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).
Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL. Genet. Med. Published online November 6, 2019. doi:10.1038/s41436-019-0686-8
Frequency of Cystic Fibrosis Transmembrane Conductance Regulator Variants in Individuals Evaluated for Primary Ciliary Dyskinesia.
Hannah WB, Truty R, Gonzales V, Kithcart GP, Ouyang K, Zeman MK, Li C, Drumm M, Nykamp K, Gaston BM. J Pediatr. Published online Oct 11, 2019. doi: 10.1016/j.jpeds.2019.08.039.
Novel heterozygous mutation in the PTEN gene associated with ovarian germ cell tumor complicated by growing teratoma syndrome and overgrowth in a two-year-old female.
Tullius, BP, Shankar SP, Cole S, Triano V, Aradhya S, Huang EC, Sanchez T, Pawar A. Pediatr. Blood Cancer. 2019;66(8):e27788. doi:10.1002/pbc.27788.
A novel TTN deletion in a family with skeletal myopathy, facial weakness, and dilated cardiomyopathy.
Roggenbuck J, Rich K, Morales A, Tan CA, Eck D, King W, Vatta M, Winder T, Elsheikh B, Hershberger RE, Kissel JT. Mol Genet Genomic Med. Published online September 5, 2019: e924. doi: 10.1002/mgg3.924
Recurring large deletion in DRC1 (CCDC164) identified as causing primary ciliary dyskinesia in two Asian patients.
Morimoto K, Hijikata M, Zariwala MA, Nykamp K, Inaba A, Guo TC, Yamada H, Truty R, Sasaki Y, Ohta K, Kudoh S, Leigh MW, Knowles MR, Keicho N. Mol Genet Genomic Med. Published online July 4, 2019: e838. doi: 10.1002/mgg3.838
Response to "The use of ACMG secondary findings recommendations for general population screening: a policy statement of the American College of Medical Genetics and Genomics (ACMG)."
Nussbaum RL, Haverfield E, Esplin ED, Aradhya S. Genet Med. Published online June 26, 2019. doi:10.1038/s41436-019-0572-4 Possible precision medicine implications from genetic testing using combined detection of sequence and intragenic copy number variants in a large cohort with childhood epilepsy.
Truty, R, Patil, N, Sankar, R, Sullivan, J, Millichap, J, Carvill, G, Entezam, A, Esplin, ED, Fuller, A, Hogue, M, Johnson, B, Khouzam, A, Kobayashi, Y, Lewis, R, Nykamp, K, Riethmaier, D, Westbrook, J, Zeman, M, Nussbaum, RL, Aradhya, S.Epilepsia Open. Published online June 22, 2019. doi:10.1002/epi4.12348 An online survey on burden of illness among families with post-stem cell transplant mucopolysaccharidosis type I children in the United States.
Conner T, Cook F, Fernandez V, Rascati K, Rangel-Miller V. J Rare Dis. Published online February 18, 2019. doi:10.1186/s13023-019-1027-3 Prevalence of germline variants in prostate cancer and implications for current genetic testing guidelines.
Nicolosi P, Ledet E, Yang S, Michalski S, Freschi B, O'Leary E, Esplin ED, Nussbaum RL, Sartor O. JAMA Oncol. Published online February 7, 2019. doi:10.1001/jamaoncol.2018.6760 A rigorous interlaboratory examination of the need to confirm next-generation sequencing-detected variants with an orthogonal method in clinical genetic testing.
Lincoln SE, Truty R, Lin CF, Zook JM, Paul J, Ramey VH, Salit M, Rehm HL, Nussbaum RL, Lebo MS. J Mol Diagn. Published online January 2, 2019. doi:10.1016/j.jmoldx.2018.10.009 BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2.
Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, Antoniou A, Baxter S, Brody L, Cook-Deegan R, Coffin A, Couch FJ, Craft B, Currie R1, Dlott CC, Dolman L, den Dunnen JT, Dyke SOM, Domchek SM, Easton D, Fischmann Z, Foulkes WD, Garber J, Goldgar D, Goldman MJ, Goodhand P, Harrison S, Haussler D, Kato K, Knoppers B, Markello C, Nussbaum R, Offit K, Plon SE, Rashbass J, Rehm HL, Robson M, Rubinstein WS, Stoppa-Lyonnet D, Tavtigian S, Thorogood A, Zhang C, Zimmermann M; BRCA Challenge Authors, Burn J, Chanock S, Rätsch G, Spurdle AB. PLoS Genet. Published online December 26, 2018. doi:10.1371/journal.pgen.1007752 Underdiagnosis of hereditary breast cancer: Are genetic testing guidelines a tool or an obstacle?
Beitsch PD, Whitworth PW, Hughes K, Patel R, Rosen B, Compagnoni G, Baron P, Simmons R, Smith LA, Grady I, Kinney M, Coomer C, Barbosa K, Holmes DR, Brown E, Gold L, Clark P, Riley L, Lyons S, Ruiz A, Kahn S, MacDonald H, Curcio L, Hardwick MK; Yang S, Esplin ED, Nussbaum RL. J Clin Oncol. Published online December 7, 2018. doi:10.1200/JCO.18.01631 Secondary findings on virtual panels: opportunities, challenges, and potential for preventive medicine.
Esplin ED, Haverfield E, Yang S, Aradhya S, Nussbaum RL. Genet Med. Published online September 24, 2018. doi:10.1038/s41436-018-0302-3ClinGen's GenomeConnect registry enables patient-centered data sharing.
Savatt JM, Azzariti DR, Faucett WA, Harrison S, Hart J, Kattman B, Landrum MJ, Ledbetter DH, Miller VR, Palen E, Rehm HL, Rhode J, Turner S, Vidal JA, Wain KE, Riggs ER, Martin CL. Human Mutation. 2018;39(11):1668-1676. doi:10.1002/humu.23633Underdiagnosis of hereditary breast and ovarian cancer in Medicare patients: Genetic testing criteria miss the mark.
Yang S, Axilbund JE, O'Leary E, Michalski ST, Evans R, Lincoln SE, Esplin ED, Nussbaum RL. Annals of Surgical Oncology. Published online July 11, 2018. doi:10.1245/s10434-018-6621-4 Prevalence and properties of intragenic copy-number variation in Mendelian disease genes.
Truty R, Paul J, Kennemer M, Lincoln SE, Olivares E, Nussbaum RL, Aradhya S. Genetics in Medicine. Published online June 12, 2018. doi:10.1038/s41436-018-0033-5Genetics in mainstream medicine: Finally within grasp to influence healthcare globally.
Aradhya S, Nussbaum RL.Molecular Genetics and Genomic Medicine. Published online May 28, 2018. doi:110.1002/mgg3.415Genetic evaluation of cardiomyopathy - a Heart Failure Society of America Practice Guideline.
Hershberger RE, Givertz M, Ho CY, Judge DP, Kantor P, McBride KL, Morales A, Taylor MRG, Vatta M, Ware SM. Cardiac Failure. Published online March 19, 2018. doi:10.1038/s41379-018-0031-9The genetics of recurrent hydatidiform moles: New insights and lessons from a comprehensive analysis of 113 patients.
Nguyen NMP, Khawajkie Y, Mechtouf N, Rezaei M, Breguet M, Kurvinen E, Jagadeesh S, Solmaz AE, Aguinaga M, Hemida R, Harma MI, Rittore C, Rahimi K, Arseneau J, Hovanes K, Clisham R, Lenzi T, Scurry B, Addor MC, Bagga R, Nendaz GG, Finci V, Poke G, Grimes L, Gregersen N, York K, Bolze PA, Patel C, Mozdarani H, Puechberty J, Scotchie J, Fardaei M, Harma M, Gardner RJM, Sahoo T, Dudding-Byth T, Srinivasan R, Sauthier P, Slim R. Modern Pathology. Published online February 20, 2018. doi: 10.1016/j.cardfail.2018.03.004 ACOG and SMFM guidelines for prenatal diagnosis: Is karyotyping really sufficient?
Hay SB, Sahoo T, Travis MK, Hovanes K, Dzidic N, Doherty C, Strecker MN. Prenatal Dignosis. 2018;38(3):184-9. doi:10.1002/pd.5212 Adaptation and validation of the ACMG/AMP variant classification framework for MYH7-associated inherited cardiomyopathies: recommendations by ClinGen's Inherited Cardiomyopathy Expert Panel.
Kelly MA, Caleshu C, Morales A, Buchan J, Wolf Z, Harrison SM, Cook S, Dillon MW, Garcia J, Haverfield E, Jongbloed JDH, Macaya D, Manrai A, Orland K, Richard G, Spoonamore K, Thomas M, Thomson K, Vincent LM, Walsh R, Watkins H, Whiffin N, Ingles J, van Tintelen JP, Semsarian C, Ware JS, Hershberger R, Funke B. Genetics in Medicine. 2018;20(3):351-9. doi:10.1038/gim.2017.218 Germline mutation prevalence in individuals with pancreatic cancer and a history of previous malignancy
Dudley B, Karloski E, Monzon FA, Singhi AD, Lincoln SE, Bahary N, Brand RE. Cancer. 2018;124(8):1691-1700. doi: 10.1002/cncr.31242 Standards and guidelines for validating next-generation sequencing bioinformatics pipelines: A joint recommendation of the Association for Molecular Pathology and the College of American Pathologists.
Roy S, Coldren C, Karunamurthy A, Kip NS, Klee EW, Lincoln SE, Leon A, Pullambhatla M, Temple-Smolkin RL, Voelkerding KV, Wang C, Carter AB. The Journal of Molecular Diagnostics. 2018;20(1):4-27. doi:10.1016/j.jmoldx.2017.11.003 Conflicts of interest in genetic counseling: addressing and delivering.
Iacoboni D. Genetics in Medicine. Published online January 4, 2018. doi:10.1038/gim.2017.234 Sources of discordance among germ-line variant classifications in ClinVar.
Yang S, Lincoln SE, Kobayashi Y, Nykamp K, Nussbaum RL, Topper S.
Genetics in Medicine. Published online June 1, 2017. doi:10.1038/gim.2017.60 Expanded gene panel use for women with breast cancer: Identification and intervention beyond breast cancer risk.
O'Leary E, Iacoboni D, Holle J, Michalski ST, Esplin ED, Yang S, Ouyang K.
Annals of Surgical Oncology. Published online August 1, 2017. doi:10.1245/s10434-017-5963-7 Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.
Genetics in Medicine. Published online May 11, 2017. doi:10.1038/gim.2017.37 Consistency of BRCA1 and BRCA2 variant classifications among clinical diagnostic laboratories.
Lincoln SE, Yang S, Cline MS, Kobayashi Y, Zhang C, Topper S, Haussler D, Paten B, Nussbaum RL.
JCO Precision Oncology. Published online April 11, 2017. doi:10.1200/PO.16.00020 Pathogenic variant burden in the ExAC database: An empirical approach to evaluating population data for clinical variant interpretation.
Kobayashi Y, Yang S, Nykamp K, Garcia J, Lincoln SE, Topper SE.
Genome Medicine. 2017, 9, 13. doi:10.1186/S13073-017-0403-7 Comprehensive genetic analysis of pregnancy loss by chromosomal microarrays: outcomes, benefits, and challenges.
Sahoo T, Dzidic N, Strecker MN, Commander S, Travis MK, Doherty C, Tyson RW, Mendoza AE, Stephenson M, Dise CA, Benito CW, Ziadie MS, Hovanes K.
Genetics in Medicine. 2017;19(1):83-9. doi:10.1038/gim.2016.69 Clinical genetics testing laboratories have a remarkably low rate of clinically significant discordance when interpreting variants in hereditary cancer syndrome genes.
Nussbaum RL, Yang S, Lincoln SE.
Journal of Clinical Oncology. Published online January 30, 2017. doi:10.1200/JCO.2016.70.9451 Data sharing and reproducible clinical genetic data: Success and challenges.
Yang S, Cline M, Zhang C, Paten B, Lincoln SE.
Pacific Symposium on Biocomput. 2016, 22, 166-176. doi:10.1142/9789813207813_0017 Clinical genetic testing for the cardiomyopathies and arrhythmias: A systematic framework for establishing clinical validity and addressing genotypic and phenotypic heterogeneity.
Garcia J, Tahiliani J, Johnson NM, Aguilar S, Beltran D, Daly A, Decker E, Haverfield E, Herrera B, Murillo L, Nykamp K, Topper S.
Frontiers in Cardiovascular Medicine. 2016, 3(20). doi:10.3389/fcvm.2016.00020 Germline hemizygous deletion of CDKN2A–CDKN2B locus in a patient presenting with Li–Fraumeni syndrome.
Chan SH, Lim WK, Michalski ST, Lim JQ, Binte Ishak ND, Met-Domestici M, Chuan Young CN, Vikstrom K, Esplin ED, Fulbright J, Ang MK, Wee J, Sittampalam K, Farid M, Lincoln SE, Itahana K, Abdullah S, Teh BT, Ngeow J.
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Bales ND, Johnson NM, Judge DP, Murphy AM.
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Cohen SA, Tan CA, Bisson R.
Frontiers in Genetics. 2016, 7, 1. doi:10.3389/fgene.2016.00036 Autosomal recessive MFN2-related Charcot-Marie-Tooth disease with diaphragmatic weakness: Case report and literature review.
Tan CA, Rabideau M, Blevins A, Westbrook MJ, Ekstein T, Nykamp K, Deucher A, Harper A, Demmer L.
American Journal of Medical Genetics Part A. 2016, 170(6), 1552-4833. doi:10.1002/ajmg.a.37611 Genetic counselors in startup companies: Redefining the genetic counselor role.
Rabideau MM, Wong K, Gordon ES, Ryan L.
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Sahoo T, Hovanes K, Strecker MN, Dzidic N, Commander S, Travis MK.
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Desmond A, Kurian AW, Gabree M, Mills MA, Anderson MJ, Kobayashi Y, Horick N, Yang S, Shannon KM, Tung N, Ford JM, Lincoln SE, Ellisen LW.
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Lincoln S, Kobayashi Y, Anderson M, Yang S, Desmond AJ, Mills MA, Nilsen GB, Jacobs KB, Monzon FA, Kurian AW, Ford JM, Ellisen LW.
The Journal of Molecular Diagnostics. 2015, 17(5), 533-544. doi:10.1016/j.jmoldx.2015.04.009 Low-level constitutional mosaicism of a de novo BRCA1 gene mutation.
Friedman E, Efrat N, Soussan-Gutman L, Dvir A, Kaplan Y, Ekstein T, Nykamp K, Powers M, Rabideau M, Sorenson J, Topper S.
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PRESENTATIONSAn international interlaboratory study of complex pathogenic variants In hereditary breast/ovarian cancer
POSTERSDetection of NF1 variants by NGS panels with SMV and CNV identification exceeds published estimates and improves clinical utility Multigene panel screening for hereditary disease risk in healthy individuals
PRESENTATIONSSecondary findings in hereditary cancer genes from multigene panel data: A new frontier unanticipated by the ACMGAn interlaboratory study of complex variant detection in clinical testing
Molecular diagnostic findings of lysosomal storage diseases in children and adults suspected to have inborn errors of metabolism Genetic testing for lysosomal storage disorders in a commercial laboratory: Use of pathognomonic criteria in variant interpretation ConnectMPS registry project: Connecting mucopolysaccharidosis and mucolipidosis patients
POSTERSAneuploidy rates in embryos generated from fresh versus frozen donor oocytes
POSTERSBroadening the scope: Expanding ordering patterns in suspected hereditary CRC
POSTERSPaperwork matters! The importance of clinical phenotype information in variant interpretation
PRESENTATIONSGenetic screening for healthy individuals: Preliminary results from a medically actionable genetic screening panel An inter-laboratory study of complex variant detection in clinical testing
POSTERSPaperwork matters! The importance of clinical phenotype information in variant interpretation
PRESENTATIONSFollowing somatic tumor testing with germline analysis: Considerations for genetic counseling practice The elephant in the room: TTN
PRESENTATIONSCopy number variant analysis enhances molecular diagnostic yield of inborn errors of metabolism
POSTERSDetermining the clinical value of germline genetic testing coupled with tumor mutation profiling
PRESENTATIONPathogenic variants in calmodulin associated with resuscitated childhood cardiac arrest
POSTERACOG and SMFM guidelines for prenatal diagnosis: Is karyotyping really sufficient?
POSTERSExpanded gene panel utilization in women with breast cancer: identification and intervention beyond breast cancer risk Hereditary cancer risk: A growing body of evidence supporting broader testing
POSTERSAttitudes of healthy early adopters toward professional genome sequencing: Observations from the PeopleSeq Consortium The benefit of a medically actionable genetic screening panel in healthy individuals: A case report
PRESENTATIONSThe spectrum of pathogenic variants underlying multiple conditions in 80,000 patients: Implications for test implementation, utilization and validation Tracing the dark matter: Prevalence of copy number and structural variants across Mendelian disorders
posterMale breast cancer: The role of next-generation sequencing panels in determining biology
POSTERSAccurate detection of copy-number changes in the highly conserved regions of PMS2 using NGSAttitudes regarding personal genomic sequencing among healthy early adopters: Findings from the PeopleSeq ConsortiumCreating a medically actionable genetic screening panel for healthy individuals
POSTERSMammalian species conservation data and the implications for clinical variant classificationNovel large rearrangement of RAD51D in an ovarian and breast cancer family
presentationsBioinformatics for genetic counselors, version 2.0
posterCopy number variation in clinical tests for inherited cardiomyopathies and arrhythmias
presentationWhat have public databases taught us about variant classification?
postersVariant classifications for BRCA1 and BRCA2 are substantially concordant across major clinical testing laboratories The expanding phenotype of PALB2-related cancer: clinical presentations of 144 identified carriers
presentationMosaic genetic variants in hereditary germline genetic testing: the expected and the unexpected
posterClinical presentation and management considerations for 77 breast cancer patients with germline PALB2 mutations
posterClinical actionability of panel tests for genes in the NCCN Guidelines for Hereditary Breast and Ovarian Cancer Clinical presentations of 111 patients with germline PALB2 mutations: Looking beyond breast and ovarian cancer
posterPreparing for the unexpected: Panel-based testing of ovarian cancer patients reveals actionable variants in non-canonical genes
postersClinical actionability of non-BRCA1/2 mutations uncovered in multigene tests for hereditary breast cancer Variant classifications for BRCA1 and BRCA2 are highly concordant across major clinical testing laboratories Clinical presentation and management considerations for 68 breast cancer patients with germline PALB2 mutations
postersAllele frequency distribution of pathogenic sequence variants in ExAC and the implications for clinical genetic testing Expanding phenotypes of cancer predisposition genes: CDKN2A Detection of novel Alu insertions by next-generation sequencing of hereditary cancer genes Challenges of content expansion with panel testing: incorporating informatics into the clinical report Rare disease diagnosis obstacles: patient perspectives and physician findings To include or not to include: RASopathy genes in cardiomyopathy genetic testing To confirm or not to confirm, that is the question: a rigorous approach to evaluating the importance of Sanger confirmation of clinical NGS findings
presentationDon't believe everything you hear: Variant classifications for BRCA1 and BRCA2 are highly concordant across major clinical testing laboratories
postersAn opportunity or dilemma? Customizable panel tests and clinician ordering behavior Establishing and evaluating a framework for describing variant evidence in clinical genomic reports Sherloc- Evaluation of a score-based implementation of the AMP-ACMG ISV guidelines in a scalable genetic diagnostic laboratory
PresentationsAnalytic validation standards for NGS assays and new reference materials needed A rigorous approach to evaluating the importance of Sanger Confirmation of NGS findings
postersClinical actionability of multigene tests for hereditary breast and ovarian cancer Integration of the ACMG ISV guidelines into clinical variant analysis and interpretation processes- A model for diagnostic standardization Moving beyond the 1%- incorporating the Exome Aggregation Consortium (ExAC) data into variant interpretation and classification To confirm or not confirm, that is the question: A rigorous approach to evaluating the importance of sanger confirmation of clinical NGS findings Understanding psychiatrists’ perceptions surrounding psychiatric genetics and genetic counseling services
PresentationsFinding just right- Balancing payer and provider goals for hereditary genetic testing Next generation sequencing- Challenges and strategies in testing patients with circulating hematopoietic malignancies Validation of clinical genetic tests - or – How to stop worrying and love the data!