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.

• Äyräväinen A, Pasanen A, Ahvenainen T, Heikkinen T, Pakarinen P, Härkki P, Vahteristo P. Systematic molecular and clinical analysis of uterine leiomyomas from fertile-aged women undergoing myomectomy. Human Reproduction, 2020, deaa187:1–17.