim.2012.21_bb0015) Guttmacher (10.1038/gim.2012.21_bb0010) Korf (10.1038/gim.2012.21_bb0025) Berg (10.1038/gim.2012.21_bb0090) |
| References_xml | – ident: CR18 – volume: 11 start-page: 161 year: 2010 end-page: 165 ident: CR1 article-title: Personalized genomic information: preparing for the future of genetic medicine publication-title: Nat Rev Genet doi: 10.1038/nrg2735 – volume: 362 start-page: 2001 year: 2010 end-page: 2011 ident: CR2 article-title: Genomic medicine–an updated primer publication-title: N Engl J Med doi: 10.1056/NEJMra0907175 – ident: CR14 – ident: CR15 – volume: 13 start-page: 201 year: 2011 end-page: 202 ident: CR4 article-title: Genetics and genomics education: the next generation publication-title: Genet Med doi: 10.1097/GIM.0b013e31820986cd – ident: CR13 – volume: 305 start-page: 1568 year: 2011 end-page: 1576 ident: CR10 article-title: Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML publication-title: JAMA doi: 10.1001/jama.2011.473 – volume: 13 start-page: 206 year: 2011 end-page: 209 ident: CR5 article-title: Public health genomics: the end of the beginning publication-title: Genet Med doi: 10.1097/GIM.0b013e31821024ca – volume: 3 start-page: 87re3 year: 2011 ident: CR11 article-title: Whole-genome sequencing for optimized patient management publication-title: Sci Transl Med doi: 10.1126/scitranslmed.3002243 – volume: 13 start-page: 218 year: 2011 end-page: 229 ident: CR12 article-title: Next generation massively parallel sequencing of targeted exomes to identify genetic mutations in primary ciliary dyskinesia: implications for application to clinical testing publication-title: Genet Med doi: 10.1097/GIM.0b013e318203cff2 – volume: 296 start-page: 212 year: 2006 end-page: 215 ident: CR16 article-title: The incidentalome: a threat to genomic medicine publication-title: JAMA doi: 10.1001/jama.296.2.212 – volume: 154 start-page: 277 year: 2009 end-page: 287 ident: CR3 article-title: Genomic and personalized medicine: foundations and applications publication-title: Transl Res doi: 10.1016/j.trsl.2009.09.005 – volume: 470 start-page: 204 year: 2011 end-page: 213 ident: CR6 article-title: Charting a course for genomic medicine from base pairs to bedside publication-title: Nature doi: 10.1038/nature09764 – volume: 13 start-page: 499 year: 2011 end-page: 504 ident: CR17 article-title: Deploying whole genome sequencing in clinical practice and public health: meeting the challenge one bin at a time publication-title: Genet Med doi: 10.1097/GIM.0b013e318220aaba – volume: 362 start-page: 1181 year: 2010 end-page: 1191 ident: CR8 article-title: Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy publication-title: N Engl J Med doi: 10.1056/NEJMoa0908094 – volume: 13 start-page: 255 year: 2011 end-page: 262 ident: CR9 article-title: Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease publication-title: Genet Med doi: 10.1097/GIM.0b013e3182088158 – volume: 13 start-page: 195 year: 2011 end-page: 196 ident: CR7 article-title: A timely arrival for genomic medicine publication-title: Genet Med doi: 10.1097/GIM.0b013e3182095089 – ident: 10.1038/gim.2012.21_bb0095 – ident: 10.1038/gim.2012.21_bb0025 – ident: 10.1038/gim.2012.21_bb0090 – ident: 10.1038/gim.2012.21_bb0035 – ident: 10.1038/gim.2012.21_bb0070 – ident: 10.1038/gim.2012.21_bb0040 – ident: 10.1038/gim.2012.21_bb0050 – ident: 10.1038/gim.2012.21_bb0055 – ident: 10.1038/gim.2012.21_bb0010 – ident: 10.1038/gim.2012.21_bb0015 – ident: 10.1038/gim.2012.21_bb0045 – ident: 10.1038/gim.2012.21_bb0020 – ident: 10.1038/gim.2012.21_bb0080 – ident: 10.1038/gim.2012.21_bb0085 – ident: 10.1038/gim.2012.21_bb0030 – ident: 10.1038/gim.2012.21_bb0075 – ident: 10.1038/gim.2012.21_bb0060 – ident: 10.1038/gim.2012.21_bb0065 |
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| Title | Exploring concordance and discordance for return of incidental findings from clinical sequencing |
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