Exome sequencing reveals frequent inactivating mutations in ARID1A, ARID1B, ARID2 and ARID4A in microsatellite unstable colorectal cancer Tatiana Cajuso 1* , Ulrika A. H€ anninen 1* , Johanna Kondelin 1 , Alexandra E. Gylfe 1 , Tomas Tanskanen 1 , Riku Katainen 1 , Esa Pitk€ anen 1 , Heikki Ristolainen 1 , Eevi Kaasinen 1 , Minna Taipale 2,3 , Jussi Taipale 2,3 , Jan B€ ohm 4 , Laura Renkonen-Sinisalo 5 , Jukka-Pekka Mecklin 4 , Heikki J€ arvinen 5 , Sari Tuupanen 1 , Outi Kilpivaara 1 and Pia Vahteristo 1 1 Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland 2 Institute of Biomedicine, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland 3 Science for Life Center, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden 4 Department of Surgery, Jyv€ askyl€ a Central Hospital and University of Eastern Finland, Jyv€ askyl€ a, Finland 5 Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland ARID1A has been identified as a novel tumor suppressor gene in ovarian cancer and subsequently in various other tumor types. ARID1A belongs to the ARID domain containing gene family, which comprises of 15 genes involved, for example, in transcriptional regulation, proliferation and chromatin remodeling. In this study, we used exome sequencing data to analyze the mutation frequency of all the ARID domain containing genes in 25 microsatellite unstable (MSI) colorectal cancers (CRCs) as a first systematic effort to characterize the mutation pattern of the whole ARID gene family. Genes which fulfilled the selec- tion criteria in this discovery set (mutations in at least 4/25 [16%] samples, including at least one nonsense or splice site mutation) were chosen for further analysis in an independent validation set of 21 MSI CRCs. We found that in addition to ARID1A, which was mutated in 39% of the tumors (18/46), also ARID1B (13%, 6/46), ARID2 (13%, 6/46) and ARID4A (20%, 9/46) were frequently mutated. In all these genes, the mutations were distributed along the entire length of the gene, thus distinguishing them from typical MSI target genes previously described. Our results indicate that in addition to ARID1A, other members of the ARID gene family may play a role in MSI CRC. Colorectal cancer (CRC) ranks among the three most com- mon cancers in industrialized countries. The annual global incidence is around 1 million with a nearly 50% mortality rate. 1 There are two genetically and clinically distinct sub- types of CRCs; tumors showing chromosome instability (CIN) and those exhibiting microsatellite instability (MSI). The majority of the tumors display CIN and approximately 15% are MSI. In MSI tumors, the mismatch repair (MMR) system, which normally corrects the numerous errors that occur during DNA replication, is defective. This results in a large number of small insertions and deletions in repetitive areas around the genome, especially in short tandem repeats called microsatellites. The overall mutation rate in MSI CRC has been estimated to be approximately tenfold when com- pared to that in microsatellite stable (MSS) CRC. 2,3 The high background mutation rate makes MSI tumors challenging to study as it is difficult to distinguish true driver mutations from passenger mutations. To date, MSI target genes have mostly been recognized through searches focused on genes with a repetitive tract in their coding region. When these repeats are affected by small insertions and deletions, it typi- cally leads to inactivation of tumor suppressors by shifting the reading frame and thus generating a premature stop codon. Only a few oncogenic changes with a confirmed role Key words: colorectal cancer, ARID1A, ARID1B, ARID2, ARID4A Abbreviations: ARID: AT rich interactive domain; BWA: Burrow- Wheeler aligner; CIN: chromosome instability; CRC: colorectal cancer; dbSNP: database of single nucleotide polymorphisms; GATK: genome analysis toolkit; MMR: mismatch repair; MSI: microsatellite instability; MSS: microsatellite stable; PCR: polymer- ase chain reaction; pRB: retinoblastoma protein; SNV: single nucleotide variant; SWI/SNF: switch/sucrose nonfermentable; VEP: variant effect predictor *T.C. and U.A.H. contributed equally to this work Grant sponsor: Academy of Finland (Finnish Centre of Excellence Programs 2006–2011 and 2012–2017); Grant number: 260370 (P.V.), 137680 (O.K.) and 218053 (M.T.); Grant sponsors: University of Helsinki (post-doctoral grant for S.T.), EU FP7 project SYSCOL, the Finnish Cancer Society, the Sigrid Juselius Foundation, the Finnish Medical Society Duodecim, the Cancer Foundation of Irja Karvonen and the Foundation of Jalmari and Rauha Ahokas. DOI: 10.1002/ijc.28705 History: Received 16 Sep 2013; Accepted 12 Dec 2013; Online 31 Dec 2013 Correspondence to: Pia Vahteristo, Department of Medical Genetics, Biomedicum Helsinki, P.O. Box 63 (Haartmaninkatu 8), FIN-00014 University of Helsinki, Finland, Tel.: 1358-9-19125600, Fax: 1358-9-19125105, E-mail: pia.vahteristo@helsinki.fi Cancer Genetics Int. J. Cancer: 135, 611–623 (2014) V C 2013 UICC International Journal of Cancer IJC