Colorectal_organoids_and_tumour_tissue - EGA European Genome-Phenome Archive

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Dataset ID	Description	Technology	Samples
EGAD00001001447	Whole genome sequencing of single cell derived organoids from normal colon tissue and colorectal cancer.	HiSeq X Ten	19
EGAD00001015406	A paradigm of childhood cancers is that they have a low mutation burden, with some ostensibly bearing fewer mutations than the normal tissues from which they derive. We set out to resolve this paradox by examining paediatric renal cancers with exceptionally few mutations using high resolution, high depth sequencing approaches. We found that apparent hypomutation was the result of unusual clonal architecture due to a normal tissue-like mode of tumour evolution, raising the possibility that the mutation burden of some cancers has been systematically misjudged.	HiSeq X Ten Illumina NovaSeq 6000	-

Publications	Citations
Tissue-specific mutation accumulation in human adult stem cells during life. Blokzijl F, de Ligt J, Jager M, Sasselli V, Roerink S, Sasaki N, Huch M, Boymans S, Kuijk E, Prins P, Nijman IJ, Martincorena I, Mokry M, Wiegerinck CL, Middendorp S, Sato T, Schwank G, Nieuwenhuis EE, Verstegen MM, van der Laan LJ, de Jonge J, IJzermans JN, Vries RG, van de Wetering M, Stratton MR, Clevers H, Cuppen E, van Boxtel R. Nature 538: 2016 260-264	599
Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer. Drost J, van Boxtel R, Blokzijl F, Mizutani T, Sasaki N, Sasselli V, de Ligt J, Behjati S, Grolleman JE, van Wezel T, Nik-Zainal S, Kuiper RP, Cuppen E, Clevers H. Science 358: 2017 234-238	273
The mutational impact of culturing human pluripotent and adult stem cells. Kuijk E, Jager M, van der Roest B, Locati MD, Van Hoeck A, Korzelius J, Janssen R, Besselink N, Boymans S, van Boxtel R, Cuppen E. Nat Commun 11: 2020 2493	64
Human induced pluripotent stem cells display a similar mutation burden as embryonic pluripotent cells <i>in vivo</i>. Hasaart KAL, Manders F, Ubels J, Verheul M, van Roosmalen MJ, Groenen NM, Oka R, Kuijk E, Lopes SMCS, Boxtel RV. iScience 25: 2022 103736	6
Common anti-cancer therapies induce somatic mutations in stem cells of healthy tissue. Kuijk E, Kranenburg O, Cuppen E, Van Hoeck A. Nat Commun 13: 2022 5915	12
Mutation accumulation in mtDNA of cancers resembles mutagenesis in normal stem cells. Manders F, van Dinter J, van Boxtel R. iScience 25: 2022 105610	2
Patient-derived organoids (PDOs) and PDO-derived xenografts (PDOXs): New opportunities in establishing faithful pre-clinical cancer models. Wang E, Xiang K, Zhang Y, Wang XF. J Natl Cancer Cent 2: 2022 263-276	19
Recapitulating the adenoma-carcinoma sequence by selection of four spontaneous oncogenic mutations in mismatch-repair-deficient human colon organoids. Mizutani T, Boretto M, Lim S, Drost J, González DM, Oka R, Geurts MH, Begthel H, Korving J, van Es JH, van Boxtel R, Clevers H. Nat Cancer 5: 2024 1852-1867	0