Lucinda Antonacci-Fulton

2022

Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data

TOPMed Anthropometry Working Group & NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Mar 2022, In: Nature Genetics. 54, 3, p. 263-273 11 p.

Research output: Contribution to journal › Article › peer-review

32 Scopus citations

Nine out of ten samples were mistakenly switched by The Orang-utan Genome Consortium

Banes, G. L., Fountain, E. D., Karklus, A., Fulton, R., Antonacci-Fulton, L. & Nelson, J. O., Dec 2022, In: Scientific data. 9, 1, 485.

Research output: Contribution to journal › Article › peer-review

Open Access

Rare coding variants in 35 genes associate with circulating lipid levels—A multi-ancestry analysis of 170,000 exomes

AMP-T2D-GENES, Myocardial Infarction Genetics Consortium, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium & NHLBI TOPMed Lipids Working Group, Jan 6 2022, In: American journal of human genetics. 109, 1, p. 81-96 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Scopus citations

Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer

Cui Zhou, D., Jayasinghe, R. G., Chen, S., Herndon, J. M., Iglesia, M. D., Navale, P., Wendl, M. C., Caravan, W., Sato, K., Storrs, E., Mo, C. K., Liu, J., Southard-Smith, A. N., Wu, Y., Naser Al Deen, N., Baer, J. M., Fulton, R. S., Wyczalkowski, M. A., Liu, R., Fronick, C. C., & 46 othersFulton, L. A., Shinkle, A., Thammavong, L., Zhu, H., Sun, H., Wang, L. B., Li, Y., Zuo, C., McMichael, J. F., Davies, S. R., Appelbaum, E. L., Robbins, K. J., Chasnoff, S. E., Yang, X., Reeb, A. N., Oh, C., Serasanambati, M., Lal, P., Varghese, R., Mashl, J. R., Ponce, J., Terekhanova, N. V., Yao, L., Wang, F., Chen, L., Schnaubelt, M., Lu, R. J. H., Schwarz, J. K., Puram, S. V., Kim, A. H., Song, S. K., Shoghi, K. I., Lau, K. S., Ju, T., Chen, K., Chatterjee, D., Hawkins, W. G., Zhang, H., Achilefu, S., Chheda, M. G., Oh, S. T., Gillanders, W. E., Chen, F., DeNardo, D. G., Fields, R. C. & Ding, L., Sep 2022, In: Nature Genetics. 54, 9, p. 1390-1405 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Scopus citations

Whole genome sequence analysis of blood lipid levels in >66,000 individuals

NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Dec 2022, In: Nature communications. 13, 1, 5995.

Research output: Contribution to journal › Article › peer-review

Open Access

2021

A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Oct 2021, In: Nature Genetics. 53, 10, p. 1504-1516 13 p.

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices

NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium & FinnGen, Dec 1 2021, In: Nature communications. 12, 1, 2182.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Scopus citations

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium

NHLBI SubPopulations and InteRmediate Outcome Measures In COPD Study (SPIROMICS), Dec 2021, In: Genome medicine. 13, 1, 66.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

Genome sequencing unveils a regulatory landscape of platelet reactivity

NHLBI Trans-Omics for Precision (TOPMed) Consortium, Dec 1 2021, In: Nature communications. 12, 1, 3626.

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus citations

Genomic Profiling of Lung Adenocarcinoma in Never-Smokers

Devarakonda, S., Li, Y., Martins Rodrigues, F., Sankararaman, S., Kadara, H., Goparaju, C., Lanc, I., Pepin, K., Waqar, S. N., Morgensztern, D., Ward, J., Masood, A., Fulton, R., Fulton, L., Gillette, M. A., Satpathy, S., Carr, S. A., Wistuba, I., Pass, H., Wilson, R. K., & 2 othersDing, L. & Govindan, R., Nov 20 2021, In: Journal of Clinical Oncology. 39, 33, p. 3747-3758 12 p.

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Feb 11 2021, In: Nature. 590, 7845, p. 290-299 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

369 Scopus citations

Variant-specific inflation factors for assessing population stratification at the phenotypic variance level

NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Dec 1 2021, In: Nature communications. 12, 1, 3506.

Research output: Contribution to journal › Article › peer-review

Open Access

Whole-genome association analyses of sleep-disordered breathing phenotypes in the NHLBI TOPMed program

TOPMed Sleep Working Group & NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Dec 2021, In: Genome medicine. 13, 1, 136.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

2020

Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale

NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium & TOPMed Lipids Working Group, Sep 1 2020, In: Nature Genetics. 52, 9, p. 969-983 15 p.

Research output: Contribution to journal › Article › peer-review

51 Scopus citations

Inherited causes of clonal haematopoiesis in 97,691 whole genomes

NHLBI Trans-Omics for Precision Medicine Consortium, Oct 29 2020, In: Nature. 586, 7831, p. 763-768 6 p.

Research output: Contribution to journal › Article › peer-review

184 Scopus citations

Mapping and characterization of structural variation in 17,795 human genomes

NHGRI Centers for Common Disease Genomics, Jul 2 2020, In: Nature. 583, 7814, p. 83-89 7 p.

Research output: Contribution to journal › Article › peer-review

80 Scopus citations

Pan-cancer analysis of whole genomes

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Feb 6 2020, In: Nature. 578, 7793, p. 82-93 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1038 Scopus citations

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 4748.

Research output: Contribution to journal › Article › peer-review

Open Access

18 Scopus citations

Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

Hughes, J. F., Skaletsky, H., Pyntikova, T., Koutseva, N., Raudsepp, T., Brown, L. G., Bellott, D. W., Cho, T. J., Dugan-Rocha, S., Khan, Z., Kremitzki, C., Fronick, C., Graves-Lindsay, T. A., Fulton, L., Warren, W. C., Wilson, R. K., Owens, E., Womack, J. E., Murphy, W. J., Muzny, D. M., & 4 othersWorley, K. C., Chowdhary, B. P., Gibbs, R. A. & Page, D. C., Nov 18 2020, In: Genome research. 31, 12, p. 1716-1726 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

13 Scopus citations

Sex differences in oncogenic mutational processes

PCAWG Tumour Subtypes and Clinical Translation & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 4330.

Research output: Contribution to journal › Article › peer-review

Open Access

33 Scopus citations

Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation

Alzheimer’s Disease Sequencing Project, Aug 1 2020, In: Molecular Psychiatry. 25, 8, p. 1859-1875 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

114 Scopus citations

2019

A rare missense variant of CASP7 is associated with familial late-onset Alzheimer's disease

Alzheimer's Disease Sequencing Project, Mar 2019, In: Alzheimer's and Dementia. 15, 3, p. 441-452 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

23 Scopus citations

Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma

National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Consortium, Dec 2019, In: CHEST. 156, 6, p. 1068-1079 12 p.

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

2018

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

The Cancer Genome Atlas Research Network, Apr 9 2018, In: Cancer Cell. 33, 4, p. 690-705.e9

Research output: Contribution to journal › Article › peer-review

Open Access

296 Scopus citations

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 400-416.e11

Research output: Contribution to journal › Article › peer-review

Open Access

1297 Scopus citations

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 386-399.e12

Research output: Contribution to journal › Article › peer-review

Open Access

148 Scopus citations

A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily

The Cancer Genome Atlas Research Network, Oct 24 2018, In: Cell Systems. 7, 4, p. 422-437.e7

Research output: Contribution to journal › Article › peer-review

Open Access

92 Scopus citations

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

The Cancer Genome Atlas Network, Apr 5 2018, In: Cell. 173, 2, p. 291-304.e6

Research output: Contribution to journal › Article › peer-review

Open Access

1028 Scopus citations

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

The Cancer Genome Atlas Research Network, Apr 9 2018, In: Cancer Cell. 33, 4, p. 721-735.e8

Research output: Contribution to journal › Article › peer-review

Open Access

268 Scopus citations

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

The Cancer Genome Atlas Research Network, Aug 13 2018, In: Cancer Cell. 34, 2, p. 211-224.e6

Research output: Contribution to journal › Article › peer-review

Open Access

381 Scopus citations

Comprehensive Characterization of Cancer Driver Genes and Mutations

The MC3 Working Group & The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 371-385.e18

Research output: Contribution to journal › Article › peer-review

Open Access

941 Scopus citations

Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer

The Cancer Genome Atlas Research Network, Oct 30 2018, In: Cell Reports. 25, 5, p. 1304-1317.e5

Research output: Contribution to journal › Article › peer-review

Open Access

188 Scopus citations

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

NHLBI TOPMed Lipids Working Group, Dec 1 2018, In: Nature communications. 9, 1, 3391.

Research output: Contribution to journal › Article › peer-review

Open Access

93 Scopus citations

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

Zekavat, S. M., Ruotsalainen, S., Handsaker, R. E., Alver, M., Bloom, J., Poterba, T., Seed, C., Ernst, J., Chaffin, M., Engreitz, J., Peloso, G. M., Manichaikul, A., Yang, C., Ryan, K. A., Fu, M., Johnson, W. C., Tsai, M., Budoff, M., Ramachandran, V. S., Cupples, L. A., & 323 othersRotter, J. I., Rich, S. S., Post, W., Mitchell, B. D., Correa, A., Metspalu, A., Wilson, J. G., Salomaa, V., Kellis, M., Daly, M. J., Neale, B. M., McCarroll, S., Surakka, I., Esko, T., Ganna, A., Ripatti, S., Kathiresan, S., Natarajan, P., Abe, N., Abecasis, G., Albert, C., Allred, N. P., Almasy, L., Alonso, A., Ament, S., Anderson, P., Anugu, P., Applebaum-Bowden, D., Arking, D., Arnett, D. K., Ashley-Koch, A., Aslibekyan, S., Assimes, T., Auer, P., Avramopoulos, D., Barnard, J., Barnes, K., Barr, R. G., Barron-Casella, E., Beaty, T., Becker, D., Becker, L., Beer, R., Begum, F., Beitelshees, A., Benjamin, E., Bezerra, M., Bielak, L., Bis, J., Blackwell, T., Blangero, J., Boerwinkle, E., Borecki, I., Bowler, R., Brody, J., Broeckel, U., Broome, J., Bunting, K., Burchard, E., Cardwell, J., Carty, C., Casaburi, R., Casella, J., Chang, C., Chasman, D., Chavan, S., Chen, B. J., Chen, W. M., Chen, Y. D. I., Cho, M., Choi, S. H., Chuang, L. M., Chung, M., Cornell, E., Crandall, C., Crapo, J., Curran, J., Curtis, J., Custer, B., Damcott, C., Darbar, D., Das, S., David, S., Davis, C., Daya, M., Andrade, M. D., Debaun, M., Deka, R., Demeo, D., Devine, S., Do, R., Duan, Q., Duggirala, R., Durda, P., Dutcher, S., Eaton, C., Ekunwe, L., Ellinor, P., Emery, L., Farber, C., Farnam, L., Fingerlin, T., Flickinger, M., Fornage, M., Franceschini, N., Fullerton, S. M., Fulton, L., Gabriel, S., Gan, W., Gao, Y., Gass, M., Gelb, B., Geng, X., Germer, S., Gignoux, C., Gladwin, M., Glahn, D., Gogarten, S., Gong, D. W., Goring, H., Gu, C. C., Guan, Y., Guo, X., Haessler, J., Hall, M., Harris, D., Hawley, N., He, J., Heavner, B., Heckbert, S., Hernandez, R., Herrington, D., Hersh, C., Hidalgo, B., Hixson, J., Hokanson, J., Hong, E., Hoth, K., Hsiung, C., Huston, H., Hwu, C. M., Irvin, M. R., Jackson, R., Jain, D., Jaquish, C., Jhun, M. A., Johnsen, J., Johnson, A., Johnston, R., Jones, K., Kang, H. M., Kaplan, R., Kardia, S., Kaufman, L., Kelly, S., Kenny, E., Kessler, M., Khan, A., Kinney, G., Konkle, B., Kooperberg, C., Kramer, H., Krauter, S., Lange, C., Lange, E., Lange, L., Laurie, C., Laurie, C., Leboff, M., Lee, S. S., Lee, W. J., Lefaive, J., Levine, D., Levy, D., Lewis, J., Li, Y., Lin, H., Lin, K. H., Liu, S., Liu, Y., Loos, R., Lubitz, S., Lunetta, K., Luo, J., Mahaney, M., Make, B., Manson, J. A., Margolin, L., Martin, L., Mathai, S., Mathias, R., McArdle, P., McDonald, M. L., McFarland, S., McGarvey, S., Mei, H., Meyers, D. A., Mikulla, J., Min, N., Minear, M., Minster, R. L., Montasser, M. E., Musani, S., Mwasongwe, S., Mychaleckyj, J. C., Nadkarni, G., Naik, R., Nekhai, S., Nickerson, D., North, K., O'connell, J., O'connor, T., Ochs-Balcom, H., Pankow, J., Papanicolaou, G., Parker, M., Parsa, A., Penchev, S., Peralta, J. M., Perez, M., Perry, J., Peters, U., Peyser, P., Phillips, L., Phillips, S., Pollin, T., Becker, J. P., Boorgula, M. P., Preuss, M., Prokopenko, D., Psaty, B., Qasba, P., Qiao, D., Qin, Z., Rafaels, N., Raffield, L., Rao, D. C., Rasmussen-Torvik, L., Ratan, A., Redline, S., Reed, R., Regan, E., Reiner, A., Rice, K., Roden, D., Roselli, C., Ruczinski, I., Russell, P., Ruuska, S., Sakornsakolpat, P., Salimi, S., Salzberg, S., Sandow, K., Sankaran, V., Scheller, C., Schmidt, E., Schwander, K., Schwartz, D., Sciurba, F., Seidman, C., Sheehan, V., Shetty, A., Shetty, A., Sheu, W. H. H., Shoemaker, M. B., Silver, B., Silverman, E., Smith, J., Smith, J., Smith, N., Smith, T., Smoller, S., Snively, B., Sofer, T., Sotoodehnia, N., Stilp, A., Streeten, E., Sung, Y. J., Sylvia, J., Szpiro, A., Sztalryd, C., Taliun, D., Tang, H., Taub, M., Taylor, K., Taylor, S., Telen, M., Thornton, T. A., Tinker, L., Tirschwell, D., Tiwari, H., Tracy, R., Vaidya, D., Vandehaar, P., Vrieze, S., Walker, T., Wallace, R., Walts, A., Wan, E., Wang, F. F., Watson, K., Weeks, D. E., Weir, B., Weiss, S., Weng, L. C., Willer, C., Williams, K., Williams, L. K., Wilson, C., Wong, Q., Xu, H., Yanek, L., Yang, I., Yang, R., Zaghloul, N., Zhang, Y., Zhao, S. X., Zhao, W., Zheng, X., Zhi, D., Zhou, X., Zody, M. & Zoellner, S., Dec 1 2018, In: Nature communications. 9, 1, 2606.

Research output: Contribution to journal › Article › peer-review

Open Access

54 Scopus citations

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

The Fusion Analysis Working Group & The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 227-238.e3

Research output: Contribution to journal › Article › peer-review

Open Access

272 Scopus citations

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 194-212.e6

Research output: Contribution to journal › Article › peer-review

Open Access

166 Scopus citations

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

The Cancer Genome Atlas Research Network, Apr 9 2018, In: Cancer Cell. 33, 4, p. 676-689.e3

Research output: Contribution to journal › Article › peer-review

Open Access

417 Scopus citations

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 239-254.e6

Research output: Contribution to journal › Article › peer-review

Open Access

482 Scopus citations

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 213-226.e3

Research output: Contribution to journal › Article › peer-review

Open Access

62 Scopus citations

lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer

The Cancer Genome Atlas Research Network, Apr 9 2018, In: Cancer Cell. 33, 4, p. 706-720.e9

Research output: Contribution to journal › Article › peer-review

Open Access

304 Scopus citations

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 172-180.e3

Research output: Contribution to journal › Article › peer-review

Open Access

77 Scopus citations

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 338-354.e15

Research output: Contribution to journal › Article › peer-review

Open Access

749 Scopus citations

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers

The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 255-269.e4

Research output: Contribution to journal › Article › peer-review

Open Access

126 Scopus citations

Oncogenic Signaling Pathways in The Cancer Genome Atlas

The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 321-337.e10

Research output: Contribution to journal › Article › peer-review

Open Access

1280 Scopus citations

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

The Cancer Genome Atlas Network, Mar 28 2018, In: Cell Systems. 6, 3, p. 282-300.e2

Research output: Contribution to journal › Article › peer-review

Open Access

183 Scopus citations

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 297-312.e12

Research output: Contribution to journal › Article › peer-review

Open Access

163 Scopus citations

Pathogenic Germline Variants in 10,389 Adult Cancers

The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 355-370.e14

Research output: Contribution to journal › Article › peer-review

Open Access

393 Scopus citations

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 305-320.e10

Research output: Contribution to journal › Article › peer-review

Open Access

173 Scopus citations

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

MC3 Working Group & The Cancer Genome Atlas Research Network, Mar 28 2018, In: Cell Systems. 6, 3, p. 271-281.e7

Research output: Contribution to journal › Article › peer-review

Open Access

345 Scopus citations

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 282-296.e4

Research output: Contribution to journal › Article › peer-review

Open Access

214 Scopus citations

Lucinda Antonacci-Fulton

Research output

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