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Publications
2020
Abul-Husn NS, Soper ER, Odgis JA, Cullina S, Bobo D, Moscati A, Rodriguez JE; CBIPM Genomics Team.; Regeneron Genetics Center., Loos RJF, Cho JH, Belbin GM, Suckiel SA, Kenny EE.
Exome sequencing reveals a high prevalence of BRCA1 and BRCA2 founder variants in a diverse population-based biobank.
Genome Med. 2019 Dec 31;12(1):2. doi: 10.1186/s13073-019-0691-1. PMID: 31892343.
Brnich SE, Abou Tayoun AN, Couch FJ, Cutting GR, Greenblatt MS, Heinen CD, Kanavy DM, Luo X, McNulty SM, Starita LM, Tavtigian SV, Wright MW, Harrison SM, Biesecker LG, Berg JS; Clinical Genome Resource Sequence Variant Interpretation Working Group..
Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework.
Genome Med. 2019 Dec 31;12(1):3. doi: 10.1186/s13073-019-0690-2. PMID: 31892348.
Kraft SA, McMullen C, Lindberg NM, Bui D, Shipman K, Anderson K, Joseph G, Duenas DM, Porter KM, Kauffman TL, Koomas A, Ransom CL, Jackson P, Goddard KAB, Wilfond BS, Lee SS.
Integrating stakeholder feedback in translational genomics research: an ethnographic analysis of a study protocol's evolution.
Genet Med. 2020 Feb 24. doi: 10.1038/s41436-020-0763-z. [Epub ahead of print]. PMID: 32089547.
Scott TM, Guo H, Eichler EE, Rosenfeld JA, Pang K, Liu Z, Lalani S, Bi W, Yang Y, Bacino CA, Streff H, Lewis AM, Koenig MK, Thiffault I, Bellomo A, Everman DB, Jones JR, Stevenson RE, Bernier R, Gilissen C, Pfundt R, Hiatt SM, et al.
BAZ2B haploinsufficiency as a cause of developmental delay, intellectual disability, and autism spectrum disorder.
Hum Mutat. 2020 Jan 30. doi: 10.1002/humu.23992. [Epub ahead of print]. PMID: 31999386.
2019
Baudhuin LM, Biesecker LG, Burke W, Green ED, Green RC.
Predictive and Precision Medicine with Genomic Data.
Clin Chem. 2019 Dec 16. pii: clinchem.2019.304345. doi: 10.1373/clinchem.2019.304345. [Epub ahead of print] No abstract available. PMID: 31843866.
Carapito R, Ivanova EL, Morlon A, Meng L, Molitor A, Erdmann E, Kieffer B, Pichot A, Naegely L, Kolmer A, Paul N, Hanauer A, Tran Mau-Them F, Jean-Marçais N, Hiatt SM, Cooper GM, Tvrdik T, Muir AM, Dimartino C, Chopra M, Amiel J, Gordon CT, et al.
ZMIZ1 Variants Cause a Syndromic Neurodevelopmental Disorder.
Am J Hum Genet. 2019 Feb 7;104(2):319-330. doi: 10.1016/j.ajhg.2018.12.007. Epub 2019 Jan 10. Erratum in: Am J Hum Genet. 2020 Jan 2;106(1):137. PMID: 30639322.
Hiatt SM, Thompson ML, Prokop JW, Lawlor JMJ, Gray DE, Bebin EM, Rinne T, Kempers M, Pfundt R, van Bon BW, Mignot C, Nava C, Depienne C, Kalsner L, Rauch A, Joset P, Bachmann-Gagescu R, Wentzensen IM, McWalter K, Cooper GM.
Deleterious Variation in BRSK2 Associates with a Neurodevelopmental Disorder.
Am J Hum Genet. 2019 Apr 4;104(4):701-708. doi: 10.1016/j.ajhg.2019.02.002. Epub 2019 Mar 14. PMID: 30879638.
Horowitz CR, Orlando LA, Slavotinek AM, Peterson J, Angelo F, Biesecker B, Bonham VL, Cameron LD, Fullerton SM, Gelb BD, Goddard KAB, Hailu B, Hart R, Hindorff LA, Jarvik GP, Kaufman D, Kenny EE, Knight SJ, Koenig BA, Korf BR, Madden E, McGuire AL, et al.
The Genomic Medicine Integrative Research Framework: A Conceptual Framework for Conducting Genomic Medicine Research.
Am J Hum Genet. 2019 Jun 6;104(6):1088-1096. doi: 10.1016/j.ajhg.2019.04.006. Epub 2019 May 16. PMID: 31104772.
Le Duc D, Giulivi C, Hiatt SM, Napoli E, Panoutsopoulos A, Harlan De Crescenzo A, Kotzaeridou U, Syrbe S, Anagnostou E, Azage M, Bend R, Begtrup A, Brown NJ, Büttner B, Cho MT, Cooper GM, Doering JH, Dubourg C, Everman DB, Hildebrand MS, Santos FJR, Kellam B, et al.
Pathogenic WDFY3 variants cause neurodevelopmental disorders and opposing effects on brain size.
Brain. 2019 Sep 1;142(9):2617-2630. doi: 10.1093/brain/awz198. Erratum in: Brain. 2019 Nov 1;142(11):e63. PMID: 31327001.
Mak CCY, Doherty D, Lin AE, Vegas N, Cho MT, Viot G, Dimartino C, Weisfeld-Adams JD, Lessel D, Joss S, Li C, Gonzaga-Jauregui C, Zarate YA, Ehmke N, Horn D, Troyer C, Kant SG, Lee Y, Ishak GE, Leung G, Barone Pritchard A, Yang S, et al.
MN1 C-terminal truncation syndrome is a novel neurodevelopmental and craniofacial disorder with partial rhombencephalosynapsis.
Brain. 2020 Jan 1;143(1):55-68. doi: 10.1093/brain/awz379. PMID: 31834374.
Mendelsohn BA, Beleford DT, Abu-El-Haija A, Alsaleh NS, Rahbeeni Z, Martin PM, Rego S, Huang A, Capodanno G, Shieh JT, Van Ziffle J, Risch N, Alkuraya FS, Slavotinek AM.
A novel truncating variant in ring finger protein 113A (RNF113A) confirms the association of this gene with X-linked trichothiodystrophy.
Am J Med Genet A. 2020 Mar;182(3):513-520. doi: 10.1002/ajmg.a.61450. Epub 2019 Dec 27. PMID: 31880405.
Niu X, Amendola LM, Hart R, Bennette CS, Heagerty P, Horike-Pyne M, Trinidad SB, Rosenthal EA, Comstock B, Nefcy C, Hisama FM, Bennett RL, Grady WM, Gallego CJ, Tarczy-Hornoch P, Fullerton SM, Burke W, Regier DA, Dorschner MO, Shirts BH, Robertson PD, Nickerson DA, et al.
Clinical exome sequencing vs. usual care for hereditary colorectal cancer diagnosis: A pilot comparative effectiveness study.
Contemp Clin Trials. 2019 Sep;84:105820. doi: 10.1016/j.cct.2019.105820. Epub 2019 Aug 7. PMID: 31400517.
Nizon M, Laugel V, Flanigan KM, Pastore M, Waldrop MA, Rosenfeld JA, Marom R, Xiao R, Gerard A, Pichon O, Le Caignec C, Gérard M, Dieterich K, Truitt Cho M, McWalter K, Hiatt S, Thompson ML, Bézieau S, Wadley A, Wierenga KJ, Egly JM, Isidor B.
Variants in MED12L, encoding a subunit of the mediator kinase module, are responsible for intellectual disability associated with transcriptional defect.
Genet Med. 2019 Dec;21(12):2713-2722. doi: 10.1038/s41436-019-0557-3. Epub 2019 Jun 3. Erratum in: Genet Med. 2019 Jul 3;:. PMID: 31155615.
Orlando LA, Voils C, Horowitz CR, Myers RA, Arwood MJ, Cicali EJ, McDonough CW, Pollin TI, Guan Y, Levy KD, Ramirez A, Quittner A, Madden EB.
IGNITE network: Response of patients to genomic medicine interventions.
Mol Genet Genomic Med. 2019 May;7(5):e636. doi: 10.1002/mgg3.636. Epub 2019 Mar 20. PMID: 30895746.
Robinson JO, Wynn J, Biesecker B, Biesecker LG, Bernhardt B, Brothers KB, Chung WK, Christensen KD, Green RC, McGuire AL, Hart MR, Griesemer I, Patrick DL, Rini C, Veenstra D, Cronin AM, Gray SW.
Psychological outcomes related to exome and genome sequencing result disclosure: a meta-analysis of seven Clinical Sequencing Exploratory Research (CSER) Consortium studies.
Genet Med. 2019 Dec;21(12):2781-2790. doi: 10.1038/s41436-019-0565-3. Epub 2019 Jun 13. PMID: 31189963.
Torti E, Keren B, Palmer EE, Zhu Z, Afenjar A, Anderson IJ, Andrews MV, Atkinson C, Au M, Berry SA, Bowling KM, Boyle J, Buratti J, Cathey SS, Charles P, Cogne B, Courtin T, Escobar LF, Finley SL, Graham JM Jr, Grange DK, Heron D, et al.
Variants in TCF20 in neurodevelopmental disability: description of 27 new patients and review of literature.
Genet Med. 2019 Sep;21(9):2036-2042. doi: 10.1038/s41436-019-0454-9. Epub 2019 Feb 11. PMID: 30739909.
Umstead KL, Han PKJ, Lewis KL, Miller IM, Hepler CL, Thompson LJ, Wolfsberg TG, Nguyen AD, Fredriksen MT, Gibney G, Turbitt E, Biesecker LG, Biesecker BB.
Perceptions of uncertainties about carrier results identified by exome sequencing in a randomized controlled trial.
Transl Behav Med. 2019 Aug 31. pii: ibz111. doi: 10.1093/tbm/ibz111. [Epub ahead of print]. PMID: 31505002.
Yu JH, Appelbaum PS, Brothers KB, Joffe S, Kauffman TL, Koenig BA, Prince AE, Scollon S, Wolf SM, Bernhardt BA, Wilfond BS; Clinical Sequencing Exploratory Research (CSER) Consortium Informed Consent and Governance Working Group..
Consent for clinical genome sequencing: considerations from the Clinical Sequencing Exploratory Research Consortium.
Per Med. 2019 Jul;16(4):325-333. doi: 10.2217/pme-2018-0076. Epub 2019 Jul 17. PMID: 31313633.
2018
Amendola LM, Berg JS, Horowitz CR, Angelo F, Bensen JT, Biesecker BB, Biesecker LG, Cooper GM, East K, Filipski K, Fullerton SM, Gelb BD, Goddard KAB, Hailu B, Hart R, Hassmiller-Lich K, Joseph G, Kenny EE, Koenig BA, Knight S, Kwok PY, Lewis KL, et al.
The Clinical Sequencing Evidence-Generating Research Consortium: Integrating Genomic Sequencing in Diverse and Medically Underserved Populations.
Am J Hum Genet. 2018 Sep 6;103(3):319-327. doi: 10.1016/j.ajhg.2018.08.007. PMID: 30193136.
Amendola LM, Robinson JO, Hart R, Biswas S, Lee K, Bernhardt BA, East K, Gilmore MJ, Kauffman TL, Lewis KL, Roche M, Scollon S, Wynn J, Blout C.
Why Patients Decline Genomic Sequencing Studies: Experiences from the CSER Consortium.
J Genet Couns. 2018 Sep;27(5):1220-1227. doi: 10.1007/s10897-018-0243-7. Epub 2018 Mar 1. PMID: 29497922.
Carvill GL, Engel KL, Ramamurthy A, Cochran JN, Roovers J, Stamberger H, Lim N, Schneider AL, Hollingsworth G, Holder DH, Regan BM, Lawlor J, Lagae L, Ceulemans B, Bebin EM, Nguyen J; EuroEPINOMICS Rare Epilepsy Syndrome, Myoclonic-Astatic Epilepsy, and Dravet Working Group., Barsh GS, Weckhuysen S, Meisler M, Berkovic SF, De Jonghe P, et al.
Aberrant Inclusion of a Poison Exon Causes Dravet Syndrome and Related SCN1A-Associated Genetic Epilepsies.
Am J Hum Genet. 2018 Dec 6;103(6):1022-1029. doi: 10.1016/j.ajhg.2018.10.023. PMID: 30526861.
Cheng H, Dharmadhikari AV, Varland S, Ma N, Domingo D, Kleyner R, Rope AF, Yoon M, Stray-Pedersen A, Posey JE, Crews SR, Eldomery MK, Akdemir ZC, Lewis AM, Sutton VR, Rosenfeld JA, Conboy E, Agre K, Xia F, Walkiewicz M, Longoni M, High FA, et al.
Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies.
Am J Hum Genet. 2018 May 3;102(5):985-994. doi: 10.1016/j.ajhg.2018.03.004. Epub 2018 Apr 12. PMID: 29656860.
Christensen KD, Bernhardt BA, Jarvik GP, Hindorff LA, Ou J, Biswas S, Powell BC, Grundmeier RW, Machini K, Karavite DJ, Pennington JW, Krantz ID, Berg JS, Goddard KAB.
Anticipated responses of early adopter genetic specialists and nongenetic specialists to unsolicited genomic secondary findings.
Genet Med. 2018 Oct;20(10):1186-1195. doi: 10.1038/gim.2017.243. Epub 2018 Feb 1. PMID: 29388940.
Hart MR, Biesecker BB, Blout CL, Christensen KD, Amendola LM, Bergstrom KL, Biswas S, Bowling KM, Brothers KB, Conlin LK, Cooper GM, Dulik MC, East KM, Everett JN, Finnila CR, Ghazani AA, Gilmore MJ, Goddard KAB, Jarvik GP, Johnston JJ, Kauffman TL, Kelley WV, et al.
Secondary findings from clinical genomic sequencing: prevalence, patient perspectives, family history assessment, and health-care costs from a multisite study.
Genet Med. 2019 May;21(5):1100-1110. doi: 10.1038/s41436-018-0308-x. Epub 2018 Oct 5. Erratum in: Genet Med. 2019 Jan 22;:. PMID: 30287922.
Haskell GT, Adams MC, Fan Z, Amin K, Guzman Badillo RJ, Zhou L, Bizon C, Chahin N, Greenwood RS, Milko LV, Shiloh-Malawsky Y, Crooks KR, Strande N, Tennison M, Tilley CR, Brandt A, Wilhelmsen KC, Weck K, Evans JP, Berg JS.
Diagnostic utility of exome sequencing in the evaluation of neuromuscular disorders.
Neurol Genet. 2018 Feb 1;4(1):e212. doi: 10.1212/NXG.0000000000000212. eCollection 2018 Feb. PMID: 29417091.
Hiatt SM, Neu MB, Ramaker RC, Hardigan AA, Prokop JW, Hancarova M, Prchalova D, Havlovicova M, Prchal J, Stranecky V, Yim DKC, Powis Z, Keren B, Nava C, Mignot C, Rio M, Revah-Politi A, Hemati P, Stong N, Iglesias AD, Suchy SF, Willaert R, et al.
De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay.
PLoS Genet. 2018 Nov 30;14(11):e1007671. doi: 10.1371/journal.pgen.1007671. eCollection 2018 Nov. PMID: 30500825.
Hiatt SM, Amaral MD, Bowling KM, Finnila CR, Thompson ML, Gray DE, Lawlor JMJ, Cochran JN, Bebin EM, Brothers KB, East KM, Kelley WV, Lamb NE, Levy SE, Lose EJ, Neu MB, Rich CA, Simmons S, Myers RM, Barsh GS, Cooper GM.
Systematic reanalysis of genomic data improves quality of variant interpretation.
Clin Genet. 2018 Jul;94(1):174-178. doi: 10.1111/cge.13259. Epub 2018 May 10. PMID: 29652076.
Lewis KL, Heidlebaugh AR, Epps S, Han PKJ, Fishler KP, Klein WMP, Miller IM, Ng D, Hepler C, Biesecker BB, Biesecker LG.
Knowledge, motivations, expectations, and traits of an African, African-American, and Afro-Caribbean sequencing cohort and comparisons to the original ClinSeq(®) cohort.
Genet Med. 2019 Jun;21(6):1355-1362. doi: 10.1038/s41436-018-0341-9. Epub 2018 Nov 1. PMID: 30382154.
Lynch FL, Himes P, Gilmore MJ, Morris EM, Schneider JL, Kauffman TL, Shuster E, Reiss JA, Dickerson JF, Leo MC, Davis JV, McMullen CK, Wilfond BS, Goddard KAB.
Time Costs for Genetic Counseling in Preconception Carrier Screening with Genome Sequencing.
J Genet Couns. 2018 Aug;27(4):823-833. doi: 10.1007/s10897-017-0205-5. Epub 2018 Feb 8. PMID: 29423569.
Mercaldo ND, Brothers KB, Carrell DS, Clayton EW, Connolly JJ, Holm IA, Horowitz CR, Jarvik GP, Kitchner TE, Li R, McCarty CA, McCormick JB, McManus VD, Myers MF, Pankratz JJ, Shrubsole MJ, Smith ME, Stallings SC, Williams JL, Schildcrout JS.
Enrichment sampling for a multi-site patient survey using electronic health records and census data.
J Am Med Inform Assoc. 2019 Mar 1;26(3):219-227. doi: 10.1093/jamia/ocy164. PMID: 30590688.
Mulhern MS, Stumpel C, Stong N, Brunner HG, Bier L, Lippa N, Riviello J, Rouhl RPW, Kempers M, Pfundt R, Stegmann APA, Kukolich MK, Telegrafi A, Lehman A; CAUSES study., Lopez-Rangel E, Houcinat N, Barth M, den Hollander N, Hoffer MJV, Weckhuysen S; EuroEPINOMICS-RES-MAE working group., et al.
NBEA: Developmental disease gene with early generalized epilepsy phenotypes.
Ann Neurol. 2018 Nov;84(5):788-795. doi: 10.1002/ana.25350. Epub 2018 Oct 25. PMID: 30269351.
Phillips KA, Trosman JR, Deverka PA, Quinn B, Tunis S, Neumann PJ, Chambers JD, Garrison LP Jr, Douglas MP, Weldon CB.
Insurance coverage for genomic tests.
Science. 2018 Apr 20;360(6386):278-279. doi: 10.1126/science.aas9268. Epub 2018 Apr 19. No abstract available. PMID: 29674586.
Porter KM, Kauffman TL, Koenig BA, Lewis KL, Rehm HL, Richards CS, Strande NT, Tabor HK, Wolf SM, Yang Y, Amendola LM, Azzariti DR, Berg JS, Bergstrom K, Biesecker LG, Biswas S, Bowling KM, Chung WK, Clayton EW, Conlin LK, Cooper GM, Dulik MC, et al.
Approaches to carrier testing and results disclosure in translational genomics research: The clinical sequencing exploratory research consortium experience.
Mol Genet Genomic Med. 2018 Nov;6(6):898-909. doi: 10.1002/mgg3.453. Epub 2018 Aug 21. PMID: 30133189.
Punj S, Akkari Y, Huang J, Yang F, Creason A, Pak C, Potter A, Dorschner MO, Nickerson DA, Robertson PD, Jarvik GP, Amendola LM, Schleit J, Simpson DK, Rope AF, Reiss J, Kauffman T, Gilmore MJ, Himes P, Wilfond B, Goddard KAB, Richards CS.
Preconception Carrier Screening by Genome Sequencing: Results from the Clinical Laboratory.
Am J Hum Genet. 2018 Jun 7;102(6):1078-1089. doi: 10.1016/j.ajhg.2018.04.004. Epub 2018 May 10. PMID: 29754767.
Roche MI, Griesemer I, Khan CM, Moore E, Lin FC, O'Daniel JM, Foreman AKM, Lee K, Powell BC, Berg JS, Evans JP, Henderson GE, Rini C.
Factors influencing NCGENES research participants' requests for non-medically actionable secondary findings.
Genet Med. 2019 May;21(5):1092-1099. doi: 10.1038/s41436-018-0294-z. Epub 2018 Sep 21. PMID: 30237575.
Rope AF, Kauffman TL, Himes P, Amendola LM, Punj S, Akkari Y, Potter A, Davis JV, Schneider JL, Reiss JA, Gilmore MJ, McMullen CK, Nickerson DA, Richards CS, Jarvik GP, Wilfond BS, Goddard KAB.
A case for expanding carrier testing to include actionable X-linked disorders.
Clin Case Rep. 2018 Sep 19;6(11):2092-2095. doi: 10.1002/ccr3.1806. eCollection 2018 Nov. PMID: 30455898.
Scollon S, Majumder MA, Bergstrom K, Wang T, McGuire AL, Robinson JO, Gutierrez AM, Lee CH, Hilsenbeck SG, Plon SE, Parsons DW, Street RL Jr.
Exome sequencing disclosures in pediatric cancer care: Patterns of communication among oncologists, genetic counselors, and parents.
Patient Educ Couns. 2019 Apr;102(4):680-686. doi: 10.1016/j.pec.2018.11.007. Epub 2018 Nov 12. PMID: 30482469.
Snijders Blok L, Hiatt SM, Bowling KM, Prokop JW, Engel KL, Cochran JN, Bebin EM, Bijlsma EK, Ruivenkamp CAL, Terhal P, Simon MEH, Smith R, Hurst JA; DDD study., McLaughlin H, Person R, Crunk A, Wangler MF, Streff H, Symonds JD, Zuberi SM, Elliott KS, et al.
De novo mutations in MED13, a component of the Mediator complex, are associated with a novel neurodevelopmental disorder.
Hum Genet. 2018 May;137(5):375-388. doi: 10.1007/s00439-018-1887-y. Epub 2018 May 8. PMID: 29740699.
Thompson ML, Finnila CR, Bowling KM, Brothers KB, Neu MB, Amaral MD, Hiatt SM, East KM, Gray DE, Lawlor JMJ, Kelley WV, Lose EJ, Rich CA, Simmons S, Levy SE, Myers RM, Barsh GS, Bebin EM, Cooper GM.
Genomic sequencing identifies secondary findings in a cohort of parent study participants.
Genet Med. 2018 Dec;20(12):1635-1643. doi: 10.1038/gim.2018.53. Epub 2018 Apr 12. PMID: 29790872.
Tripathy R, Leca I, van Dijk T, Weiss J, van Bon BW, Sergaki MC, Gstrein T, Breuss M, Tian G, Bahi-Buisson N, Paciorkowski AR, Pagnamenta AT, Wenninger-Weinzierl A, Martinez-Reza MF, Landler L, Lise S, Taylor JC, Terrone G, Vitiello G, Del Giudice E, Brunetti-Pierri N, D'Amico A, et al.
Mutations in MAST1 Cause Mega-Corpus-Callosum Syndrome with Cerebellar Hypoplasia and Cortical Malformations.
Neuron. 2018 Dec 19;100(6):1354-1368.e5. doi: 10.1016/j.neuron.2018.10.044. Epub 2018 Nov 15. PMID: 30449657.
Wilfond BS, Kauffman TL, Jarvik GP, Reiss JA, Richards CS, McMullen C, Gilmore M, Himes P, Kraft SA, Porter KM, Schneider JL, Punj S, Leo MC, Dickerson JF, Lynch FL, Clarke E, Rope AF, Lutz K, Goddard KAB.
Lessons Learned From A Study Of Genomics-Based Carrier Screening For Reproductive Decision Making.
Health Aff (Millwood). 2018 May;37(5):809-816. doi: 10.1377/hlthaff.2017.1578. PMID: 29733724.
Zebrowski AM, Ellis DE, Barg FK, Sperber NR, Bernhardt BA, Denny JC, Dexter PR, Ginsburg GS, Horowitz CR, Johnson JA, Levy MA, Orlando LA, Pollin TI, Skaar TC, Kimmel SE.
Qualitative study of system-level factors related to genomic implementation.
Genet Med. 2019 Jul;21(7):1534-1540. doi: 10.1038/s41436-018-0378-9. Epub 2018 Nov 23. PMID: 30467402.
2017
Blanchet P, Bebin M, Bruet S, Cooper GM, Thompson ML, Duban-Bedu B, Gerard B, Piton A, Suckno S, Deshpande C, Clowes V, Vogt J, Turnpenny P, Williamson MP, Alembik Y; Clinical Sequencing Exploratory Research Study Consortium.; Deciphering Developmental Disorders Consortium., Glasgow E, McNeill A.
MYT1L mutations cause intellectual disability and variable obesity by dysregulating gene expression and development of the neuroendocrine hypothalamus.
PLoS Genet. 2017 Aug 31;13(8):e1006957. doi: 10.1371/journal.pgen.1006957. eCollection 2017 Aug. PMID: 28859103.
Bowling KM, Thompson ML, Amaral MD, Finnila CR, Hiatt SM, Engel KL, Cochran JN, Brothers KB, East KM, Gray DE, Kelley WV, Lamb NE, Lose EJ, Rich CA, Simmons S, Whittle JS, Weaver BT, Nesmith AS, Myers RM, Barsh GS, Bebin EM, Cooper GM.
Genomic diagnosis for children with intellectual disability and/or developmental delay.
Genome Med. 2017 May 30;9(1):43. doi: 10.1186/s13073-017-0433-1. PMID: 28554332.
Gilmore MJ, Schneider J, Davis JV, Kauffman TL, Leo MC, Bergen K, Reiss JA, Himes P, Morris E, Young C, McMullen C, Wilfond BS, Goddard KAB.
Reasons for Declining Preconception Expanded Carrier Screening Using Genome Sequencing.
J Genet Couns. 2017 Oct;26(5):971-979. doi: 10.1007/s10897-017-0074-y. Epub 2017 Mar 17. PMID: 28315134.
Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, McGuire AL, Nussbaum RL, O'Daniel JM, Ormond KE, Rehm HL, Watson MS, Williams MS, Biesecker LG.
CORRIGENDUM: ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
Genet Med. 2017 May;19(5):606. doi: 10.1038/gim.2017.18. No abstract available. PMID: 28492529.
Haskell GT, Jensen BC, Skrzynia C, Pulikkotil T, Tilley CR, Lu Y, Marchuk DS, Ann Samsa L, Wilhelmsen KC, Lange E, Patterson C, Evans JP, Berg JS.
Genetic Complexity of Mitral Valve Prolapse Revealed by Clinical and Genetic Evaluation of a Large Family.
J Heart Valve Dis. 2017 Sep;26(5):569-580. PMID: 29762926.
Haskell GT, Jensen BC, Samsa LA, Marchuk D, Huang W, Skrzynia C, Tilley C, Seifert BA, Rivera-Muñoz EA, Koller B, Wilhelmsen KC, Liu J, Alhosaini H, Weck KE, Evans JP, Berg JS.
Whole Exome Sequencing Identifies Truncating Variants in Nuclear Envelope Genes in Patients With Cardiovascular Disease.
Circ Cardiovasc Genet. 2017 Jun;10(3). pii: e001443. doi: 10.1161/CIRCGENETICS.116.001443. PMID: 28611029.
Himes P, Kauffman TL, Muessig KR, Amendola LM, Berg JS, Dorschner MO, Gilmore M, Nickerson DA, Reiss JA, Richards CS, Rope AF, Simpson DK, Wilfond BS, Jarvik GP, Goddard KAB.
Genome sequencing and carrier testing: decisions on categorization and whether to disclose results of carrier testing.
Genet Med. 2017 Jul;19(7):803-808. doi: 10.1038/gim.2016.198. Epub 2017 Jan 12. PMID: 28079899.
Langer, M, Roche M., Brewer NT, Berg JS, Khan CM, Leos C, Moore E, Brown M, Rini, C.
Development and validation of a genomic knowledge scale to advance informed decision making research in genomic sequencing.
Medical Decision Making Policy & Practice, 2(1), 1-13.
Lyons JJ, Stotz SC, Chovanec J, Liu Y, Lewis KL, Nelson C, DiMaggio T, Jones N, Stone KD, Sung H, Biesecker LG, Colicos MA, Milner JD.
A common haplotype containing functional CACNA1H variants is frequently coinherited with increased TPSAB1 copy number.
Genet Med. 2018 Apr;20(5):503-512. doi: 10.1038/gim.2017.136. Epub 2017 Sep 21. PMID: 28933792.
Manolio TA, Fowler DM, Starita LM, Haendel MA, MacArthur DG, Biesecker LG, Worthey E, Chisholm RL, Green ED, Jacob HJ, McLeod HL, Roden D, Rodriguez LL, Williams MS, Cooper GM, Cox NJ, Herman GE, Kingsmore S, Lo C, Lutz C, MacRae CA, Nussbaum RL, et al.
Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research.
Cell. 2017 Mar 23;169(1):6-12. doi: 10.1016/j.cell.2017.03.005. PMID: 28340351.
Patel RY, Shah N, Jackson AR, Ghosh R, Pawliczek P, Paithankar S, Baker A, Riehle K, Chen H, Milosavljevic S, Bizon C, Rynearson S, Nelson T, Jarvik GP, Rehm HL, Harrison SM, Azzariti D, Powell B, Babb L, Plon SE, Milosavljevic A; ClinGen Resource..
ClinGen Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants.
Genome Med. 2017 Jan 12;9(1):3. doi: 10.1186/s13073-016-0391-z. PMID: 28081714.
Rini C, Khan CM, Moore E, Roche MI, Evans JP, Berg JS, Powell BC, Corbie-Smith G, Foreman AKM, Griesemer I, Lee K, O'Daniel JM, Henderson GE.
The who, what, and why of research participants' intentions to request a broad range of secondary findings in a diagnostic genomic sequencing study.
Genet Med. 2018 Jul;20(7):760-769. doi: 10.1038/gim.2017.176. Epub 2017 Oct 26. PMID: 29261173.
Sanghvi RV, Buhay CJ, Powell BC, Tsai EA, Dorschner MO, Hong CS, Lebo MS, Sasson A, Hanna DS, McGee S, Bowling KM, Cooper GM, Gray DE, Lonigro RJ, Dunford A, Brennan CA, Cibulskis C, Walker K, Carneiro MO, Sailsbery J, Hindorff LA, Robinson DR, et al.
Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers.
Genet Med. 2018 Aug;20(8):855-866. doi: 10.1038/gim.2017.192. Epub 2017 Nov 16. PMID: 29144510.
Vora NL, Powell B, Brandt A, Strande N, Hardisty E, Gilmore K, Foreman AKM, Wilhelmsen K, Bizon C, Reilly J, Owen P, Powell CM, Skinner D, Rini C, Lyerly AD, Boggess KA, Weck K, Berg JS, Evans JP.
Prenatal exome sequencing in anomalous fetuses: new opportunities and challenges.
Genet Med. 2017 Nov;19(11):1207-1216. doi: 10.1038/gim.2017.33. Epub 2017 May 18. PMID: 28518170.
Wolf SM, Amendola LM, Berg JS, Chung WK, Clayton EW, Green RC, Harris-Wai J, Henderson GE, Jarvik GP, Koenig BA, Lehmann LS, McGuire AL, O'Rourke P, Somkin C, Wilfond BS, Burke W.
Navigating the research-clinical interface in genomic medicine: analysis from the CSER Consortium.
Genet Med. 2018 Apr;20(5):545-553. doi: 10.1038/gim.2017.137. Epub 2017 Aug 31. PMID: 28858330.
2016
Amendola LM, Jarvik GP, Leo MC, McLaughlin HM, Akkari Y, Amaral MD, Berg JS, Biswas S, Bowling KM, Conlin LK, Cooper GM, Dorschner MO, Dulik MC, Ghazani AA, Ghosh R, Green RC, Hart R, Horton C, Johnston JJ, Lebo MS, Milosavljevic A, Ou J, et al.
Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium.
Am J Hum Genet. 2016 Jun 2;98(6):1067-1076. doi: 10.1016/j.ajhg.2016.03.024. Epub 2016 May 12. Erratum in: Am J Hum Genet. 2016 Jul 7;99(1):247. PMID: 27181684.
Amendola LM, Jarvik GP, Leo MC, McLaughlin HM, Akkari Y, Amaral MD, Berg JS, Biswas S, Bowling KM, Conlin LK, Cooper GM, Dorschner MO, Dulik MC, Ghazani AA, Ghosh R, Green RC, Hart R, Horton C, Johnston JJ, Lebo MS, Milosavljevic A, Ou J, et al.
Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium.
Am J Hum Genet. 2016 Jul 7;99(1):247. doi: 10.1016/j.ajhg.2016.06.001. No abstract available. PMID: 27392081.
Biesecker LG.
Overcalling secondary findings.
Genet Med. 2016 Apr;18(4):416. doi: 10.1038/gim.2016.19. Epub 2016 Mar 17. No abstract available. PMID: 26986879.
Bissig-Choisat B, Kettlun-Leyton C, Legras XD, Zorman B, Barzi M, Chen LL, Amin MD, Huang YH, Pautler RG, Hampton OA, Prakash MM, Yang D, Borowiak M, Muzny D, Doddapaneni HV, Hu J, Shi Y, Gaber MW, Hicks MJ, Thompson PA, Lu Y, Mills GB, et al.
Novel patient-derived xenograft and cell line models for therapeutic testing of pediatric liver cancer.
J Hepatol. 2016 Aug;65(2):325-33. doi: 10.1016/j.jhep.2016.04.009. PMID: 27117591.
Bowdin S, Gilbert A, Bedoukian E, Carew C, Adam MP, Belmont J, Bernhardt B, Biesecker L, Bjornsson HT, Blitzer M, D'Alessandro LC, Deardorff MA, Demmer L, Elliott A, Feldman GL, Glass IA, Herman G, Hindorff L, Hisama F, Hudgins L, Innes AM, Jackson L, et al.
Recommendations for the integration of genomics into clinical practice.
Genet Med. 2016 Nov;18(11):1075-1084. doi: 10.1038/gim.2016.17. Epub 2016 May 12. Review. PMID: 27171546.
Brothers KB, East KM, Kelley WV, Wright MF, Westbrook MJ, Rich CA, Bowling KM, Lose EJ, Bebin EM, Simmons S, Myers JA, Barsh G, Myers RM, Cooper GM, Pulley JM, Rothstein MA, Clayton EW.
Eliciting preferences on secondary findings: the Preferences Instrument for Genomic Secondary Results.
Genet Med. 2017 Mar;19(3):337-344. doi: 10.1038/gim.2016.110. Epub 2016 Aug 25. PMID: 27561086.
Christensen KD, Roberts JS, Whitehouse PJ, Royal CD, Obisesan TO, Cupples LA, Vernarelli JA, Bhatt DL, Linnenbringer E, Butson MB, Fasaye GA, Uhlmann WR, Hiraki S, Wang N, Cook-Deegan R, Green RC; REVEAL Study Group*..
Disclosing Pleiotropic Effects During Genetic Risk Assessment for Alzheimer Disease: A Randomized Trial.
Ann Intern Med. 2016 Feb 2;164(3):155-63. doi: 10.7326/M15-0187. Epub 2016 Jan 26. PMID: 26810768.
Delaney SK, Hultner ML, Jacob HJ, Ledbetter DH, McCarthy JJ, Ball M, Beckman KB, Belmont JW, Bloss CS, Christman MF, Cosgrove A, Damiani SA, Danis T, Delledonne M, Dougherty MJ, Dudley JT, Faucett WA, Friedman JR, Haase DH, Hays TS, Heilsberg S, Huber J, et al.
Toward clinical genomics in everyday medicine: perspectives and recommendations.
Expert Rev Mol Diagn. 2016;16(5):521-32. doi: 10.1586/14737159.2016.1146593. Epub 2016 Feb 24. PMID: 26810587.
Garofalo A, Sholl L, Reardon B, Taylor-Weiner A, Amin-Mansour A, Miao D, Liu D, Oliver N, MacConaill L, Ducar M, Rojas-Rudilla V, Giannakis M, Ghazani A, Gray S, Janne P, Garber J, Joffe S, Lindeman N, Wagle N, Garraway LA, Van Allen EM.
The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine.
Genome Med. 2016 Jul 26;8(1):79. doi: 10.1186/s13073-016-0333-9. PMID: 27460824.
Gray SW, Park ER, Najita J, Martins Y, Traeger L, Bair E, Gagne J, Garber J, Jänne PA, Lindeman N, Lowenstein C, Oliver N, Sholl L, Van Allen EM, Wagle N, Wood S, Garraway L, Joffe S.
Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study.
Genet Med. 2016 Oct;18(10):1011-9. doi: 10.1038/gim.2015.207. Epub 2016 Feb 11. PMID: 26866579.
Green RC, Goddard KA, Jarvik GP, Amendola LM, Appelbaum PS, Berg JS, Bernhardt BA, Biesecker LG, Biswas S, Blout CL, Bowling KM, Brothers KB, Burke W, Caga-Anan CF, Chinnaiyan AM, Chung WK, Clayton EW, Cooper GM, East K, Evans JP, Fullerton SM, Garraway LA, et al.
Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine.
Am J Hum Genet. 2016 Jul 7;99(1):246. doi: 10.1016/j.ajhg.2016.06.002. No abstract available. PMID: 27392080.
Green RC, Goddard KAB, Jarvik GP, Amendola LM, Appelbaum PS, Berg JS, Bernhardt BA, Biesecker LG, Biswas S, Blout CL, Bowling KM, Brothers KB, Burke W, Caga-Anan CF, Chinnaiyan AM, Chung WK, Clayton EW, Cooper GM, East K, Evans JP, Fullerton SM, Garraway LA, et al.
Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine.
Am J Hum Genet. 2016 Jun 2;98(6):1051-1066. doi: 10.1016/j.ajhg.2016.04.011. Epub 2016 May 12. Erratum in: Am J Hum Genet. 2016 Jul 7;99(1):246. PMID: 27181682.
Green RC, Goddard KA, Amendola LM, Appelbaum PS, Berg JS, Bernhardt BA, Biesecker LG, Biswas S, Blout CL, Bowling KM, Brothers KB, Burke W, Caga-Ana CF, Chinnaiyan AM, Chung WK, Clayton EW, Fullerton SM, Garraway LA, Garrett JR, Gray SW, Henderson GE, Hindorff LA, Hutter CM, Janne PA, Jarvik GP, Joffe S, Kaufman D, Knoppers BM, Koenig BA, Krantz ID, Manolio T, McCullough L, Myers RM, Nickerson DA, Ou J, Parsons DW, Petersen GM, Plon SE, Rehm HL, Roberts JS, Robinson D, Salama J, Scollon S, Sharp RR, Shirts B, Spinner NB, Tabor HK, Tarczy-Hornoch P, Veenstra DL, Wagle N, Weck K, Wilfond BS, Wilhelmsen K, Wolf SM, Wynn J, Yu JH, for the CSER Consortium..
The Clinical Sequencing Exploratory Research Consortium: Accelerating the Evidence-Based Practice of Genomic Medicine.
Am J Hum Genet. 2016 May 12. pii: S0002-9297(16)30106-9. doi: 10.1016/j.ajhg.2016.04.011. PMID: 27181682.
Guella I, Huh L, McKenzie MB, Toyota EB, Bebin EM, Thompson ML, Cooper GM, Evans DM, Buerki SE, Adam S, Van Allen MI, Nelson TN, Connolly MB, Farrer MJ, Demos M.
De novo FGF12 mutation in 2 patients with neonatal-onset epilepsy.
Neurol Genet. 2016 Nov 10;2(6):e120. eCollection 2016 Dec. PMID: 27872899.
Hunter JE, Irving SA, Biesecker LG, Buchanan A, Jensen B, Lee K, Martin CL, Milko L, Muessig K, Niehaus AD, O'Daniel J, Piper MA, Ramos EM, Schully SD, Scott AF, Slavotinek A, Sobreira N, Strande N, Weaver M, Webber EM, Williams MS, Berg JS, et al.
A standardized, evidence-based protocol to assess clinical actionability of genetic disorders associated with genomic variation.
Genet Med. 2016 Dec;18(12):1258-1268. doi: 10.1038/gim.2016.40. Epub 2016 Apr 28. PMID: 27124788.
Jarvik GP, Evans JP.
Mastering genomic terminology.
Genet Med. 2017 May;19(5):491-492. doi: 10.1038/gim.2016.139. Epub 2016 Sep 22. No abstract available. PMID: 27657676.
Kauffman TL, Wilfond BS, Jarvik GP, Leo MC, Lynch FL, Reiss JA, Richards CS, McMullen C, Nickerson D, Dorschner MO, Goddard KA.
Design of a randomized controlled trial for genomic carrier screening in healthy patients seeking preconception genetic testing.
Contemp Clin Trials. 2017 Feb;53:100-105. doi: 10.1016/j.cct.2016.12.007. Epub 2016 Dec 7. PMID: 27940182.
Korngiebel DM, McMullen CK, Amendola LM, Berg JS, Davis JV, Gilmore MJ, Harding CO, Himes P, Jarvik GP, Kauffman TL, Kennedy KA, Simpson DK, Leo MC, Lynch FL, Quigley DI, Reiss JA, Richards CS, Rope AF, Schneider JL, Goddard KA, Wilfond BS.
Generating a taxonomy for genetic conditions relevant to reproductive planning.
Am J Med Genet A. 2016 Mar;170(3):565-73. doi: 10.1002/ajmg.a.37513. PMID: 26889673.
Kullo IJ, Jouni H, Austin EE, Brown SA, Kruisselbrink TM, Isseh IN, Haddad RA, Marroush TS, Shameer K, Olson JE, Broeckel U, Green RC, Schaid DJ, Montori VM, Bailey KR.
Incorporating a Genetic Risk Score Into Coronary Heart Disease Risk Estimates: Effect on Low-Density Lipoprotein Cholesterol Levels (the MI-GENES Clinical Trial).
Circulation. 2016 Mar 22;133(12):1181-8. doi: 10.1161/CIRCULATIONAHA.115.020109. Epub 2016 Feb 25. PMID: 26915630.
Leo MC, McMullen C, Wilfond BS, Lynch FL, Reiss JA, Gilmore MJ, Himes P, Kauffman TL, Davis JV, Jarvik GP, Berg JS, Harding C, Kennedy KA, Simpson DK, Quigley DI, Richards CS, Rope AF, Goddard KA.
Patients' ratings of genetic conditions validate a taxonomy to simplify decisions about preconception carrier screening via genome sequencing.
Am J Med Genet A. 2016 Mar;170(3):574-82. doi: 10.1002/ajmg.a.37477. Epub 2016 Jan 21. PMID: 26792268.
Lin FY, Bergstrom K, Person R, Bavle A, Ballester LY, Scollon S, Raesz-Martinez R, Jea A, Birchansky S, Wheeler DA, Berg SL, Chintagumpala MM, Adesina AM, Eng C, Roy A, Plon SE, Parsons DW.
Integrated tumor and germline whole-exome sequencing identifies mutations in MAPK and PI3K pathway genes in an adolescent with rosette-forming glioneuronal tumor of the fourth ventricle.
Cold Spring Harb Mol Case Stud. 2016 Sep;2(5):a001057. doi: 10.1101/mcs.a001057. PMID: 27626068.
Lupo PJ, Robinson JO, Diamond PM, Jamal L, Danysh HE, Blumenthal-Barby J, Lehmann LS, Vassy JL, Christensen KD, Green RC, McGuire AL; MedSeq Project team..
Patients' perceived utility of whole-genome sequencing for their healthcare: findings from the MedSeq project.
Per Med. 2016 Jan 1;13(1):13-20. Epub 2016 Jan 8. PMID: 27019659.
Lyons JJ, Yu X, Hughes JD, Le QT, Jamil A, Bai Y, Ho N, Zhao M, Liu Y, O'Connell MP, Trivedi NN, Nelson C, DiMaggio T, Jones N, Matthews H, Lewis KL, Oler AJ, Carlson RJ, Arkwright PD, Hong C, Agama S, Wilson TM, et al.
Elevated basal serum tryptase identifies a multisystem disorder associated with increased TPSAB1 copy number.
Nat Genet. 2016 Dec;48(12):1564-1569. doi: 10.1038/ng.3696. Epub 2016 Oct 17. PMID: 27749843.
Mehra R, Vats P, Cieslik M, Cao X, Su F, Shukla S, Udager AM, Wang R, Pan J, Kasaian K, Lonigro R, Siddiqui J, Premkumar K, Palapattu G, Weizer A, Hafez KS, Wolf JS Jr, Sangoi AR, Trpkov K, Osunkoya AO, Zhou M, Giannico G, et al.
Biallelic Alteration and Dysregulation of the Hippo Pathway in Mucinous Tubular and Spindle Cell Carcinoma of the Kidney.
Cancer Discov. 2016 Nov;6(11):1258-1266. Epub 2016 Sep 7. PMID: 27604489.
Møller RS, Weckhuysen S, Chipaux M, Marsan E, Taly V, Bebin EM, Hiatt SM, Prokop JW, Bowling KM, Mei D, Conti V, de la Grange P, Ferrand-Sorbets S, Dorfmüller G, Lambrecq V, Larsen LH, Leguern E, Guerrini R, Rubboli G, Cooper GM, Baulac S.
Germline and somatic mutations in the MTOR gene in focal cortical dysplasia and epilepsy.
Neurol Genet. 2016 Oct 31;2(6):e118. eCollection 2016 Dec. PMID: 27830187.
Ng BG, Shiryaev SA, Rymen D, Eklund EA, Raymond K, Kircher M, Abdenur JE, Alehan F, Midro AT, Bamshad MJ, Barone R, Berry GT, Brumbaugh JE, Buckingham KJ, Clarkson K, Cole FS, O'Connor S, Cooper GM, Van Coster R, Demmer LA, Diogo L, Fay AJ, et al.
ALG1-CDG: Clinical and Molecular Characterization of 39 Unreported Patients.
Hum Mutat. 2016 Jul;37(7):653-60. doi: 10.1002/humu.22983. Epub 2016 Mar 21. PMID: 26931382.
O'Daniel JM, McLaughlin HM, Amendola LM, Bale SJ, Berg JS, Bick D, Bowling KM, Chao EC, Chung WK, Conlin LK, Cooper GM, Das S, Deignan JL, Dorschner MO, Evans JP, Ghazani AA, Goddard KA, Gornick M, Farwell Hagman KD, Hambuch T, Hegde M, Hindorff LA, et al.
A survey of current practices for genomic sequencing test interpretation and reporting processes in US laboratories.
Genet Med. 2017 May;19(5):575-582. doi: 10.1038/gim.2016.152. Epub 2016 Nov 3. PMID: 27811861.
Parsons DW, Roy A, Yang Y, Wang T, Scollon S, Bergstrom K, Kerstein RA, Gutierrez S, Petersen AK, Bavle A, Lin FY, López-Terrada DH, Monzon FA, Hicks MJ, Eldin KW, Quintanilla NM, Adesina AM, Mohila CA, Whitehead W, Jea A, Vasudevan SA, Nuchtern JG, et al.
Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors.
JAMA Oncol. 2016 May 1;2(5):616-624. doi: 10.1001/jamaoncol.2015.5699. PMID: 26822237.
Posey JE, Harel T, Liu P, Rosenfeld JA, James RA, Coban Akdemir ZH, Walkiewicz M, Bi W, Xiao R, Ding Y, Xia F, Beaudet AL, Muzny DM, Gibbs RA, Boerwinkle E, Eng CM, Sutton VR, Shaw CA, Plon SE, Yang Y, Lupski JR.
Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation.
N Engl J Med. 2017 Jan 5;376(1):21-31. doi: 10.1056/NEJMoa1516767. Epub 2016 Dec 7. PMID: 27959697.
Potter SL, Venkatramani R, Wenderfer S, Graham BH, Vasudevan SA, Sher A, Wu H, Wheeler DA, Yang Y, Eng CM, Gibbs RA, Roy A, Plon SE, Parsons DW.
Renal cell carcinoma harboring somatic TSC2 mutations in a child with methylmalonic acidemia.
Pediatr Blood Cancer. 2016 Oct 17. doi: 10.1002/pbc.26286. [Epub ahead of print]. PMID: 27748010.
Rasmussen LV, Overby CL, Connolly J, Chute CG, Denny JC, Freimuth R, Hartzler AL, Holm IA, Manzi S, Pathak J, Peissig PL, Smith M, Williams MS, Shirts BH, Stoffel EM, Tarczy-Hornoch P, Rohrer Vitek CR, Wolf WA, Starren J.
Practical considerations for implementing genomic information resources. Experiences from eMERGE and CSER.
Appl Clin Inform. 2016 Sep 21;7(3):870-82. doi: 10.4338/ACI-2016-04-RA-0060. PMID: 27652374.
Ritter DI, Roychowdhury S, Roy A, Rao S, Landrum MJ, Sonkin D, Shekar M, Davis CF, Hart RK, Micheel C, Weaver M, Van Allen EM, Parsons DW, McLeod HL, Watson MS, Plon SE, Kulkarni S, Madhavan S; ClinGen Somatic Cancer Working Group..
Somatic cancer variant curation and harmonization through consensus minimum variant level data.
Genome Med. 2016 Nov 4;8(1):117. PMID: 27814769.
Seifert BA, O'Daniel JM, Amin K, Marchuk DS, Patel NM, Parker JS, Hoyle AP, Mose LE, Marron A, Hayward MC, Bizon C, Wilhelmsen KC, Evans JP, Earp HS 3rd, Sharpless NE, Hayes DN, Berg JS.
Germline Analysis from Tumor-Germline Sequencing Dyads to Identify Clinically Actionable Secondary Findings.
Clin Cancer Res. 2016 Aug 15;22(16):4087-4094. doi: 10.1158/1078-0432.CCR-16-0015. Epub 2016 Apr 15. PMID: 27083775.
Tan N, Amendola LM, O'Daniel JM, Burt A, Horike-Pyne MJ, Boshe L, Henderson GE, Rini C, Roche MI, Hisama FM, Burke W, Wilfond B, Jarvik GP.
Is "incidental finding" the best term?: a study of patients' preferences.
Genet Med. 2017 Feb;19(2):176-181. doi: 10.1038/gim.2016.96. Epub 2016 Aug 4. PMID: 27490114.
2015
Amendola LM, Dorschner MO, Robertson PD, Salama JS, Hart R, Shirts BH, Murray ML, Tokita MJ, Gallego CJ, Kim DS, Bennett JT, Crosslin DR, Ranchalis J, Jones KL, Rosenthal EA, Jarvik ER, Itsara A, Turner EH, Herman DS, Schleit J, Burt A, Jamal SM, et al.
Actionable exomic incidental findings in 6503 participants: challenges of variant classification.
Genome Res. 2015 Mar;25(3):305-15. doi: 10.1101/gr.183483.114. Epub 2015 Jan 30. PMID: 25637381.
Amendola LM, Lautenbach D, Scollon S, Bernhardt B, Biswas S, East K, Everett J, Gilmore MJ, Himes P, Raymond VM, Wynn J, Hart R; CSER Genetic Counseling Working Group., Jarvik GP.
Illustrative case studies in the return of exome and genome sequencing results.
Per Med. 2015;12(3):283-295. PMID: 26478737.
Berg JS, Foreman AK, O'Daniel JM, Booker JK, Boshe L, Carey T, Crooks KR, Jensen BC, Juengst ET, Lee K, Nelson DK, Powell BC, Powell CM, Roche MI, Skrzynia C, Strande NT, Weck KE, Wilhelmsen KC, Evans JP.
A semiquantitative metric for evaluating clinical actionability of incidental or secondary findings from genome-scale sequencing.
Genet Med. 2016 May;18(5):467-75. doi: 10.1038/gim.2015.104. Epub 2015 Aug 13. PMID: 26270767.
Berg JS, Foreman AKM, O'Daniel JM, Booker JK, Boshe L, Carye T, Crooks KR, Jensen JC, Juengst ET, Lee K, Nelson DK, Powell BC, Powell CM, Roche MI, Skrzynia C, Strande NT, Weck KE, Wilhelmsen KC, Evans JP.
A semiquantitative metric for evaluating clinical actionability of incidental or secondary findings from genome-scale sequencing.
PMID: 26270767. PMCID: 4752935.
Berkman BE, Hull SC, Biesecker LG.
Scrutinizing the Right Not to Know.
Am J Bioeth. 2015;15(7):17-9. doi: 10.1080/15265161.2015.1039733. No abstract available. PMID: 26147256.
Botkin JR, Belmont JW, Berg JS, Berkman BE, Bombard Y, Holm IA, Levy HP, Ormond KE, Saal HM, Spinner NB, Wilfond BS, McInerney JD.
Points to Consider: Ethical, Legal, and Psychosocial Implications of Genetic Testing in Children and Adolescents.
Am J Hum Genet. 2015 Jul 2;97(1):6-21. doi: 10.1016/j.ajhg.2015.05.022. Review. Erratum in: Am J Hum Genet. 2015 Sep 3;97(3):501. PMID: 26140447.
Brothers KB, Holm IA, Childerhose JE, Antommaria AH, Bernhardt BA, Clayton EW, Gelb BD, Joffe S, Lynch JA, McCormick JB, McCullough LB, Parsons DW, Sundaresan AS, Wolf WA, Yu JH, Wilfond BS; Pediatrics Workgroup of the Clinical Sequencing Exploratory Research (CSER) Consortium.; Pediatrics Workgroup of the Clinical Sequencing Exploratory Research CSER Consortium..
When Participants in Genomic Research Grow Up: Contact and Consent at the Age of Majority.
J Pediatr. 2016 Jan;168:226-31.e1. doi: 10.1016/j.jpeds.2015.09.020. Epub 2015 Oct 23. No abstract available. PMID: 26477867.
Christensen KD, Vassy JL, Jamal L, Lehmann LS, Slashinski MJ, Perry DL, Robinson JO, Blumenthal-Barby J, Feuerman LZ, Murray MF, Green RC, McGuire AL; MedSeq Project Team..
Are physicians prepared for whole genome sequencing? a qualitative analysis.
Clin Genet. 2016 Feb;89(2):228-34. doi: 10.1111/cge.12626. Epub 2015 Jul 7. PMID: 26080898.
Cieslik M, Chugh R, Wu YM, Wu M, Brennan C, Lonigro R, Su F, Wang R, Siddiqui J, Mehra R, Cao X, Lucas D, Chinnaiyan AM, Robinson D.
The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing.
Genome Res. 2015 Sep;25(9):1372-81. doi: 10.1101/gr.189621.115. Epub 2015 Aug 7. PMID: 26253700.
Cohen SA, Laurino M, Bowen DJ, Upton MP, Pritchard C, Hisama F, Jarvik G, Fichera A, Sjoding B, Bennett RL, Naylor L, Jacobson A, Burke W, Grady WM.
Initiation of universal tumor screening for Lynch syndrome in colorectal cancer patients as a model for the implementation of genetic information into clinical oncology practice.
Cancer. 2016 Feb 1;122(3):393-401. doi: 10.1002/cncr.29758. Epub 2015 Oct 19. PMID: 26480326.
Cooper GM.
Parlez-vous VUS?.
Genome Res. 2015 Oct;25(10):1423-6. doi: 10.1101/gr.190116.115. PMID: 26430151.
Couser NL, Masood MM, Strande NT, Foreman AK, Crooks K, Weck KE, Lu M, Wilhelmsen KC, Roche M, Evans JP, Berg JS, Powell CM.
The phenotype of multiple congenital anomalies-hypotonia-seizures syndrome 1: report and review.
Am J Med Genet A. 2015 Sep;167A(9):2176-81. doi: 10.1002/ajmg.a.37129. Epub 2015 Apr 29. PMID: 25920937.
Dauriz M, Porneala BC, Guo X, Bielak LF, Peyser PA, Durant NH, Carnethon MR, Bonadonna RC, Bonora E, Bowden DW, Florez JC, Fornage M, Hivert MF, Jacobs DR Jr, Kabagambe EK, Lewis CE, Murabito JM, Rasmussen-Torvik LJ, Rich SS, Vassy JL, Yao J, Carr JJ, et al.
Association of a 62 Variants Type 2 Diabetes Genetic Risk Score With Markers of Subclinical Atherosclerosis: A Transethnic, Multicenter Study.
Circ Cardiovasc Genet. 2015 Jun;8(3):507-15. doi: 10.1161/CIRCGENETICS.114.000740. Epub 2015 Mar 24. PMID: 25805414.
Gallego CJ, Shirts BH, Bennette CS, Guzauskas G, Amendola LM, Horike-Pyne M, Hisama FM, Pritchard CC, Grady WM, Burke W, Jarvik GP, Veenstra DL.
Next-Generation Sequencing Panels for the Diagnosis of Colorectal Cancer and Polyposis Syndromes: A Cost-Effectiveness Analysis.
J Clin Oncol. 2015 Jun 20;33(18):2084-91. doi: 10.1200/JCO.2014.59.3665. Epub 2015 May 4. PMID: 25940718.
Gargis AS, Kalman L, Bick DP, da Silva C, Dimmock DP, Funke BH, Gowrisankar S, Hegde MR, Kulkarni S, Mason CE, Nagarajan R, Voelkerding KV, Worthey EA, Aziz N, Barnes J, Bennett SF, Bisht H, Church DM, Dimitrova Z, Gargis SR, Hafez N, Hambuch T, et al.
Good laboratory practice for clinical next-generation sequencing informatics pipelines.
Nat Biotechnol. 2015 Jul;33(7):689-93. doi: 10.1038/nbt.3237. No abstract available. PMID: 26154004.
Harms PW, Vats P, Verhaegen ME, Robinson DR, Wu YM, Dhanasekaran SM, Palanisamy N, Siddiqui J, Cao X, Su F, Wang R, Xiao H, Kunju LP, Mehra R, Tomlins SA, Fullen DR, Bichakjian CK, Johnson TM, Dlugosz AA, Chinnaiyan AM.
The Distinctive Mutational Spectra of Polyomavirus-Negative Merkel Cell Carcinoma.
Cancer Res. 2015 Sep 15;75(18):3720-3727. doi: 10.1158/0008-5472.CAN-15-0702. Epub 2015 Aug 3. PMID: 26238782.
Johnston JJ, Lewis KL, Ng D, Singh LN, Wynter J, Brewer C, Brooks BP, Brownell I, Candotti F, Gonsalves SG, Hart SP, Kong HH, Rother KI, Sokolic R, Solomon BD, Zein WM, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG.
Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations.
Am J Hum Genet. 2015 Jun 4;96(6):913-25. doi: 10.1016/j.ajhg.2015.04.013. PMID: 26046366.
Keppler-Noreuil KM, Rios JJ, Parker VE, Semple RK, Lindhurst MJ, Sapp JC, Alomari A, Ezaki M, Dobyns W, Biesecker LG.
PIK3CA-related overgrowth spectrum (PROS): diagnostic and testing eligibility criteria, differential diagnosis, and evaluation.
Am J Med Genet A. 2015 Feb;167A(2):287-95. doi: 10.1002/ajmg.a.36836. Epub 2014 Dec 31. PMID: 25557259.
Lee K, Berg JS, Milko L, Crooks K, Lu M, Bizon C, Owen P, Wilhelmsen KC, Weck KE, Evans JP, Garg S.
High Diagnostic Yield of Whole Exome Sequencing in Participants With Retinal Dystrophies in a Clinical Ophthalmology Setting.
Am J Ophthalmol. 2015 Aug;160(2):354-363.e9. doi: 10.1016/j.ajo.2015.04.026. Epub 2015 Apr 22. PMID: 25910913.
Li MH, Abrudan JL, Dulik MC, Sasson A, Brunton J, Jayaraman V, Dugan N, Haley D, Rajagopalan R, Biswas S, Sarmady M, DeChene ET, Deardorff MA, Wilkens A, Noon SE, Scarano MI, Santani AB, White PS, Pennington J, Conlin LK, Spinner NB, Krantz ID, et al.
Utility and limitations of exome sequencing as a genetic diagnostic tool for conditions associated with pediatric sudden cardiac arrest/sudden cardiac death.
Hum Genomics. 2015 Jul 19;9:15. doi: 10.1186/s40246-015-0038-y. PMID: 26187847.
McLaughlin HM, Ceyhan-Birsoy O, Christensen KD, Kohane IS, Krier J, Lane WJ, Lautenbach D, Lebo MS, Machini K, MacRae CA, Azzariti DR, Murray MF, Seidman CE, Vassy JL, Green RC, Rehm HL; MedSeq Project..
A systematic approach to the reporting of medically relevant findings from whole genome sequencing.
BMC Med Genet. 2014 Dec 14;15:134. doi: 10.1186/s12881-014-0134-1. PMID: 25714468.
Mody RJ, Wu YM, Lonigro RJ, Cao X, Roychowdhury S, Vats P, Frank KM, Prensner JR, Asangani I, Palanisamy N, Dillman JR, Rabah RM, Kunju LP, Everett J, Raymond VM, Ning Y, Su F, Wang R, Stoffel EM, Innis JW, Roberts JS, Robertson PL, et al.
Integrative Clinical Sequencing in the Management of Refractory or Relapsed Cancer in Youth.
JAMA. 2015 Sep 1;314(9):913-25. doi: 10.1001/jama.2015.10080. PMID: 26325560.
Rehm HL, Berg JS, Brooks LD, Bustamante CD, Evans JP, Landrum MJ, Ledbetter DH, Maglott DR, Martin CL, Nussbaum RL, Plon SE, Ramos EM, Sherry ST, Watson MS; ClinGen..
ClinGen--the Clinical Genome Resource.
N Engl J Med. 2015 Jun 4;372(23):2235-42. doi: 10.1056/NEJMsr1406261. No abstract available. PMID: 26014595.
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; 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. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5. PMID: 25741868.
Rinaldi C, Schmidt T, Situ AJ, Johnson JO, Lee PR, Chen KL, Bott LC, Fadó R, Harmison GH, Parodi S, Grunseich C, Renvoisé B, Biesecker LG, De Michele G, Santorelli FM, Filla A, Stevanin G, Dürr A, Brice A, Casals N, Traynor BJ, Blackstone C, et al.
Mutation in CPT1C Associated With Pure Autosomal Dominant Spastic Paraplegia.
JAMA Neurol. 2015 May;72(5):561-70. doi: 10.1001/jamaneurol.2014.4769. Erratum in: JAMA Neurol. 2015 May;72(5):608. PMID: 25751282.
Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, Vinson J, Cao X, Vats P, Kunju LP, Hussain M, Feng FY, Tomlins SA, Cooney KA, Smith DC, et al.
Integrative clinical genomics of advanced prostate cancer.
Cell. 2015 May 21;161(5):1215-1228. doi: 10.1016/j.cell.2015.05.001. Erratum in: Cell. 2015 Jul 16;162(2):454. PMID: 26000489.
Roy A, Kumar V, Zorman B, Fang E, Haines KM, Doddapaneni H, Hampton OA, White S, Bavle AA, Patel NR, Eldin KW, John Hicks M, Rakheja D, Leavey PJ, Skapek SX, Amatruda JF, Nuchtern JG, Chintagumpala MM, Wheeler DA, Plon SE, Sumazin P, Parsons DW.
Recurrent internal tandem duplications of BCOR in clear cell sarcoma of the kidney.
Nat Commun. 2015 Nov 17;6:8891. doi: 10.1038/ncomms9891. PMID: 26573325.
Schneider JL, Goddard KA, Davis J, Wilfond B, Kauffman TL, Reiss JA, Gilmore M, Himes P, Lynch FL, Leo MC, McMullen C.
Is It Worth Knowing?" Focus Group Participants' Perceived Utility of Genomic Preconception Carrier Screening.
J Genet Couns. 2016 Feb;25(1):135-45. doi: 10.1007/s10897-015-9851-7. Epub 2015 Jun 21. PMID: 26093606.
Schneider JL, Davis J, Kauffman TL, Reiss JA, McGinley C, Arnold K, Zepp J, Gilmore M, Muessig KR, Syngal S, Acheson L, Wiesner GL, Peterson SK, Goddard KA.
Stakeholder perspectives on implementing a universal Lynch syndrome screening program: a qualitative study of early barriers and facilitators.
Genet Med. 2016 Feb;18(2):152-61. doi: 10.1038/gim.2015.43. Epub 2015 Apr 16. PMID: 25880440.
Shirts BH, Salama JS, Aronson SJ, Chung WK, Gray SW, Hindorff LA, Jarvik GP, Plon SE, Stoffel EM, Tarczy-Hornoch PZ, Van Allen EM, Weck KE, Chute CG, Freimuth RR, Grundmeier RW, Hartzler AL, Li R, Peissig PL, Peterson JF, Rasmussen LV, Starren JB, Williams MS, et al.
CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record.
J Am Med Inform Assoc. 2015 Nov;22(6):1231-42. doi: 10.1093/jamia/ocv065. Epub 2015 Jul 3. PMID: 26142422.
Trinidad SB, Fullerton SM, Burke W.
Looking for Trouble and Finding It.
Am J Bioeth. 2015;15(7):15-7. doi: 10.1080/15265161.2015.1039731. No abstract available. PMID: 26147255.
Vassy JL, Christensen KD, Slashinski MJ, Lautenbach DM, Raghavan S, Robinson JO, Blumenthal-Barby J, Feuerman LZ, Lehmann LS, Murray MF, Green RC, McGuire AL.
'Someday it will be the norm': physician perspectives on the utility of genome sequencing for patient care in the MedSeq Project.
Per Med. 2015;12(1):23-32. PMID: 25642274.
Vassy JL, McLaughlin HM, MacRae CA, Seidman CE, Lautenbach D, Krier JB, Lane WJ, Kohane IS, Murray MF, McGuire AL, Rehm HL, Green RC.
A one-page summary report of genome sequencing for the healthy adult.
Public Health Genomics. 2015;18(2):123-9. doi: 10.1159/000370102. Epub 2015 Jan 21. Erratum in: Public Health Genomics. 2015 Apr;18(3):191. McLaughlin, Heather L [corrected to McLaughlin, Heather M]. PMID: 25612602.
Wassif CA, Cross JL, Iben J, Sanchez-Pulido L, Cougnoux A, Platt FM, Ory DS, Ponting CP, Bailey-Wilson JE, Biesecker LG, Porter FD.
High incidence of unrecognized visceral/neurological late-onset Niemann-Pick disease, type C1, predicted by analysis of massively parallel sequencing data sets.
Genet Med. 2016 Jan;18(1):41-8. doi: 10.1038/gim.2015.25. Epub 2015 Mar 12. PMID: 25764212.
Wolf SM, Branum R, Koenig BA, Petersen GM, Berry SA, Beskow LM, Daly MB, Fernandez CV, Green RC, LeRoy BS, Lindor NM, O'Rourke PP, Breitkopf CR, Rothstein MA, Van Ness B, Wilfond BS.
Returning a Research Participant's Genomic Results to Relatives: Analysis and Recommendations.
J Law Med Ethics. 2015 Fall;43(3):440-63. doi: 10.1111/jlme.12288. PMID: 26479555.
Zhou S, Hertel PM, Finegold MJ, Wang L, Kerkar N, Wang J, Wong LJ, Plon SE, Sambrotta M, Foskett P, Niu Z, Thompson RJ, Knisely AS.
Hepatocellular carcinoma associated with tight-junction protein 2 deficiency.
Hepatology. 2015 Dec;62(6):1914-6. doi: 10.1002/hep.27872. Epub 2015 Jun 19. No abstract available. PMID: 25921221.
2014
Botkin JR, Lewis MH, Watson MS, Swoboda KJ, Anderson R, Berry SA, Bonhomme N, Brosco JP, Comeau AM, Goldenberg A, Goldman E, Therrell B, Levy-Fisch J, Tarini B, Wilfond B; Bioethics and Legal Work Group of the Newborn Screening Translational Research Network..
Parental permission for pilot newborn screening research: guidelines from the NBSTRN.
Pediatrics. 2014 Feb;133(2):e410-7. doi: 10.1542/peds.2013-2271. Epub 2014 Jan 6. PMID: 24394680.
Brothers KB, Lynch JA, Aufox SA, Connolly JJ, Gelb BD, Holm IA, Sanderson SC, McCormick JB, Williams JL, Wolf WA, Antommaria AH, Clayton EW.
Practical guidance on informed consent for pediatric participants in a biorepository.
Mayo Clin Proc. 2014 Nov;89(11):1471-80. doi: 10.1016/j.mayocp.2014.07.006. Epub 2014 Sep 26. No abstract available. PMID: 25264176.
Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, et al.
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
Genome Biol. 2014 Mar 25;15(3):R53. doi: 10.1186/gb-2014-15-3-r53. PMID: 24667040.
Carere DA, Couper MP, Crawford SD, Kalia SS, Duggan JR, Moreno TA, Mountain JL, Roberts JS, Green RC; PGen Study Group..
Design, methods, and participant characteristics of the Impact of Personal Genomics (PGen) Study, a prospective cohort study of direct-to-consumer personal genomic testing customers.
Genome Med. 2014 Dec 3;6(12):96. doi: 10.1186/s13073-014-0096-0. eCollection 2014. PMID: 25484922.
Fan Z, Greenwood R, Felix AC, Shiloh-Malawsky Y, Tennison M, Roche M, Crooks K, Weck K, Wilhelmsen K, Berg J, Evans J.
GCH1 heterozygous mutation identified by whole-exome sequencing as a treatable condition in a patient presenting with progressive spastic paraplegia.
J Neurol. 2014 Mar;261(3):622-4. doi: 10.1007/s00415-014-7265-3. Epub 2014 Feb 8. No abstract available. PMID: 24509643.
Gallego CJ, Bennette CS, Heagerty P, Comstock B, Horike-Pyne M, Hisama F, Amendola LM, Bennett RL, Dorschner MO, Tarczy-Hornoch P, Grady WM, Fullerton SM, Trinidad SB, Regier DA, Nickerson DA, Burke W, Patrick DL, Jarvik GP, Veenstra DL.
Comparative effectiveness of next generation genomic sequencing for disease diagnosis: design of a randomized controlled trial in patients with colorectal cancer/polyposis syndromes.
Contemp Clin Trials. 2014 Sep;39(1):1-8. doi: 10.1016/j.cct.2014.06.016. Epub 2014 Jul 3. PMID: 24997220.
Garralda E, Paz K, López-Casas PP, Jones S, Katz A, Kann LM, López-Rios F, Sarno F, Al-Shahrour F, Vasquez D, Bruckheimer E, Angiuoli SV, Calles A, Diaz LA, Velculescu VE, Valencia A, Sidransky D, Hidalgo M.
Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment.
Clin Cancer Res. 2014 May 1;20(9):2476-84. doi: 10.1158/1078-0432.CCR-13-3047. Epub 2014 Mar 14. PMID: 24634382.
Green RC, Christensen KD, Cupples LA, Relkin NR, Whitehouse PJ, Royal CD, Obisesan TO, Cook-Deegan R, Linnenbringer E, Butson MB, Fasaye GA, Levinson E, Roberts JS; REVEAL Study Group..
A randomized noninferiority trial of condensed protocols for genetic risk disclosure of Alzheimer's disease.
Alzheimers Dement. 2015 Oct;11(10):1222-30. doi: 10.1016/j.jalz.2014.10.014. Epub 2014 Dec 9. PMID: 25499536.
Hwang KB, Lee IH, Park JH, Hambuch T, Choe Y, Kim M, Lee K, Song T, Neu MB, Gupta N, Kohane IS, Green RC, Kong SW.
Reducing false-positive incidental findings with ensemble genotyping and logistic regression based variant filtering methods.
Hum Mutat. 2014 Aug;35(8):936-44. doi: 10.1002/humu.22587. Epub 2014 Jun 24. PMID: 24829188.
Jarvik GP, Amendola LM, Berg JS, Brothers K, Clayton EW, Chung W, Evans BJ, Evans JP, Fullerton SM, Gallego CJ, Garrison NA, Gray SW, Holm IA, Kullo IJ, Lehmann LS, McCarty C, Prows CA, Rehm HL, Sharp RR, Salama J, Sanderson S, Van Driest SL, et al.
Return of genomic results to research participants: the floor, the ceiling, and the choices in between.
Am J Hum Genet. 2014 Jun 5;94(6):818-26. doi: 10.1016/j.ajhg.2014.04.009. Epub 2014 May 8. PMID: 24814192.
Lee IH, Lee K, Hsing M, Choe Y, Park JH, Kim SH, Bohn JM, Neu MB, Hwang KB, Green RC, Kohane IS, Kong SW.
Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline.
Hum Mutat. 2014 May;35(5):537-47. doi: 10.1002/humu.22520. Epub 2014 Mar 6. PMID: 24478219.
MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, et al.
Guidelines for investigating causality of sequence variants in human disease.
Nature. 2014 Apr 24;508(7497):469-76. doi: 10.1038/nature13127. PMID: 24759409.
Overby CL, Rasmussen LV, Hartzler A, Connolly JJ, Peterson JF, Hedberg RE, Freimuth RR, Shirts BH, Denny JC, Larson EB, Chute CG, Jarvik GP, Ralston JD, Shuldiner AR, Starren J, Kullo IJ, Tarczy-Hornoch P, Williams MS.
A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project.
AMIA Annu Symp Proc. 2014 Nov 14;2014:944-53. eCollection 2014. PMID: 25954402.
Peters TL, Kumar V, Polikepahad S, Lin FY, Sarabia SF, Liang Y, Wang WL, Lazar AJ, Doddapaneni H, Chao H, Muzny DM, Wheeler DA, Okcu MF, Plon SE, Hicks MJ, López-Terrada D, Parsons DW, Roy A.
BCOR-CCNB3 fusions are frequent in undifferentiated sarcomas of male children.
Mod Pathol. 2015 Apr;28(4):575-86. doi: 10.1038/modpathol.2014.139. Epub 2014 Oct 31. PMID: 25360585.
Scollon S, Bergstrom K, Kerstein RA, Wang T, Hilsenbeck SG, Ramamurthy U, Gibbs RA, Eng CM, Chintagumpala MM, Berg SL, McCullough LB, McGuire AL, Plon SE, Parsons DW.
Obtaining informed consent for clinical tumor and germline exome sequencing of newly diagnosed childhood cancer patients.
Genome Med. 2014 Sep 17;6(9):69. doi: 10.1186/s13073-014-0069-3. eCollection 2014. PMID: 25317207.
Sparks JA, Iversen MD, Miller Kroouze R, Mahmoud TG, Triedman NA, Kalia SS, Atkinson ML, Lu B, Deane KD, Costenbader KH, Green RC, Karlson EW.
Personalized Risk Estimator for Rheumatoid Arthritis (PRE-RA) Family Study: rationale and design for a randomized controlled trial evaluating rheumatoid arthritis risk education to first-degree relatives.
Contemp Clin Trials. 2014 Sep;39(1):145-57. doi: 10.1016/j.cct.2014.08.007. Epub 2014 Aug 20. PMID: 25151341.
Teutsch SM, Fielding JE, Khoury MJ, Evans JP.
Utility before business.
Genet Med. 2014 Dec;16(12):869-70. doi: 10.1038/gim.2014.71. Epub 2014 Jul 10. No abstract available. PMID: 25010054.
Van Allen EM, Mouw KW, Kim P, Iyer G, Wagle N, Al-Ahmadie H, Zhu C, Ostrovnaya I, Kryukov GV, O'Connor KW, Sfakianos J, Garcia-Grossman I, Kim J, Guancial EA, Bambury R, Bahl S, Gupta N, Farlow D, Qu A, Signoretti S, Barletta JA, Reuter V, et al.
Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma.
Cancer Discov. 2014 Oct;4(10):1140-53. doi: 10.1158/2159-8290.CD-14-0623. Epub 2014 Aug 5. PMID: 25096233.
Van Allen EM, Wagle N, Stojanov P, Perrin DL, Cibulskis K, Marlow S, Jane-Valbuena J, Friedrich DC, Kryukov G, Carter SL, McKenna A, Sivachenko A, Rosenberg M, Kiezun A, Voet D, Lawrence M, Lichtenstein LT, Gentry JG, Huang FW, Fostel J, Farlow D, Barbie D, et al.
Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.
Nat Med. 2014 Jun;20(6):682-8. doi: 10.1038/nm.3559. Epub 2014 May 18. PMID: 24836576.
Vassy JL, Hivert MF, Porneala B, Dauriz M, Florez JC, Dupuis J, Siscovick DS, Fornage M, Rasmussen-Torvik LJ, Bouchard C, Meigs JB.
Polygenic type 2 diabetes prediction at the limit of common variant detection.
Diabetes. 2014 Jun;63(6):2172-82. doi: 10.2337/db13-1663. Epub 2014 Feb 11. Erratum in: Diabetes. 2018 Apr 18;:. PMID: 24520119.
Vassy JL, Lautenbach DM, McLaughlin HM, Kong SW, Christensen KD, Krier J, Kohane IS, Feuerman LZ, Blumenthal-Barby J, Roberts JS, Lehmann LS, Ho CY, Ubel PA, MacRae CA, Seidman CE, Murray MF, McGuire AL, Rehm HL, Green RC; MedSeq Project..
The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine.
Trials. 2014 Mar 20;15:85. doi: 10.1186/1745-6215-15-85. PMID: 24645908.
Xia F, Bainbridge MN, Tan TY, Wangler MF, Scheuerle AE, Zackai EH, Harr MH, Sutton VR, Nalam RL, Zhu W, Nash M, Ryan MM, Yaplito-Lee J, Hunter JV, Deardorff MA, Penney SJ, Beaudet AL, Plon SE, Boerwinkle EA, Lupski JR, Eng CM, Muzny DM, et al.
De novo truncating mutations in AHDC1 in individuals with syndromic expressive language delay, hypotonia, and sleep apnea.
Am J Hum Genet. 2014 May 1;94(5):784-9. doi: 10.1016/j.ajhg.2014.04.006. PMID: 24791903.
Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, Veeraraghavan N, Hawes A, Chiang T, Leduc M, Beuten J, Zhang J, He W, Scull J, Willis A, Landsverk M, Craigen WJ, Bekheirnia MR, et al.
Molecular findings among patients referred for clinical whole-exome sequencing.
JAMA. 2014 Nov 12;312(18):1870-9. doi: 10.1001/jama.2014.14601. PMID: 25326635.
2013
Berg JS, Amendola LM, Eng C, Van Allen E, Gray SW, Wagle N, Rehm HL, DeChene ET, Dulik MC, Hisama FM, Burke W, Spinner NB, Garraway L, Green RC, Plon S, Evans JP, Jarvik GP; Members of the CSER Actionability and Return of Results Working Group..
Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the Clinical Sequencing Exploratory Research Consortium.
Genet Med. 2013 Nov;15(11):860-7. doi: 10.1038/gim.2013.133. Epub 2013 Oct 24. Review. Erratum in: Genet Med. 2014 Feb;16(2):203. PMID: 24195999.
Burke W, Antommaria AH, Bennett R, Botkin J, Clayton EW, Henderson GE, Holm IA, Jarvik GP, Khoury MJ, Knoppers BM, Press NA, Ross LF, Rothstein MA, Saal H, Uhlmann WR, Wilfond B, Wolf SM, Zimmern R.
Recommendations for returning genomic incidental findings? We need to talk!.
Genet Med. 2013 Nov;15(11):854-9. doi: 10.1038/gim.2013.113. Epub 2013 Aug 1. Review. PMID: 23907645.
Caulfield T, Evans J, McGuire A, McCabe C, Bubela T, Cook-Deegan R, Fishman J, Hogarth S, Miller FA, Ravitsky V, Biesecker B, Borry P, Cho MK, Carroll JC, Etchegary H, Joly Y, Kato K, Lee SS, Rothenberg K, Sankar P, Szego MJ, Ossorio P, et al.
Reflections on the cost of "low-cost" whole genome sequencing: framing the health policy debate.
PLoS Biol. 2013 Nov;11(11):e1001699. doi: 10.1371/journal.pbio.1001699. PMID: 24223516.
Dorschner MO, Amendola LM, Turner EH, Robertson PD, Shirts BH, Gallego CJ, Bennett RL, Jones KL, Tokita MJ, Bennett JT, Kim JH, Rosenthal EA, Kim DS; National Heart, Lung, and Blood Institute Grand Opportunity Exome Sequencing Project., Tabor HK, Bamshad MJ, Motulsky AG, Scott CR, Pritchard CC, Walsh T, Burke W, Raskind WH, et al.
Actionable, pathogenic incidental findings in 1,000 participants' exomes.
Am J Hum Genet. 2013 Oct 3;93(4):631-40. doi: 10.1016/j.ajhg.2013.08.006. Epub 2013 Sep 19. PMID: 24055113.
Goddard KA, Whitlock EP, Berg JS, Williams MS, Webber EM, Webster JA, Lin JS, Schrader KA, Campos-Outcalt D, Offit K, Feigelson HS, Hollombe C.
Description and pilot results from a novel method for evaluating return of incidental findings from next-generation sequencing technologies.
Genet Med. 2013 Sep;15(9):721-8. doi: 10.1038/gim.2013.37. Epub 2013 Apr 4. PMID: 23558254.
Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, McGuire AL, Nussbaum RL, O'Daniel JM, Ormond KE, Rehm HL, Watson MS, Williams MS, Biesecker LG; American College of Medical Genetics and Genomics..
ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
Genet Med. 2013 Jul;15(7):565-74. doi: 10.1038/gim.2013.73. Epub 2013 Jun 20. Erratum in: Genet Med. 2017 May;19(5):606. PMID: 23788249.
Hartzler A, McCarty CA, Rasmussen LV, Williams MS, Brilliant M, Bowton EA, Clayton EW, Faucett WA, Ferryman K, Field JR, Fullerton SM, Horowitz CR, Koenig BA, McCormick JB, Ralston JD, Sanderson SC, Smith ME, Trinidad SB.
Stakeholder engagement: a key component of integrating genomic information into electronic health records.
Genet Med. 2013 Oct;15(10):792-801. doi: 10.1038/gim.2013.127. Epub 2013 Sep 12. Review. PMID: 24030437.
Hazin R, Brothers KB, Malin BA, Koenig BA, Sanderson SC, Rothstein MA, Williams MS, Clayton EW, Kullo IJ.
Ethical, legal, and social implications of incorporating genomic information into electronic health records.
Genet Med. 2013 Oct;15(10):810-6. doi: 10.1038/gim.2013.117. Epub 2013 Sep 12. Review. PMID: 24030434.
Johannessen CM, Johnson LA, Piccioni F, Townes A, Frederick DT, Donahue MK, Narayan R, Flaherty KT, Wargo JA, Root DE, Garraway LA.
A melanocyte lineage program confers resistance to MAP kinase pathway inhibition.
Nature. 2013 Dec 5;504(7478):138-42. doi: 10.1038/nature12688. Epub 2013 Nov 3. PMID: 24185007.
McGuire AL, Joffe S, Koenig BA, Biesecker BB, McCullough LB, Blumenthal-Barby JS, Caulfield T, Terry SF, Green RC.
Point-counterpoint. Ethics and genomic incidental findings.
Science. 2013 May 31;340(6136):1047-8. doi: 10.1126/science.1240156. Epub 2013 May 16. No abstract available. PMID: 23686340.
Overby CL, Kohane I, Kannry JL, Williams MS, Starren J, Bottinger E, Gottesman O, Denny JC, Weng C, Tarczy-Hornoch P, Hripcsak G.
Opportunities for genomic clinical decision support interventions.
Genet Med. 2013 Oct;15(10):817-23. doi: 10.1038/gim.2013.128. Epub 2013 Sep 19. No abstract available. PMID: 24051479.
Peterson D, Munger C, Crowley J, Corcoran C, Cruchaga C, Goate AM, Norton MC, Green RC, Munger RG, Breitner JC, Welsh-Bohmer KA, Lyketsos C, Tschanz J, Kauwe JS; Alzheimer's Disease Neuroimaging Initiative..
Variants in PPP3R1 and MAPT are associated with more rapid functional decline in Alzheimer's disease: the Cache County Dementia Progression Study.
Alzheimers Dement. 2014 May;10(3):366-71. doi: 10.1016/j.jalz.2013.02.010. Epub 2013 May 30. PMID: 23727081.
Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, Friez MJ, Funke BH, Hegde MR, Lyon E; Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Commitee..
ACMG clinical laboratory standards for next-generation sequencing.
Genet Med. 2013 Sep;15(9):733-47. doi: 10.1038/gim.2013.92. PMID: 23887774.
Robinson DR, Wu YM, Vats P, Su F, Lonigro RJ, Cao X, Kalyana-Sundaram S, Wang R, Ning Y, Hodges L, Gursky A, Siddiqui J, Tomlins SA, Roychowdhury S, Pienta KJ, Kim SY, Roberts JS, Rae JM, Van Poznak CH, Hayes DF, Chugh R, Kunju LP, et al.
Activating ESR1 mutations in hormone-resistant metastatic breast cancer.
Nat Genet. 2013 Dec;45(12):1446-51. doi: 10.1038/ng.2823. Epub 2013 Nov 3. PMID: 24185510.
Tarczy-Hornoch P, Amendola L, Aronson SJ, Garraway L, Gray S, Grundmeier RW, Hindorff LA, Jarvik G, Karavite D, Lebo M, Plon SE, Van Allen E, Weck KE, White PS, Yang Y.
A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record.
Genet Med. 2013 Oct;15(10):824-32. doi: 10.1038/gim.2013.120. Epub 2013 Sep 26. PMID: 24071794.
Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, et al.
Clinical whole-exome sequencing for the diagnosis of mendelian disorders.
N Engl J Med. 2013 Oct 17;369(16):1502-11. doi: 10.1056/NEJMoa1306555. Epub 2013 Oct 2. PMID: 24088041.
Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, Romano-Adesman A, Bjornson RD, Breitbart RE, Brown KK, Carriero NJ, Cheung YH, Deanfield J, DePalma S, Fakhro KA, Glessner J, Hakonarson H, Italia MJ, Kaltman JR, Kaski J, Kim R, Kline JK, et al.
De novo mutations in histone-modifying genes in congenital heart disease.
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2012
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2010
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