CLL Genome

Description: Description from EGA:

"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"

Subject(s)

Leukemia, Lymphocytic, Chronic, B-Cell

Mutation/genetics

RNA Splicing Factors

Whole Genome Sequencing

OncoTree Cancer Type(s)

Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma

Access via EGA

Accession #: EGAS00000000092
Access Restrictions: Application Required
Access Instructions: It is possible to submit an access request to data stored at the EGA. The DAC assigned to the study will assess the request and, if approved, grant access to the data. Requesters must provide sufficient justification for your request and comply with the intended data usage in order to get access to it.

Each dataset is covered by a Data Access Agreement (DAA) that defines the terms and conditions of use for the specified datasets. The DAA is created and provided by the DAC, and must be signed by the individual requesting access to the given dataset.
Associated Publications: Rustad E, Nadeu F, Angelopoulos N, Ziccheddu B, Bolli N, Puente X, Campo E, Landgren O, Maura F. mmsig: A fitting approach to accurately identify somatic mutational signatures in hematological malignancies. Communications Biology. 2021; 4(1):424.

Puente XS, Pinyol M, Quesada V, et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature. 2011 Jun 5;475(7354):101-5. PMID: 21642962; PMCID: PMC3322590.

Valdés-Mas R, Bea S, Puente DA, López-Otín C, Puente XS. Estimation of copy number alterations from exome sequencing data. PLoS One. 2012;7(12):e51422. Epub 2012 Dec 19. PMID: 23284693; PMCID: PMC3526607.

Garcia-Alonso L, Jiménez-Almazán J, Carbonell-Caballero J, Vela-Boza A, Santoyo-López J, Antiñolo G, Dopazo J. The role of the interactome in the maintenance of deleterious variability in human populations. Mol Syst Biol. 2014 Sep 26;10(9):752. PMID: 25261458; PMCID: PMC4299661.

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. Genetic Predisposition to Chronic Lymphocytic Leukemia Is Mediated by a BMF Super-Enhancer Polymorphism. Cell Rep. 2016 Aug 23;16(8):2061-2067. Epub 2016 Aug 11. PMID: 27524613; PMCID: PMC4999417.

Muyas F, Bosio M, Puig A, Susak H, Domènech L, Escaramis G, Zapata L, Demidov G, Estivill X, Rabionet R, Ossowski S. Allele balance bias identifies systematic genotyping errors and false disease associations. Hum Mutat. 2019 Jan;40(1):115-126. Epub 2018 Nov 23. PMID: 30353964; PMCID: PMC6587442.

Patel MB, Wang J. The Identification and Interpretation of cis-Regulatory Noncoding Mutations in Cancer. High Throughput. 2018 Dec 20;8(1):1. PMID: 30577431; PMCID: PMC6473693.

Sahraeian SME, Liu R, Lau B, Podesta K, Mohiyuddin M, Lam HYK. Deep convolutional neural networks for accurate somatic mutation detection. Nat Commun. 2019 Mar 4;10(1):1041. PMID: 30833567; PMCID: PMC6399298.

Maura F, Degasperi A, Nadeu F, Leongamornlert D, Davies H, Moore L, Royo R, Ziccheddu B, Puente X, Avet-Loiseau H, Campbell P, Nik-Zainal S, Campo E, Munshi N, Bolli N. A practical guide for mutational signature analysis in hematological malignancies. Nature Communications. 2019; 10(1):2969.

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. Insight into genetic predisposition to chronic lymphocytic leukemia from integrative epigenomics. Nat Commun. 2019 Aug 9;10(1):3615. PMID: 31399598; PMCID: PMC6689100.

Muyas F, Zapata L, Guigó R, Ossowski S. The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues. Genome Med. 2020 May 27;12(1):49. PMID: 32460841; PMCID: PMC7254727.

Susak H, Serra-Saurina L, Demidov G, Rabionet R, Domènech L, Bosio M, Muyas F, Estivill X, Escaramís G, Ossowski S. Efficient and flexible Integration of variant characteristics in rare variant association studies using integrated nested Laplace approximation. PLoS Comput Biol. 2021 Feb 19;17(2):e1007784. PMID: 33606672; PMCID: PMC7928502.

Duran-Ferrer M, Clot G, Nadeu F, et al. The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome. Nat Cancer. 2020 Nov;1(11):1066-1081. Epub 2020 Nov 2. PMID: 34079956; PMCID: PMC8168619.

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. PanCancer analysis of somatic mutations in repetitive regions reveals recurrent mutations in snRNA U2. NPJ Genom Med. 2022 Mar 14;7(1):19. PMID: 35288589; PMCID: PMC8921233.

Knisbacher B, Lin Z, Hahn C, et al. Molecular map of chronic lymphocytic leukemia and its impact on outcome. Nature Genetics. 2022; 54(11):1664-1674.

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. SF3B1 mutation-mediated sensitization to H3B-8800 splicing inhibitor in chronic lymphocytic leukemia. Life Sci Alliance. 2023 Aug 10;6(11):e202301955. PMID: 37562845; PMCID: PMC10415613.
Equipment Used: Affymetrix GeneChip Human Genome U133 plus 2.0
Benefits of the first and most comprehensive whole human genome expression array

Affymetrix snp 6.0
For performing association studies with large sample sizes in both initial scan and replication phases

Illumina Genome Analyzer IIx
Dataset Format(s): FASTQ, CEL, gzip, TXT
Dataset Size: 2.36 TB

Data Catalog Record Updated: 2024-05-30