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For: Pawliczek P, Patel RY, Ashmore LR, Jackson AR, Bizon C, Nelson T, Powell B, Freimuth RR, Strande N, Shah N, Paithankar S, Wright MW, Dwight S, Zhen J, Landrum M, McGarvey P, Babb L, Plon SE, Milosavljevic A. ClinGen Allele Registry links information about genetic variants. Hum Mutat 2018;39:1690-1701. [PMID: 30311374 PMCID: PMC6519371 DOI: 10.1002/humu.23637] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/01/2018] [Accepted: 08/28/2018] [Indexed: 11/18/2022]
Number Cited by Other Article(s)
1
Arbesfeld JA, Da EY, Stevenson JS, Kuzma K, Paul A, Farris T, Capodanno BJ, Grindstaff SB, Riehle K, Saraiva-Agostinho N, Safer JF, Milosavljevic A, Foreman J, Firth HV, Hunt SE, Iqbal S, Cline MS, Rubin AF, Wagner AH. Mapping MAVE data for use in human genomics applications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.20.545702. [PMID: 38979347 PMCID: PMC11230167 DOI: 10.1101/2023.06.20.545702] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
2
Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie ME, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D’Eustachio P, Wu G. Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. Database (Oxford) 2024;2024:baae031. [PMID: 38713862 PMCID: PMC11184451 DOI: 10.1093/database/baae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/23/2024] [Accepted: 04/01/2024] [Indexed: 05/09/2024]
3
Claussnitzer M, Parikh VN, Wagner AH, Arbesfeld JA, Bult CJ, Firth HV, Muffley LA, Nguyen Ba AN, Riehle K, Roth FP, Tabet D, Bolognesi B, Glazer AM, Rubin AF. Minimum information and guidelines for reporting a multiplexed assay of variant effect. Genome Biol 2024;25:100. [PMID: 38641812 PMCID: PMC11027375 DOI: 10.1186/s13059-024-03223-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 03/25/2024] [Indexed: 04/21/2024]  Open
4
El Kassaby B, Castellanos F, Gerring M, Kunde-Ramamoorthy G, Bult CJ. MVAR: A Mouse Variation Registry. J Mol Biol 2024:168518. [PMID: 38458603 DOI: 10.1016/j.jmb.2024.168518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/01/2024] [Indexed: 03/10/2024]
5
Walton NA, Nagarajan R, Wang C, Sincan M, Freimuth RR, Everman DB, Walton DC, McGrath SP, Lemas DJ, Benos PV, Alekseyenko AV, Song Q, Gamsiz Uzun E, Taylor CO, Uzun A, Person TN, Rappoport N, Zhao Z, Williams MS. Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. J Am Med Inform Assoc 2024;31:536-541. [PMID: 38037121 PMCID: PMC10797281 DOI: 10.1093/jamia/ocad211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 10/09/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023]  Open
6
Pitz V, Makarious MB, Bandres-Ciga S, Iwaki H, Singleton AB, Nalls M, Heilbron K, Blauwendraat C. Analysis of rare Parkinson's disease variants in millions of people. NPJ Parkinsons Dis 2024;10:11. [PMID: 38191580 PMCID: PMC10774311 DOI: 10.1038/s41531-023-00608-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/24/2023] [Indexed: 01/10/2024]  Open
7
Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie M, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D'Eustachio P, Wu G. Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562964. [PMID: 37904913 PMCID: PMC10614924 DOI: 10.1101/2023.10.18.562964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
8
Pitz V, Makarious M, Bandrés-Ciga S, Iwaki H, Singleton A, Nalls M, Heilbron K, Blauwendraat C. Analysis of rare Parkinson's disease variants in millions of people. RESEARCH SQUARE 2023:rs.3.rs-2743857. [PMID: 37090536 PMCID: PMC10120789 DOI: 10.21203/rs.3.rs-2743857/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
9
Croucher DC, Devasia AJ, Abelman DD, Mahdipour-Shirayeh A, Li Z, Erdmann N, Tiedemann R, Pugh TJ, Trudel S. Single-cell profiling of multiple myeloma reveals molecular response to FGFR3 inhibitor despite clinical progression. Cold Spring Harb Mol Case Stud 2023;9:a006249. [PMID: 36639200 PMCID: PMC10240837 DOI: 10.1101/mcs.a006249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/29/2022] [Indexed: 01/15/2023]  Open
10
Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell 2023;186:1493-1511.e40. [PMID: 37001506 PMCID: PMC10074325 DOI: 10.1016/j.cell.2023.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 10/16/2022] [Accepted: 02/10/2023] [Indexed: 04/03/2023]
11
Krysiak K, Danos A, Saliba J, McMichael J, Coffman A, Kiwala S, Barnell E, Sheta L, Grisdale C, Kujan L, Pema S, Lever J, Ridd S, Spies N, Andric V, Chiorean A, Rieke D, Clark K, Reisle C, Venigalla A, Evans M, Jani P, Takahashi H, Suda A, Horak P, Ritter D, Zhou X, Ainscough B, Delong S, Kesserwan C, Lamping M, Shen H, Marr A, Hoang M, Singhal K, Khanfar M, Li B, Lin WH, Terraf P, Corson L, Salama Y, Campbell K, Farncombe K, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, King I, Cotto K, Skidmore Z, Walker J, Zhang J, Milosavljevic A, Patel R, Giles R, Kim R, Schriml L, Mardis E, Jones SJM, Raca G, Rao S, Madhavan S, Wagner A, Griffith M, Griffith O. CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. Nucleic Acids Res 2023;51:D1230-D1241. [PMID: 36373660 PMCID: PMC9825608 DOI: 10.1093/nar/gkac979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/15/2022]  Open
12
Fan S, Zhao T, Sun L. The global prevalence and ethnic heterogeneity of iron-refractory iron deficiency anaemia. Orphanet J Rare Dis 2023;18:2. [PMID: 36604716 PMCID: PMC9814447 DOI: 10.1186/s13023-022-02612-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023]  Open
13
Goar W, Babb L, Chamala S, Cline M, Freimuth RR, Hart RK, Kuzma K, Lee J, Nelson T, Prlić A, Riehle K, Smith A, Stahl K, Yates AD, Rehm HL, Wagner AH. Development and application of a computable genotype model in the GA4GH Variation Representation Specification. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2023;28:383-394. [PMID: 36540993 PMCID: PMC9782714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
14
Tudini E, Andrews J, Lawrence DM, King-Smith SL, Baker N, Baxter L, Beilby J, Bennetts B, Beshay V, Black M, Boughtwood TF, Brion K, Cheong PL, Christie M, Christodoulou J, Chong B, Cox K, Davis MR, Dejong L, Dinger ME, Doig KD, Douglas E, Dubowsky A, Ellul M, Fellowes A, Fisk K, Fortuno C, Friend K, Gallagher RL, Gao S, Hackett E, Hadler J, Hipwell M, Ho G, Hollway G, Hooper AJ, Kassahn KS, Krishnaraj R, Lau C, Le H, San Leong H, Lundie B, Lunke S, Marty A, McPhillips M, Nguyen LT, Nones K, Palmer K, Pearson JV, Quinn MC, Rawlings LH, Sadedin S, Sanchez L, Schreiber AW, Sigalas E, Simsek A, Soubrier J, Stark Z, Thompson BA, U J, Vakulin CG, Wells AV, Wise CA, Woods R, Ziolkowski A, Brion MJ, Scott HS, Thorne NP, Spurdle AB. Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation. Am J Hum Genet 2022;109:1960-1973. [PMID: 36332611 PMCID: PMC9674965 DOI: 10.1016/j.ajhg.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]  Open
15
Wei CH, Allot A, Riehle K, Milosavljevic A, Lu Z. tmVar 3.0: an improved variant concept recognition and normalization tool. Bioinformatics 2022;38:4449-4451. [PMID: 35904569 PMCID: PMC9477515 DOI: 10.1093/bioinformatics/btac537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/07/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022]  Open
16
Zhang D, Wu J, Yuan Y, Li X, Gao X, Han M, Gao S, Huang S, Dai P. A novel missense variant in CEACAM16 gene causes autosomal dominant nonsyndromic hearing loss. Ann Hum Genet 2022;86:207-217. [PMID: 35292975 PMCID: PMC9314904 DOI: 10.1111/ahg.12463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 11/27/2022]
17
Horak P, Griffith M, Danos AM, Pitel BA, Madhavan S, Liu X, Chow C, Williams H, Carmody L, Barrow-Laing L, Rieke D, Kreutzfeldt S, Stenzinger A, Tamborero D, Benary M, Rajagopal PS, Ida CM, Lesmana H, Satgunaseelan L, Merker JD, Tolstorukov MY, Campregher PV, Warner JL, Rao S, Natesan M, Shen H, Venstrom J, Roy S, Tao K, Kanagal-Shamanna R, Xu X, Ritter DI, Pagel K, Krysiak K, Dubuc A, Akkari YM, Li XS, Lee J, King I, Raca G, Wagner AH, Li MM, Plon SE, Kulkarni S, Griffith OL, Chakravarty D, Sonkin D. Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC). Genet Med 2022;24:986-998. [PMID: 35101336 PMCID: PMC9081216 DOI: 10.1016/j.gim.2022.01.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/22/2021] [Accepted: 01/03/2022] [Indexed: 01/21/2023]  Open
18
Krysiak K, Danos AM, Kiwala S, McMichael JF, Coffman AC, Barnell EK, Sheta L, Saliba J, Grisdale CJ, Kujan L, Pema S, Lever J, Spies NC, Chiorean A, Rieke DT, Clark KA, Jani P, Takahashi H, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Lamping M, Marr AR, Li BV, Lin WH, Terraf P, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith OL, Griffith M. A community approach to the cancer-variant-interpretation bottleneck. NATURE CANCER 2022;3:522-525. [PMID: 35624339 PMCID: PMC9872366 DOI: 10.1038/s43018-022-00379-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
19
Preston CG, Wright MW, Madhavrao R, Harrison SM, Goldstein JL, Luo X, Wand H, Wulf B, Cheung G, Mandell ME, Tong H, Cheng S, Iacocca MA, Pineda AL, Popejoy AB, Dalton K, Zhen J, Dwight SS, Babb L, DiStefano M, O’Daniel JM, Lee K, Riggs ER, Zastrow DB, Mester JL, Ritter DI, Patel RY, Subramanian SL, Milosavljevic A, Berg JS, Rehm HL, Plon SE, Cherry JM, Bustamante CD, Costa HA. ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines. Genome Med 2022;14:6. [PMID: 35039090 PMCID: PMC8764818 DOI: 10.1186/s13073-021-01004-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 11/12/2021] [Indexed: 12/29/2022]  Open
20
Harrison SM, Austin-Tse CA, Kim S, Lebo M, Leon A, Murdock D, Radhakrishnan A, Shirts BH, Steeves M, Venner E, Gibbs RA, Jarvik GP, Rehm HL. Harmonizing variant classification for return of results in the All of Us Research Program. Hum Mutat 2021;43:1114-1121. [PMID: 34923710 PMCID: PMC9206690 DOI: 10.1002/humu.24317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 11/24/2021] [Accepted: 12/15/2021] [Indexed: 11/18/2022]
21
Ware SM. Pediatric cardiomyopathy and the PCM Genes study: A summary with insights on genetic testing, variant interpretation, race and ethnicity. PROGRESS IN PEDIATRIC CARDIOLOGY 2021. [DOI: 10.1016/j.ppedcard.2021.101468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
22
Wagner AH, Babb L, Alterovitz G, Baudis M, Brush M, Cameron DL, Cline M, Griffith M, Griffith OL, Hunt SE, Kreda D, Lee JM, Li S, Lopez J, Moyer E, Nelson T, Patel RY, Riehle K, Robinson PN, Rynearson S, Schuilenburg H, Tsukanov K, Walsh B, Konopko M, Rehm HL, Yates AD, Freimuth RR, Hart RK. The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification. CELL GENOMICS 2021;1. [PMID: 35311178 PMCID: PMC8929418 DOI: 10.1016/j.xgen.2021.100027] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
23
Murugan M, Babb LJ, Overby Taylor C, Rasmussen LV, Freimuth RR, Venner E, Yan F, Yi V, Granite SJ, Zouk H, Aronson SJ, Power K, Fedotov A, Crosslin DR, Fasel D, Jarvik GP, Hakonarson H, Bangash H, Kullo IJ, Connolly JJ, Nestor JG, Caraballo PJ, Wei W, Wiley K, Rehm HL, Gibbs RA. Genomic considerations for FHIR®; eMERGE implementation lessons. J Biomed Inform 2021;118:103795. [PMID: 33930535 PMCID: PMC8583906 DOI: 10.1016/j.jbi.2021.103795] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/06/2021] [Accepted: 04/25/2021] [Indexed: 01/17/2023]
24
Palmisano A, Vural S, Zhao Y, Sonkin D. MutSpliceDB: A database of splice sites variants with RNA-seq based evidence on effects on splicing. Hum Mutat 2021;42:342-345. [PMID: 33600011 PMCID: PMC9867871 DOI: 10.1002/humu.24185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/02/2020] [Accepted: 02/13/2021] [Indexed: 01/26/2023]
25
Holmes JB, Moyer E, Phan L, Maglott D, Kattman B. SPDI: data model for variants and applications at NCBI. Bioinformatics 2020;36:1902-1907. [PMID: 31738401 DOI: 10.1093/bioinformatics/btz856] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/04/2019] [Accepted: 11/15/2019] [Indexed: 11/13/2022]  Open
26
Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nat Genet 2020;52:448-457. [PMID: 32246132 PMCID: PMC7127986 DOI: 10.1038/s41588-020-0603-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
27
Nie A, Pineda AL, Wright MW, Wand H, Wulf B, Costa H, Patel R, Bustamante CD, Zou J. LitGen: Genetic Literature Recommendation Guided by Human Explanations. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2020;25:67-78. [PMID: 31797587 PMCID: PMC7478937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
28
A pediatric perspective on genomics and prevention in the twenty-first century. Pediatr Res 2020;87:338-344. [PMID: 31578042 DOI: 10.1038/s41390-019-0597-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022]
29
Gelman H, Dines JN, Berg J, Berger AH, Brnich S, Hisama FM, James RG, Rubin AF, Shendure J, Shirts B, Fowler DM, Starita LM. Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation. Genome Med 2019;11:85. [PMID: 31862013 PMCID: PMC6925490 DOI: 10.1186/s13073-019-0698-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/20/2019] [Indexed: 01/31/2023]  Open
30
Danos AM, Krysiak K, Barnell EK, Coffman AC, McMichael JF, Kiwala S, Spies NC, Sheta LM, Pema SP, Kujan L, Clark KA, Wollam AZ, Rao S, Ritter DI, Sonkin D, Raca G, Lin WH, Grisdale CJ, Kim RH, Wagner AH, Madhavan S, Griffith M, Griffith OL. Standard operating procedure for curation and clinical interpretation of variants in cancer. Genome Med 2019;11:76. [PMID: 31779674 PMCID: PMC6883603 DOI: 10.1186/s13073-019-0687-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/07/2019] [Indexed: 02/04/2023]  Open
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Bizon C, Cox S, Balhoff J, Kebede Y, Wang P, Morton K, Fecho K, Tropsha A. ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources. J Chem Inf Model 2019;59:4968-4973. [DOI: 10.1021/acs.jcim.9b00683] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bergom C, West CM, Higginson DS, Abazeed ME, Arun B, Bentzen SM, Bernstein JL, Evans JD, Gerber NK, Kerns SL, Keen J, Litton JK, Reiner AS, Riaz N, Rosenstein BS, Sawakuchi GO, Shaitelman SF, Powell SN, Woodward WA. The Implications of Genetic Testing on Radiation Therapy Decisions: A Guide for Radiation Oncologists. Int J Radiat Oncol Biol Phys 2019;105:698-712. [PMID: 31381960 DOI: 10.1016/j.ijrobp.2019.07.026] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 06/21/2019] [Accepted: 07/08/2019] [Indexed: 02/06/2023]
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Maroilley T, Tarailo-Graovac M. Uncovering Missing Heritability in Rare Diseases. Genes (Basel) 2019;10:E275. [PMID: 30987386 PMCID: PMC6523881 DOI: 10.3390/genes10040275] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022]  Open
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Pawliczek P, Patel RY, Ashmore LR, Jackson AR, Bizon C, Nelson T, Powell B, Freimuth RR, Strande N, Shah N, Paithankar S, Wright MW, Dwight S, Zhen J, Landrum M, McGarvey P, Babb L, Plon SE, Milosavljevic A. ClinGen Allele Registry links information about genetic variants. Hum Mutat 2018;39:1690-1701. [PMID: 30311374 PMCID: PMC6519371 DOI: 10.1002/humu.23637] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/01/2018] [Accepted: 08/28/2018] [Indexed: 11/18/2022]
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Rehm HL, Berg JS, Plon SE. ClinGen and ClinVar – Enabling Genomics in Precision Medicine. Hum Mutat 2018. [DOI: 10.1002/humu.23654] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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