CLL Genome

The Chronic Lymphocytic Leukemia (CLL) Genome Project aims to identify genetic alterations involved in the development and progression of the CLL, which are still unknown, with the objective of generating a comprehensive catalogue of genetic alterations in 500 independent tumours. The CLL Genome Project, as a contributing member of the International Cancer Genome Consortium (ICGC), has the purposes of creating diagnostic tools, discovering therapeutic targets and developing new strategies that will allow a customized therapy for CLL in order to make it more precise and effective. This study consists of two datasets. EGAD00001000023 described in the Nature paper (2011), Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia, and the dataset EGA00001000044 & & EGAD00001000083 described in the Nature (2011) paper, Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia.Additional data generated within the ICGC-CLL genome project can be found in studies EGAS00001000374 and EGAS00001001306

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

6 Datasets 16 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001000023	Recurrent Somatic Mutations in CLL	Illumina Genome Analyzer IIx	11
EGAD00001000044	Recurrent Somatic Mutations in CLL	Illumina Genome Analyzer IIx	212
EGAD00001000083	Recurrent Somatic Mutations in CLL	Illumina Genome Analyzer II Illumina Genome Analyzer IIx	61
EGAD00010000238	CLL Expression array	Affymetrix GeneChip Human Genome U133 plus 2.0	64
EGAD00010000280	CLL Expression array	Affymetrix snp 6.0	4
EGAD00010000470	CLL Expression Array	GPL570	20

Publications	Citations
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Puente XS, Pinyol M, Quesada V, Conde L, Ordóñez GR, Villamor N, Escaramis G, Jares P, Beà S, González-Díaz M, Bassaganyas L, Baumann T, Juan M, López-Guerra M, Colomer D, Tubío JM, López C, Navarro A, Tornador C, Aymerich M, Rozman M, Hernández JM, Puente DA, Freije JM, Velasco G, Gutiérrez-Fernández A, Costa D, Carrió A, Guijarro S, Enjuanes A, Hernández L, Yagüe J, Nicolás P, Romeo-Casabona CM, Himmelbauer H, Castillo E, Dohm JC, de Sanjosé S, Piris MA, de Alava E, San Miguel J, Royo R, Gelpí JL, Torrents D, Orozco M, Pisano DG, Valencia A, Guigó R, Bayés M, Heath S, Gut M, Klatt P, Marshall J, Raine K, Stebbings LA, Futreal PA, Stratton MR, Campbell PJ, Gut I, López-Guillermo A, Estivill X, Montserrat E, López-Otín C, Campo E. Nature 475: 2011 101-105	980
Estimation of copy number alterations from exome sequencing data. Valdés-Mas R, Bea S, Puente DA, López-Otín C, Puente XS. PLoS One 7: 2012 e51422	16
The role of the interactome in the maintenance of deleterious variability in human populations. Garcia-Alonso L, Jiménez-Almazán J, Carbonell-Caballero J, Vela-Boza A, Santoyo-López J, Antiñolo G, Dopazo J. Mol Syst Biol 10: 2014 752	22
Genetic Predisposition to Chronic Lymphocytic Leukemia Is Mediated by a BMF Super-Enhancer Polymorphism. Kandaswamy R, Sava GP, Speedy HE, Beà S, Martín-Subero JI, Studd JB, Migliorini G, Law PJ, Puente XS, Martín-García D, Salaverria I, Gutiérrez-Abril J, López-Otín C, Catovsky D, Allan JM, Campo E, Houlston RS. Cell Rep 16: 2016 2061-2067	38
Allele balance bias identifies systematic genotyping errors and false disease associations. Muyas F, Bosio M, Puig A, Susak H, Domènech L, Escaramis G, Zapata L, Demidov G, Estivill X, Rabionet R, Ossowski S. Hum Mutat 40: 2019 115-126	15
The Identification and Interpretation of cis-Regulatory Noncoding Mutations in Cancer. Patel MB, Wang J. High Throughput 8: 2018 E1	4
Deep convolutional neural networks for accurate somatic mutation detection. Sahraeian SME, Liu R, Lau B, Podesta K, Mohiyuddin M, Lam HYK. Nat Commun 10: 2019 1041	48
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	115
Insight into genetic predisposition to chronic lymphocytic leukemia from integrative epigenomics. Speedy HE, Beekman R, Chapaprieta V, Orlando G, Law PJ, Martín-García D, Gutiérrez-Abril J, Catovsky D, Beà S, Clot G, Puiggròs M, Torrents D, Puente XS, Allan JM, López-Otín C, Campo E, Houlston RS, Martín-Subero JI. Nat Commun 10: 2019 3615	19
The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues. Muyas F, Zapata L, Guigó R, Ossowski S. Genome Med 12: 2020 49	13
Efficient and flexible Integration of variant characteristics in rare variant association studies using integrated nested Laplace approximation. Susak H, Serra-Saurina L, Demidov G, Rabionet R, Domènech L, Bosio M, Muyas F, Estivill X, Escaramís G, Ossowski S. PLoS Comput Biol 17: 2021 e1007784	3
mmsig: a fitting approach to accurately identify somatic mutational signatures in hematological malignancies. Rustad EH, Nadeu F, Angelopoulos N, Ziccheddu B, Bolli N, Puente XS, Campo E, Landgren O, Maura F. Commun Biol 4: 2021 424	20
The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome. Duran-Ferrer M, Clot G, Nadeu F, Beekman R, Baumann T, Nordlund J, Marincevic-Zuniga Y, Lönnerholm G, Rivas-Delgado A, Martín S, Ordoñez R, Castellano G, Kulis M, Queirós AC, Lee ST, Wiemels J, Royo R, Puiggrós M, Lu J, Giné E, Beà S, Jares P, Agirre X, Prosper F, López-Otín C, Puente XS, Oakes CC, Zenz T, Delgado J, López-Guillermo A, Campo E, Martín-Subero JI. Nat Cancer 1: 2020 1066-1081	38
PanCancer analysis of somatic mutations in repetitive regions reveals recurrent mutations in snRNA U2. Bousquets-Muñoz P, Díaz-Navarro A, Nadeu F, Sánchez-Pitiot A, López-Tamargo S, Shuai S, Balbín M, Tubio JMC, Beà S, Martin-Subero JI, Gutiérrez-Fernández A, Stein LD, Campo E, Puente XS. NPJ Genom Med 7: 2022 19	5
Molecular map of chronic lymphocytic leukemia and its impact on outcome. Knisbacher BA, Lin Z, Hahn CK, Nadeu F, Duran-Ferrer M, Stevenson KE, Tausch E, Delgado J, Barbera-Mourelle A, Taylor-Weiner A, Bousquets-Muñoz P, Diaz-Navarro A, Dunford A, Anand S, Kretzmer H, Gutierrez-Abril J, López-Tamargo S, Fernandes SM, Sun C, Sivina M, Rassenti LZ, Schneider C, Li S, Parida L, Meissner A, Aguet F, Burger JA, Wiestner A, Kipps TJ, Brown JR, Hallek M, Stewart C, Neuberg DS, Martín-Subero JI, Puente XS, Stilgenbauer S, Wu CJ, Campo E, Getz G. Nat Genet 54: 2022 1664-1674	48
<i>SF3B1</i> mutation-mediated sensitization to H3B-8800 splicing inhibitor in chronic lymphocytic leukemia. López-Oreja I, Gohr A, Playa-Albinyana H, Giró A, Arenas F, Higashi M, Tripathi R, López-Guerra M, Irimia M, Aymerich M, Valcárcel J, Bonnal S, Colomer D. Life Sci Alliance 6: 2023 e202301955	5