Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium

American Journal of Human Genetics

Volumn 98, Issue 6, 2016, Pages 1067-1076

  Amendola, Laura M ^a   Jarvik, Gail P ^a   Leo, Michael C ^b   McLaughlin, Heather M ^c   Akkari, Yassmine ^d   Amaral, Michelle D ^e   Berg, Jonathan S ^f   Biswas, Sawona ^g   Bowling, Kevin M ^e   Conlin, Laura K ^g   Cooper, Greg M ^e   Dorschner, Michael O ^h   Dulik, Matthew C ^g   Ghazani, Arezou A ⁱ   Ghosh, Rajarshi ^j   Green, Robert C ^c,k,n   Hart, Ragan ^a   Horton, Carrie ^l   Johnston, Jennifer J ^m   Lebo, Matthew S ^c,k   Milosavljevic, Aleksandar ^j   Ou, Jeffrey ^a   Pak, Christine M ^d   Patel, Ronak Y ^j   Punj, Sumit ^d   Richards, Carolyn Sue ^d   Salama, Joseph ^a   Strande, Natasha T ^f   Yang, Yaping ^j   Plon, Sharon E ^j   Biesecker, Leslie G ^m   Rehm, Heidi L ^c,k,n   more..

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b CENTER FOR HEALTH RESEARCH   (United States)

^c LABORATORY FOR MOLECULAR MEDICINE   (United States)

^d OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^e HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^f UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^g CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^h UNIVERSITY OF WASHINGTON   (United States)

ⁱ DANA FARBER CANCER INSTITUTE   (United States)

^j BAYLOR COLLEGE OF MEDICINE   (United States)

^k BRIGHAM AND WOMEN S HOSPITAL   (United States)

^l AMBRY GENETICS   (United States)

^m NATIONAL INSTITUTE OF MENTAL HEALTH   (United States)

ⁿ BROAD INSTITUTE OF MIT AND HARVARD   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLASSIFICATION; CONSENSUS; EXPLORATORY RESEARCH; GENE SEQUENCE; GENETIC VARIATION; HUMAN; INDEL MUTATION; LABORATORY; MOLECULAR DIAGNOSIS; MONOGENIC DISORDER; PATHOGENICITY; PRACTICE GUIDELINE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; DNA SEQUENCE; EVIDENCE BASED PRACTICE; EXOME; GENETIC SCREENING; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; INCIDENTAL FINDING; MEDICAL RESEARCH; MUTATION; PROCEDURES; SOFTWARE; STANDARDS; STATISTICAL ANALYSIS; UNITED STATES;

BIOMEDICAL RESEARCH; DATA INTERPRETATION, STATISTICAL; EVIDENCE-BASED PRACTICE; EXOME; GENETIC TESTING; GENETIC VARIATION; GENOME, HUMAN; GENOMICS; GUIDELINES AS TOPIC; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INCIDENTAL FINDINGS; LABORATORIES; MUTATION; SEQUENCE ANALYSIS, DNA; SOFTWARE; UNITED STATES;

EID: 84966639523     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2016.03.024     Document Type: Article

References (26)

1. I.S. Kohane, M. Hsing, and S.W. Kong Taxonomizing, sizing, and overcoming the incidentalome Genet. Med. 14 2012 399 404
2. B.J. Evans, W. Burke, and G.P. Jarvik The FDA and genomic tests - getting regulation right N. Engl. J. Med. 372 2015 2258 2264
3. H.L. Rehm, J.S. Berg, L.D. Brooks, C.D. Bustamante, J.P. Evans, M.J. Landrum, D.H. Ledbetter, D.R. Maglott, C.L. Martin, R.L. Nussbaum, et al. ClinGen ClinGen - the Clinical Genome Resource N. Engl. J. Med. 372 2015 2235 2242
4. L.M. Amendola, M.O. Dorschner, P.D. Robertson, J.S. Salama, R. Hart, B.H. Shirts, M.L. Murray, M.J. Tokita, C.J. Gallego, D.S. Kim, and et al. Actionable exomic incidental findings in 6503 participants: challenges of variant classification Genome Res. 25 2015 305 315
5. A. Yorczyk, L.S. Robinson, and T.S. Ross Use of panel tests in place of single gene tests in the cancer genetics clinic Clin. Genet. 88 2015 278 282
6. C.S. Richards, S. Bale, D.B. Bellissimo, S. Das, W.W. Grody, M.R. Hegde, E. Lyon, B.E. Ward Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007 Genet. Med. 10 2008 294 300
7. I. Karbassi, G.A. Maston, A. Love, C. DiVincenzo, C.D. Braastad, C.D. Elzinga, A.R. Bright, D. Previte, K. Zhang, C.M. Rowland, and et al. A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders Hum. Mutat. 37 2016 127 134
8. B.A. Thompson, A.B. Spurdle, J.P. Plazzer, M.S. Greenblatt, K. Akagi, F. Al-Mulla, B. Bapat, I. Bernstein, G. Capellá, J.T. den Dunnen, et al. InSiGHT Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database Nat. Genet. 46 2014 107 115
9. D.E. Goldgar, D.F. Easton, G.B. Byrnes, A.B. Spurdle, E.S. Iversen, M.S. Greenblatt IARC Unclassified Genetic Variants Working Group Genetic evidence and integration of various data sources for classifying uncertain variants into a single model Hum. Mutat. 29 2008 1265 1272
10. S. Richards, N. Aziz, S. Bale, D. Bick, S. Das, J. Gastier-Foster, W.W. Grody, M. Hegde, E. Lyon, E. Spector, et al. ACMG Laboratory Quality Assurance Committee 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 Genet. Med. 17 2015 405 424
11. L.G. Biesecker, J.C. Mullikin, F.M. Facio, C. Turner, P.F. Cherukuri, R.W. Blakesley, G.G. Bouffard, P.S. Chines, P. Cruz, N.F. Hansen, et al. NISC Comparative Sequencing Program The ClinSeq Project: piloting large-scale genome sequencing for research in genomic medicine Genome Res. 19 2009 1665 1674
12. A.F. Hayes, and K. Krippendorff Answering the call for a standard reliability measure for coding data Commun. Methods Meas. 1 2007 77 89
13. K. Krippendorff Reliability in content analysis: Some common misconceptions and recommendations Hum. Commun. Res. 30 2004 411 433
14. K. Krippendorff Content analysis: An introduction to its methodology Second Edition 2004 Sage
15. R.L. Brennan, and D.J. Prediger Coefficient kappa: Some uses, misuses, and alternatives Educ. Psychol. Meas. 41 1981 687 699
16. R. Zwick Another look at interrater agreement Psychol. Bull. 103 1988 374 378
17. mvα. http://web.asc.upenn.edu/usr/krippendorff/boot.c-Alpha.pdf.
18. H.Y. Lin, C.H. Huang, H.C. Yu, K.W. Chong, J.H. Hsu, P.C. Lee, K.H. Cheng, C.C. Chiang, H.J. Ho, S.P. Lin, and et al. Enzyme assay and clinical assessment in subjects with a Chinese hotspot late-onset Fabry mutation (IVS4c+c919G→A) J. Inherit. Metab. Dis. 33 2010 619 624
19. S. Ishii, S. Nakao, R. Minamikawa-Tachino, R.J. Desnick, and J.Q. Fan Alternative splicing in the alpha-galactosidase A gene: increased exon inclusion results in the Fabry cardiac phenotype Am. J. Hum. Genet. 70 2002 994 1002
20. W.L. Hwu, Y.H. Chien, N.C. Lee, S.C. Chiang, R. Dobrovolny, A.C. Huang, H.Y. Yeh, M.C. Chao, S.J. Lin, T. Kitagawa, and et al. Newborn screening for Fabry disease in Taiwan reveals a high incidence of the later-onset GLA mutation c.936+919G>A (IVS4+919G>A) Hum. Mutat. 30 2009 1397 1405
21. G. Casari, M. De Fusco, S. Ciarmatori, M. Zeviani, M. Mora, P. Fernandez, G. De Michele, A. Filla, S. Cocozza, R. Marconi, and et al. Spastic paraplegia and OXPHOS impairment caused by mutations in paraplegin, a nuclear-encoded mitochondrial metalloprotease Cell 93 1998 973 983
22. R.H. Roxburgh, R. Marquis-Nicholson, F. Ashton, A.M. George, R.A. Lea, D. Eccles, S. Mossman, T. Bird, K.L. van Gassen, E.J. Kamsteeg, and D.R. Love The p.Ala510Val mutation in the SPG7 (paraplegin) gene is the most common mutation causing adult onset neurogenetic disease in patients of British ancestry J. Neurol. 260 2013 1286 1294
23. N. Elleuch, C. Depienne, A. Benomar, A.M. Hernandez, X. Ferrer, B. Fontaine, D. Grid, C.M. Tallaksen, R. Zemmouri, G. Stevanin, and et al. Mutation analysis of the paraplegin gene (SPG7) in patients with hereditary spastic paraplegia Neurology 66 2006 654 659
24. K.L. van Gassen, C.D. van der Heijden, S.T. de Bot, W.F. den Dunnen, L.H. van den Berg, C.C. Verschuuren-Bemelmans, H.P. Kremer, J.H. Veldink, E.J. Kamsteeg, H. Scheffer, and B.P. van de Warrenburg Genotype-phenotype correlations in spastic paraplegia type 7: a study in a large Dutch cohort Brain 135 2012 2994 3004
25. K.J. Norrgard, R.J. Pomponio, K.L. Swango, J. Hymes, T.R. Reynolds, G.A. Buck, and B. Wolf Mutation (Q456H) is the most common cause of profound biotinidase deficiency in children ascertained by newborn screening in the United States Biochem. Mol. Med. 61 1997 22 27
26. J. Hymes, C.M. Stanley, and B. Wolf Mutations in BTD causing biotinidase deficiency Hum. Mutat. 18 2001 375 381