Applied Tumor Genomics (ATG)

Program Director

Lauri Aaltonen
Tumor Genomics
Biomedicum 1 Haartmaninkatu 8
00014 University of Helsinki
tel. 02941 25595
lauri.aaltonen@helsinki.fi

Applied Tumor Genomics Research Program aims to advance the understanding of the genetic and environmental signals that lead to neoplasia: improving the knowledge of the function of the coding and noncoding genome, exploiting the public data, and creating and analyzing new key data sets from highly selected patient populations.

Principal Investigators

Ralf Bützow
Outi Kilpivaara - Hematological Genetics
Anna Lepistö
Sirpa Leppä - Lymphoma Biology and Survival
Outi Monni - Oncogenomics
Ari Ristimäki - Gastrointestinal Tumorigenesis
Biswajyoti Sahu - Enhancer Biology
Jussi Taipale
Pia Vahteristo - Gynecological Tumor Genomics
Esa Pitkänen - Machine Learning in Biomedicine

Clinical Associated Researchers

Oskari Heikinheimo
Minna Pöyhönen
Laura Renkonen-Sinisalo
Ulla Wartiovaara-Kautto

Events

ATG Symposium 3^rd of June: "Genomic Basis of Cancer"

Seminars

CancerBio Progress report seminar series

Key Publications from ATG

Kaasinen E, Kuismin O, Rajamäki K, Ristolainen H, Aavikko M, Kondelin J, Saarinen S, Berta D, Katainen R, Hirvonen E, Karhu A, Taira A, Tanskanen T, Alkodsi A, Taipale M, Morgunova E, Franssila K, Lehtonen R, Mäkinen M, Aittomäki K, Palotie A, Kurki M, Pietiläinen O, Hilpert M, Saarentaus E, Niinimäki J, Junttila J, Kaikkonen K, Vahteristo P, Skoda R, Seppänen M, Eklund K, Taipale J, Kilpivaara O* & Aaltonen LA*. Impact of Constitutional TET2 Haploinsufficiency on Molecular and Clinical Phenotype in Humans. Nature Communications, 2019, 10:1252. *equal contribution
Cajuso T, Sulo P, Tanskanen T, Katainen R, Taira A, Hänninen U, Kondelin J, Forsström L, Välimäki N, Aavikko M, Kaasinen E, Ristimäki, Koskensalo S, Lepistö A, Renkonen-Sinisalo L, Seppälä T, Kuopio T, Böhm J, Mecklin J-P, Kilpivaara O, Pitkänen E, Palin K & Aaltonen LA. Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival. Nature Communications, 2019, 10:4022.
Olkinuora A, Nieminen TT, Mårtensson E, Rohlin A, Ristimäki A, Koskenvuo L, Lepistö A; Swedish Extended Genetic Analysis of Colorectal Neoplasia (SWEN) Study Group, Gebre-Medhin S, Nordling M, Peltomäki P. Biallelic germline nonsense variant of MLH3 underlies polyposis predisposition. Genet Med, 2019, 21:1868-1873.
Tuomainen K, Al-Samadi A, Potdar S, Turunen L, Turunen M, Karhemo PR, Bergman P, Risteli M, Åström P, Tiikkaja R, Grenman R, Wennerberg K, Monni O, Salo T. Human Tumor-Derived Matrix Improves the Predictability of Head and Neck Cancer Drug Testing. Cancers (Basel), 2019, 12(1), pii: E92.
Karjalainen EK, Renkonen-Sinisalo L, Mustonen HK, Lepistö AH. Morbidity related to diverting ileostomy after restorative proctocolectomy in patients with ulcerative colitis. Colorectal Disease, 2019, 21(6):671-678.
Douglas S.P.M, Siipola P, Kovanen P.E., Pyörälä M, Kakko S, Savolainen E-R, Salmenniemi U, Orte K, Kytölä S, Pitkänen E, Porkka K, Kilpivaara O,* Wartiovaara-Kautto U*. ERCC6L2 defines a novel entity within inherited acute myeloid leukemia. Blood, 2019, 133(25):2724-2728. *equal contribution
Hirvonen EAM, Peuhkuri S, Norberg A, Degerman S, Hannula-Jouppi K, Välimaa H, Kilpivaara O*, Wartiovaara-Kautto U*. Characterization of an X-chromosome-linked telomere biology disorder in females with DKC1 mutation. Leukemia, 2019, 33(1):275-278. *equal contribution
Leivonen S-K, Pollari M, Brück O, Pellinen T, Autio M, Vähämurto P, Karjalainen-Lindsberg M-L, Mannisto S, Kellokumpu-Lehtinen P-L, Mustjoki S, Leppä S. T-cell inflamed tumor microenvironment predicts favorable prognosis in primary testicular lymphoma. Haematologica, 2019, 104(2):338-346.
Göös H, Fogarty C.L, Sahu B, Plagnol V, Rajamäki K, Nurmi K, Liu X, Einarsdottir E, Jouppila A, Pettersson T, Vihinen H, Krjutskov K, Saavalainen P, Järvinen A, Muurinen M, Greco D, Scala G, Curtis J, Nordström D, Flaumenhaft R, Vaarala O, Kovanen P.E, Keskitalo S, Ranki A, Kere J, Lehto M, Notarangelo L.D, Nejentsev S, Eklund K.K, Varjosalo M, Taipale J, Seppanen M.R. J. / Gain-of-function CEBPE mutation causes noncanonical autoinflammatory inflammasomopathy. Journal of Allergy and Clinical Immunology. 2019, 144(5):1364-1376.
Pasanen A, Ahvenainen T, Pellinen T, Vahteristo P, Loukovaara M, Bützow R. PD-L1 expression in endometrial carcinoma cells and intratumoral immune cells: differences across histologic and TCGA-based molecular subgroups. American Journal of Surgical Pathology, 2020, 44(2):174-181.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (a large number of contributors, including members from the Aaltonen & Pitkänen group). Pan-cancer analysis of whole genomes. Nature, 2020, 578:82-93.
Quist-Paulsen P, Toft N , Heyman M, Abrahamsson J, Griškevičius J, Hallböök H, Jónsson ÓG, Palk K, Pruunsild K, Vaitkeviciene G, Vettenranta K, Åsberg A1, Frandsen TL, Opdahl S, Marquart HV, Madsen HO, Overgaard UM, Wartiovaara-Kautto U, Schmiegelow K. T cell acute lymphoblastic leukemia in patients 1-45 years treated with the pediatric NOPHO ALL2008 protocol. Leukemia, 2020, 34(2):347-357.