Genomics group publications

Penter L, Borji M, Nagler A, Lyu H, Lu WS, Cieri N, Maurer K, Oliveira G, Al’Khafaji AM, Garimella KV, Li S, Neuberg DS, Ritz J, Soiffer RJ, Garcia JS, Livak KJ, Wu CJ. Integrative genotyping of cancer and immune phenotypes by long-read sequencing. Nat Commun. 2024 Jan 2;15(1):32. doi: 10.1038/s41467-023-44137-7. PMID: 38167262; PMCID: PMC10762175.

Ten Hacken E, Gruber M, Hernández-Sánchez M, Hoffmann GB, Baranowski K, Redd RA, Clement K, Livak K, Wu CJ. Generation of mouse models carrying B cell restricted single or multiplexed loss-of-function mutations through CRISPR-Cas9 gene editing. STAR Protoc. 2023 Dec 15;4(4):102165. doi: 10.1016/j.xpro.2023.102165. Epub 2023 Sep 18. PMID: 37729058; PMCID: PMC10510057.

Penter L, Ten Hacken E, Southard J, Lareau CA, Ludwig LS, Li S, Neuberg DS, Livak KJ, Wu CJ. Mitochondrial DNA Mutations as Natural Barcodes for Lineage Tracing of Murine Tumor Models. Cancer Res. 2023 Mar 2;83(5):667-672. doi: 10.1158/0008-5472.CAN-22-0275. PMID: 36469010; PMCID: PMC9988704.

Ten Hacken E, Sewastianik T, Yin S, Hoffmann GB, Gruber M, Clement K, Penter L, Redd RA, Ruthen N, Hergalant S, Sholokhova A, Fell G, Parry EM, Broséus J, Guieze R, Lucas F, Hernández-Sánchez M, Baranowski K, Southard J, Joyal H, Billington L, Regis FFD, Witten E, Uduman M, Knisbacher BA, Li S, Lyu H, Vaisitti T, Deaglio S, Inghirami G, Feugier P, Stilgenbauer S, Tausch E, Davids MS, Getz G, Livak KJ, Bozic I, Neuberg DS, Carrasco RD, Wu CJ. In Vivo Modeling of CLL Transformation to Richter Syndrome Reveals Convergent Evolutionary Paths and Therapeutic Vulnerabilities. Blood Cancer Discov. 2023 Mar 1;4(2):150-169. doi: 10.1158/2643-3230.BCD-22-0082. PMID: 36468984; PMCID: PMC9975769.

Liu S, Iorgulescu JB, Li S, Borji M, Barrera-Lopez IA, Shanmugam V, Lyu H, Morriss JW, Garcia ZN, Murray E, Reardon DA, Yoon CH, Braun DA, Livak KJ, Wu CJ, Chen F. Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response. Immunity. 2022 Oct 11;55(10):1940-1952.e5. doi: 10.1016/j.immuni.2022.09.002. PMID: 36223726; PMCID: PMC9745674.

Song L, Ouyang Z, Cohen D, Cao Y, Altreuter J, Bai G, Hu X, Livak KJ, Li H, Tang M, Li B, Liu XS. Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies. Cancer Immunol Res. 2022 Jul 1;10(7):788-799. doi: 10.1158/2326-6066.CIR-21-0965. PMID: 35605261; PMCID: PMC9299271.

Gutierrez C, Al’Khafaji AM, Brenner E, Johnson KE, Gohil SH, Lin Z, Knisbacher BA, Durrett RE, Li S, Parvin S, Biran A, Zhang W, Rassenti L, Kipps TJ, Livak KJ, Neuberg D, Letai A, Getz G, Wu CJ, Brock A. Multifunctional barcoding with ClonMapper enables high-resolution study of clonal dynamics during tumor evolution and treatment. Nat Cancer. 2021 Jul;2(7):758-772. doi: 10.1038/s43018-021-00222-8. Epub 2021 Jul 12. PMID: 34939038; PMCID: PMC8691751.

Gohil SH, Iorgulescu JB, Braun DA, Keskin DB, Livak KJ. Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy. Nat Rev Clin Oncol. 2021 Apr;18(4):244-256. doi: 10.1038/s41571-020-00449-x. Epub 2020 Dec 4. PMID: 33277626; PMCID: PMC8415132.

Ten Hacken E, Clement K, Li S, Hernández-Sánchez M, Redd R, Wang S, Ruff D, Gruber M, Baranowski K, Jacob J, Flynn J, Jones KW, Neuberg D, Livak KJ, Pinello L, Wu CJ. High throughput single-cell detection of multiplex CRISPR-edited gene modifications. Genome Biol. 2020 Oct 20;21(1):266. doi: 10.1186/s13059-020-02174-1. PMID: 33081820; PMCID: PMC7574538.

Li S, Sun J, Allesøe R, Datta K, Bao Y, Oliveira G, Forman J, Jin R, Olsen LR, Keskin DB, Shukla SA, Wu CJ, Livak KJ. RNase H-dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis. Nat Protoc Aug;14(8):2571-2594 (2019).

Li S, Livak KJ. Targeted TCR amplification from single-cell cDNA libraries. Methods Mol Bio 2019;1979:197-224 (2019).

Keskin DB, Anandappa AJ, Sun J, Tirosh I, Mathewson ND, Li S, Oliveira G, Giobbie-Hurder A, Felt K, Gjini E, Shukla SA, Hu Z, Li L, Le PM, Allesoe RL, Richman A, Kowalczyk M, Abdelrahman S, Geduldig JE, Charbonneau A, Pelton K, Iorgulescu JB, Elagina L, Zhang W, Olive O, McCluskey C, Olsen LR, Stevens J, Lane WJ, Salazar AM, Daley H, Wen PY, Chiocca EA, Harden M, Lennon N, Gabriel S, Getz G, Lander ES, Regev A, Ritz J, Neuberg D, Rodig SJ, Ligon KL, Suva, ML, Wucherpfennig K, Hacohen N, Fritsch EF, Livak KJ, Ott PA, Wu CJ, Reardon DA. Personal Neoantigen-Targeting Vaccination for Glioblastoma (GBM) Generates Intra-Tumoral T Cell Responses. Nature Jan;565(7738):234-239 (2019).

Wang L, Livak KJ, Wu CJ. High-dimension single-cell analysis applied to cancer. Mol Aspects Med 59, 70-84. Epub 2017 Aug 30 (2018).

Hu Z, Anandappa AJ, Sun J, Kim J, Leet DE, Bozym DJ, Chen C, Williams L, Shukla SA, Zhang W, Tabbaa D, Steelman S, Olive O, Livak KJ, Kishi H, Muraguchi A, Guleria I, Stevens J, Lane WJ, Burkhardt UE, Fritsch EF, Neuberg D, Ott PA, Keskin DB, Hacohen N, Wu CJ. A cloning and expression system to probe T cell receptor specificity and assess functional avidity to neoantigens. Blood Jan (2018).

Wang L, Fan J, Francis JM, Georghiou G, Herger S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Dal Cin P, Bowden M, Kotliar D, Shukla SA, Brown JR, Neuberg D, Alessi DR, Zhang C-Z, Kharchenko PC, Livak KJ, Wu CJ. Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Res 27, 1300-1311 (2017).

Ott PA, Hu Z, Keskin DB, Shukla SA, Sun J, Bozym DJ, Zhang W, Luoma A, Giobbie-Hurder A, Peter L, Chen C, Olive O, Carter TA, Li S, Lieb DJ, Eisenhaure T, Gjini E, Stevens J, Lane WJ, Javeri I, Nellaiappan K, Salazar AM, Daley H, Seaman M, Buchbinder EI, Yoon CH, Harden M, Lennon N, Gabriel S, Rodig SJ, Barouch DH, Aster JC, Getz G, Wucherpfennig K, Neuberg D, Ritz J, Lander ES, Fritsch EF, Hacohen N, Wu CJ. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature 547(7662), 217-221 (2017).

Wang L, Brooks AN, Fan J, Wan Y, Gambe R, Li S, Hergert S, Yin S, Freeman SS, Fan L, Seiler M, Buonamici S, Smith PG, Chau KF, Cibulskis CL, Zhang W, Rassenti LZ, Ghia EM, Kipps TJ, Fernandes S, Bloch DB, Kotliar D, Landau DA, Shukla SA, Aster JC, Reed R, DeLuca DS, Brown JR, Neuberg D, Getz G, Livak KJ, Meyerson MM, Kharchenko PV, Wu CJ. Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. Cancer Cell 30, 750-763(2016).

Burger JA,  Landau DA, Taylor-Weiner A, Bozic I, Zhang H, Sarosiek K, Wang L, Stewart C, Fan J, Hoellenriegel J, Sivina M, Dubuc AM, Fraser C, Han Y, Li S, Livak KJ, Zou L, Wan Y, Konoplev S, Sougnez C, Brown JR, Abruzzo LV, Carter SL, Keating MJ, Davids MS, Wierda WG, Cibulskis K, Zenz T, Werner L, Dal Cin P, Kharchencko P, Neuberg D, Kantarjian H, Lander E, Gabriel S, O’Brien S, Letai A, Weitz D, Nowak MA, Getz G, Wu CJ. Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition. Nat Commun 7, 11589 (2016).

Landau DA, Clement K, Ziller MJ, Boyle P, Fan J, Gu H, Stevenson K, Sougnez C, Wang L, Li S, Kotliar D, Zhang W, Ghandi M, Garraway L, Fernandes SM, Livak KJ, Gabriel S, Gnirke A, Lander ES, Brown JR, Neuberg D, Kharchenko PV, Hacohen N, Getz G, Meissner A, Wu CJ. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell 26(6), 813-825 (2014).