PUBLICATIONS

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We believe that there is a new gold standard today, one that includes both high quality testing and a dedication to improving medicine. Below are some of the Peer reviewed papers of our partner laboratory.

> Clinical cohort analysis of germline EGFR T790M demonstrates penetrance across ethnicities and races, sexes, and ages.
Berry DK, Wang X, Michalski ST, Kang HC, Yang S, Creelan BC, McLeod HL, Hicks JK. JCO Precision Oncol. Published online March 6, 2020. doi.org/10.1200/PO.19.00297

> 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/s41436-018-0302-3

> ClinGen’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.23633

> Underdiagnosis 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/s41436-018-0033-5

> Genetics 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/mgg3.415

> Genetic 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/s41379-018-0031-9

> The 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.
NPJ Genomic Medicine. 2016, 1, 16015. doi:10.1038/npjgenmed.2016.15

> Who pays? Coverage challenges for cardiovascular genetic testing in U.S. patients.
Spoonamore K, Johnson NM. Frontiers in Cardiovascular Medicine. 2016, 3(14). doi:10.3389/fcvm.2016.00014

> Comprehensive versus targeted genetic testing in children with hypertrophic cardiomyopathy.
Bales ND, Johnson NM, Judge DP, Murphy AM. Pediatric Cardiology. 2016, 37(5), 845. doi:10.1007/s00246-016-1358-y

> An individual with both MUTYH-associated polyposis and Lynch syndrome identified by multi-gene hereditary cancer panel testing: A case report. 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.
Journal of Genetic Counselling. 2016, 25(4), 649–657. doi:10.1007/s10897-015-9923 8

> Expanding noninvasive prenatal testing to include microdeletions and segmental aneuploidy: cause for concern?
Sahoo T, Hovanes K, Strecker MN, Dzidic N, Commander S, Travis MK.
Genetics in Medicine. 2016;18(3):275-6. doi:0.1038/gim.2015

> Clinical actionability of multigene panel testing for hereditary breast and ovarian cancer risk assessment.
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. JAMA Oncology. 2015, 1(7), 943-951. doi:10.1001/jamaoncol.2015.2690

> A systematic comparison of traditional and multigene panel testing for hereditary breast and ovarian cancer genes in more than 1000 patients.
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.
British Journal of Cancer. 2015, 112, 765–768. doi:10.1038/bjc.2015.14

> A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.
Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA. Bioinformatics. 2015, 31(2), 268-270. doi:10.1093/bioinformatics/btu630

> Discordant noninvasive prenatal testing and cytogenetic results: a study of 109 consecutive cases.
Wang JC, Sahoo T, Schonberg S, Kopita KA, Ross L, Patek K, Strom CM.
Genetics in Medicine. 2015;17(3):234-6. doi:10.1038/gim.2014.92

> PWS/AS MS-MLPA confirms maternal origin of 15q11.2 microduplication.
Dawson AJ, Cox J, Hovanes K, Spriggs E. Care Reports in Genetics. 2015;2015:474097. doi:10.1155/2015/474097

> Clinical evaluation of a multiple-gene sequencing panel for hereditary cancer risk assessment.
Kurian AW, Hare EE, Mills MA, Kingham KE, McPherson L, Whittemore AS, McGuire V, Ladabaum U, Kobayashi Y, Lincoln SE, Cargill M, Ford JM. Journal of Clinical Oncology. 2014,32(19), 2001-2009. doi:10.1200/JCO.2013.53.6607

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