Landscape of somatic mutations in 560 breast cancer whole-genome sequences.
Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GK, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van't Veer L, Tutt A, Knappskog S, Tan BK, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR.
Nature
534 :
2016
47-54
1228
Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage.
Stork CT, Bocek M, Crossley MP, Sollier J, Sanz LA, Chédin F, Swigut T, Cimprich KA.
Elife
5 :
2016
e17548
165
The 29.5 kb APOBEC3B Deletion Polymorphism Is Not Associated with Clinical Outcome of Breast Cancer.
Liu J, Sieuwerts AM, Look MP, van der Vlugt-Daane M, Meijer-van Gelder ME, Foekens JA, Hollestelle A, Martens JW.
PLoS One
11 :
2016
e0161731
9
Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.
Smid M, Rodríguez-González FG, Sieuwerts AM, Salgado R, Prager-Van der Smissen WJ, Vlugt-Daane MV, van Galen A, Nik-Zainal S, Staaf J, Brinkman AB, van de Vijver MJ, Richardson AL, Fatima A, Berentsen K, Butler A, Martin S, Davies HR, Debets R, Gelder ME, van Deurzen CH, MacGrogan G, Van den Eynden GG, Purdie C, Thompson AM, Caldas C, Span PN, Simpson PT, Lakhani SR, Van Laere S, Desmedt C, Ringnér M, Tommasi S, Eyford J, Broeks A, Vincent-Salomon A, Futreal PA, Knappskog S, King T, Thomas G, Viari A, Langerød A, Børresen-Dale AL, Birney E, Stunnenberg HG, Stratton M, Foekens JA, Martens JW.
Nat Commun
7 :
2016
12910
65
A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.
Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S.
Nat Genet
49 :
2017
341-348
58
HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
Davies H, Glodzik D, Morganella S, Yates LR, Staaf J, Zou X, Ramakrishna M, Martin S, Boyault S, Sieuwerts AM, Simpson PT, King TA, Raine K, Eyfjord JE, Kong G, Borg Å, Birney E, Stunnenberg HG, van de Vijver MJ, Børresen-Dale AL, Martens JW, Span PN, Lakhani SR, Vincent-Salomon A, Sotiriou C, Tutt A, Thompson AM, Van Laere S, Richardson AL, Viari A, Campbell PJ, Stratton MR, Nik-Zainal S.
Nat Med
23 :
2017
517-525
528
Somatic mutations reveal asymmetric cellular dynamics in the early human embryo.
Ju YS, Martincorena I, Gerstung M, Petljak M, Alexandrov LB, Rahbari R, Wedge DC, Davies HR, Ramakrishna M, Fullam A, Martin S, Alder C, Patel N, Gamble S, O'Meara S, Giri DD, Sauer T, Pinder SE, Purdie CA, Borg Å, Stunnenberg H, van de Vijver M, Tan BK, Caldas C, Tutt A, Ueno NT, van 't Veer LJ, Martens JW, Sotiriou C, Knappskog S, Span PN, Lakhani SR, Eyfjörd JE, Børresen-Dale AL, Richardson A, Thompson AM, Viari A, Hurles ME, Nik-Zainal S, Campbell PJ, Stratton MR.
Nature
543 :
2017
714-718
150
Systems modelling of the EGFR-PYK2-c-Met interaction network predicts and prioritizes synergistic drug combinations for triple-negative breast cancer.
Shin SY, Müller AK, Verma N, Lev S, Nguyen LK.
PLoS Comput Biol
14 :
2018
e1006192
13
Mitochondrial RNA Expression and Single Nucleotide Variants in Association with Clinical Parameters in Primary Breast Cancers.
Weerts MJA, Smid M, Foekens JA, Sleijfer S, Martens JWM.
Cancers (Basel)
10 :
2018
E500
5
The Identification and Interpretation of cis-Regulatory Noncoding Mutations in Cancer.
Patel MB, Wang J.
High Throughput
8 :
2018
E1
4
The circular RNome of primary breast cancer.
Smid M, Wilting SM, Uhr K, Rodríguez-González FG, de Weerd V, Prager-Van der Smissen WJC, van der Vlugt-Daane M, van Galen A, Nik-Zainal S, Butler A, Martin S, Davies HR, Staaf J, van de Vijver MJ, Richardson AL, MacGrogan G, Salgado R, van den Eynden GGGM, Purdie CA, Thompson AM, Caldas C, Span PN, Sweep FCGJ, Simpson PT, Lakhani SR, Van Laere S, Desmedt C, Paradiso A, Eyfjord J, Broeks A, Vincent-Salomon A, Futreal AP, Knappskog S, King T, Viari A, Børresen-Dale AL, Stunnenberg HG, Stratton M, Foekens JA, Sieuwerts AM, Martens JWM.
Genome Res
29 :
2019
356-366
64
Imprint of parity and age at first pregnancy on the genomic landscape of subsequent breast cancer.
Nguyen B, Venet D, Lambertini M, Desmedt C, Salgado R, Horlings HM, Rothé F, Sotiriou C.
Breast Cancer Res
21 :
2019
25
15
A practical guide for mutational signature analysis in hematological malignancies.
Maura F, Degasperi A, Nadeu F, Leongamornlert D, Davies H, Moore L, Royo R, Ziccheddu B, Puente XS, Avet-Loiseau H, Campbell PJ, Nik-Zainal S, Campo E, Munshi N, Bolli N.
Nat Commun
10 :
2019
2969
113
The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies.
Angus L, Smid M, Wilting SM, van Riet J, Van Hoeck A, Nguyen L, Nik-Zainal S, Steenbruggen TG, Tjan-Heijnen VCG, Labots M, van Riel JMGH, Bloemendal HJ, Steeghs N, Lolkema MP, Voest EE, van de Werken HJG, Jager A, Cuppen E, Sleijfer S, Martens JWM.
Nat Genet
51 :
2019
1450-1458
170
A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies.
Degasperi A, Amarante TD, Czarnecki J, Shooter S, Zou X, Glodzik D, Morganella S, Nanda AS, Badja C, Koh G, Momen SE, Georgakopoulos-Soares I, Dias JML, Young J, Memari Y, Davies H, Nik-Zainal S.
Nat Cancer
1 :
2020
249-263
129
DNA copy number motifs are strong and independent predictors of survival in breast cancer.
Pladsen AV, Nilsen G, Rueda OM, Aure MR, Borgan Ø, Liestøl K, Vitelli V, Frigessi A, Langerød A, Mathelier A, OSBREAC, Engebråten O, Kristensen V, Wedge DC, Van Loo P, Caldas C, Børresen-Dale AL, Russnes HG, Lingjærde OC.
Commun Biol
3 :
2020
153
9
Characterization of BRCA1-deficient premalignant tissues and cancers identifies Plekha5 as a tumor metastasis suppressor.
Liu J, Adhav R, Miao K, Su SM, Mo L, Chan UI, Zhang X, Xu J, Li J, Shu X, Zeng J, Zhang X, Lyu X, Pardeshi L, Tan K, Sun H, Wong KH, Deng C, Xu X.
Nat Commun
11 :
2020
4875
19
Revealing the impact of structural variants in multiple myeloma.
Rustad EH, Yellapantula VD, Glodzik D, Maclachlan KH, Diamond B, Boyle EM, Ashby C, Blaney P, Gundem G, Hultcrantz M, Leongamornlert D, Angelopoulos N, Agnelli L, Auclair D, Zhang Y, Dogan A, Bolli N, Papaemmanuil E, Anderson KC, Moreau P, Avet-Loiseau H, Munshi NC, Keats JJ, Campbell PJ, Morgan GJ, Landgren O, Maura F.
Blood Cancer Discov
1 :
2020
258-273
64
The Prognostic Role of MYC Structural Variants Identified by NGS and FISH in Multiple Myeloma.
Sharma N, Smadbeck JB, Abdallah N, Zepeda-Mendoza C, Binder M, Pearce KE, Asmann YW, Peterson JF, Ketterling RP, Greipp PT, Bergsagel PL, Rajkumar SV, Kumar SK, Baughn LB.
Clin Cancer Res
27 :
2021
5430-5439
17
Spatial immunophenotypes predict response to anti-PD1 treatment and capture distinct paths of T cell evasion in triple negative breast cancer.
Hammerl D, Martens JWM, Timmermans M, Smid M, Trapman-Jansen AM, Foekens R, Isaeva OI, Voorwerk L, Balcioglu HE, Wijers R, Nederlof I, Salgado R, Horlings H, Kok M, Debets R.
Nat Commun
12 :
2021
5668
67
Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data.
Hoogstrate Y, Komor MA, Böttcher R, van Riet J, van de Werken HJG, van Lieshout S, Hoffmann R, van den Broek E, Bolijn AS, Dits N, Sie D, van der Meer D, Pepers F, Bangma CH, van Leenders GJLH, Smid M, French PJ, Martens JWM, van Workum W, van der Spek PJ, Janssen B, Caldenhoven E, Rausch C, de Jong M, Stubbs AP, Meijer GA, Fijneman RJA, Jenster GW.
Gigascience
10 :
2021
giab080
8
Apolipoprotein B mRNA-Editing Catalytic Polypeptide-Like-Induced Protein Changes in Estrogen Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Breast Cancer Throughout Disease Progression.
Bos MK, Smid M, Sleijfer S, Martens JWM.
JCO Precis Oncol
6 :
2022
e2100190
4
Identifying Transcripts with Tandem Duplications from RNA-Sequencing Data to Predict BRCA1-Type Primary Breast Cancer.
Qu S, Martens JWM, Hollestelle A, Smid M.
Cancers (Basel)
14 :
2022
753
1
Substitution mutational signatures in whole-genome-sequenced cancers in the UK population.
Degasperi A, Zou X, Amarante TD, Martinez-Martinez A, Koh GCC, Dias JML, Heskin L, Chmelova L, Rinaldi G, Wang VYW, Nanda AS, Bernstein A, Momen SE, Young J, Perez-Gil D, Memari Y, Badja C, Shooter S, Czarnecki J, Brown MA, Davies HR, Genomics England Research Consortium, Nik-Zainal S.
Science
376 :
2022
science.abl9283
91
Breast cancer genomes from CHEK2 c.1100delC mutation carriers lack somatic TP53 mutations and display a unique structural variant size distribution profile.
Smid M, Schmidt MK, Prager-van der Smissen WJC, Ruigrok-Ritstier K, Schreurs MAC, Cornelissen S, Garcia AM, Broeks A, Timmermans AM, Trapman-Jansen AMAC, Collée JM, Adank MA, Hooning MJ, Martens JWM, Hollestelle A.
Breast Cancer Res
25 :
2023
53
4
Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers.
Setton J, Hadi K, Choo ZN, Kuchin KS, Tian H, Da Cruz Paula A, Rosiene J, Selenica P, Behr J, Yao X, Deshpande A, Sigouros M, Manohar J, Nauseef JT, Mosquera JM, Elemento O, Weigelt B, Riaz N, Reis-Filho JS, Powell SN, Imieliński M.
Nature
621 :
2023
129-137
3
Most large structural variants in cancer genomes can be detected without long reads.
Choo ZN, Behr JM, Deshpande A, Hadi K, Yao X, Tian H, Takai K, Zakusilo G, Rosiene J, Da Cruz Paula A, Weigelt B, Setton J, Riaz N, Powell SN, Busam K, Shoushtari AN, Ariyan C, Reis-Filho J, de Lange T, Imieliński M.
Nat Genet
55 :
2023
2139-2148
8
Integrative whole-genome and transcriptome analysis of HER2-amplified metastatic breast cancer.
Verschoor N, Smid M, Jager A, Sleijfer S, Wilting SM, Martens JWM.
Breast Cancer Res
25 :
2023
145
0
GIInger predicts homologous recombination deficiency and patient response to PARPi treatment from shallow genomic profiles.
Pozzorini C, Andre G, Coletta T, Buisson A, Bieler J, Ferrer L, Kempfer R, Saintigny P, Harlé A, Vacirca D, Barberis M, Gilson P, Roma C, Saitta A, Smith E, Consales Barras F, Ripol L, Fritzsche M, Marques AC, Alkodsi A, Marin R, Normanno N, Grimm C, Müllauer L, Harter P, Pignata S, Gonzalez-Martin A, Denison U, Fujiwara K, Vergote I, Colombo N, Willig A, Pujade-Lauraine E, Just PA, Ray-Coquard I, Xu Z.
Cell Rep Med
4 :
2023
101344
2
Association of ESR1 Germline Variants with TP53 Somatic Variants in Breast Tumors in a Genome-wide Study.
Tjader NP, Beer AJ, Ramroop J, Tai MC, Ping J, Gandhi T, Dauch C, Neuhausen SL, Ziv E, Sotelo N, Ghanekar S, Meadows O, Paredes M, Gillespie JL, Aeilts AM, Hampel H, Zheng W, Jia G, Hu Q, Wei L, Liu S, Ambrosone CB, Palmer JR, Carpten JD, Yao S, Stevens P, Ho WK, Pan JW, Fadda P, Huo D, Teo SH, McElroy JP, Toland AE.
Cancer Res Commun
4 :
2024
1597-1608
0
Prediction of homologous recombination deficiency identifies colorectal tumors sensitive to PARP inhibition.
Corti G, Buzo K, Berrino E, Miotto M, Aquilano MC, Lentini M, Bellomo SE, Lorenzato A, Bartolini A, Mauri G, Lazzari L, Russo M, Di Nicolantonio F, Siena S, Marsoni S, Marchiò C, Bardelli A, Arena S.
NPJ Precis Oncol
8 :
2024
231
0
