Integrated Genomic Analysis of Chronic Lymphocytic Leukaemia

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
EGAD00001001443	RNASeq sequencing. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired-end mode with a read length of 2 × 76 bp. We generated more than 20 million paired-end reads for each sample in a fraction of a sequencing lane on HiSeq2000 (Illumina Inc.) following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files.	Illumina Genome Analyzer II	199
EGAD00001001464	Exome Sequencing. 3 μg of genomic DNA from each sample were sheared and used for the construction of a paired-end sequencing library as described in the paired-end sequencing sample preparation protocol provided by Illumina41. Enrichment of exonic sequences was then performed for each library using either the Sure Select Human All Exon 50 Mb or All Exon+UTRs v4 kits following the manufacturer’s instructions (Agilent Technologies). Exon-enriched DNA was pulled down by magnetic beads coated with streptavidin (Invitrogen), followed by washing, elution and 18 additional cycles of amplification of the captured library. Enriched libraries were sequenced (2 × 76 bp) in one lane of an Illumina GAIIx sequencer or in two lanes of a HiSeq2000 when using pools of eight samples.		-
EGAD00001001466	Whole Genome sequencing. 2 μg of genomic DNA from each sample was used for the construction of two short-insert paired-end sequencing libraries. Both types of libraries were sequenced in paired-end mode on Illumina GAIIx (2 × 151 bp) using Sequencing kit v4 or Illumina HiSeq2000 (2x101 bp) using TruSeq SBS Kit v3.		-
EGAD00010000875	CLL Expression Array	Affymetrix U219	-

Publications	Citations
Non-coding recurrent mutations in chronic lymphocytic leukaemia. Puente XS, Beà S, Valdés-Mas R, Villamor N, Gutiérrez-Abril J, Martín-Subero JI, Munar M, Rubio-Pérez C, Jares P, Aymerich M, Baumann T, Beekman R, Belver L, Carrio A, Castellano G, Clot G, Colado E, Colomer D, Costa D, Delgado J, Enjuanes A, Estivill X, Ferrando AA, Gelpí JL, González B, González S, González M, Gut M, Hernández-Rivas JM, López-Guerra M, Martín-García D, Navarro A, Nicolás P, Orozco M, Payer ÁR, Pinyol M, Pisano DG, Puente DA, Queirós AC, Quesada V, Romeo-Casabona CM, Royo C, Royo R, Rozman M, Russiñol N, Salaverría I, Stamatopoulos K, Stunnenberg HG, Tamborero D, Terol MJ, Valencia A, López-Bigas N, Torrents D, Gut I, López-Guillermo A, López-Otín C, Campo E. Nature 526: 2015 519-524	529
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
Time to Treatment Prediction in Chronic Lymphocytic Leukemia Based on New Transcriptional Patterns. Mosquera Orgueira A, Antelo Rodríguez B, Alonso Vence N, Bendaña López Á, Díaz Arias JÁ, Díaz Varela N, González Pérez MS, Pérez Encinas MM, Bello López JL. Front Oncol 9: 2019 79	5
The association of germline variants with chronic lymphocytic leukemia outcome suggests the implication of novel genes and pathways in clinical evolution. Mosquera Orgueira A, Antelo Rodríguez B, Alonso Vence N, Díaz Arias JÁ, Díaz Varela N, Pérez Encinas MM, Allegue Toscano C, Goiricelaya Seco EM, Carracedo Álvarez Á, Bello López JL. BMC Cancer 19: 2019 515	6
New Recurrent Structural Aberrations in the Genome of Chronic Lymphocytic Leukemia Based on Exome-Sequencing Data. Mosquera Orgueira A, Antelo Rodríguez B, Díaz Arias JÁ, González Pérez MS, Bello López JL. Front Genet 10: 2019 854	5
A Three-Gene Expression Signature Identifies a Cluster of Patients with Short Survival in Chronic Lymphocytic Leukemia. Mosquera Orgueira A, Antelo Rodríguez B, Díaz Arias JÁ, Díaz Varela N, Bello López JL. J Oncol 2019: 2019 9453539	6
Novel Mutation Hotspots within Non-Coding Regulatory Regions of the Chronic Lymphocytic Leukemia Genome. Mosquera Orgueira A, Rodríguez Antelo B, Díaz Arias JÁ, Díaz Varela N, Alonso Vence N, González Pérez MS, Bello López JL. Sci Rep 10: 2020 2407	1
IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms. Nadeu F, Mas-de-Les-Valls R, Navarro A, Royo R, Martín S, Villamor N, Suárez-Cisneros H, Mares R, Lu J, Enjuanes A, Rivas-Delgado A, Aymerich M, Baumann T, Colomer D, Delgado J, Morin RD, Zenz T, Puente XS, Campbell PJ, Beà S, Maura F, Campo E. Nat Commun 11: 2020 3390	25
Molecular Basis and Role of Siglec-7 Ligand Expression on Chronic Lymphocytic Leukemia B Cells. Chang LY, Liang SY, Lu SC, Tseng HC, Tsai HY, Tang CJ, Sugata M, Chen YJ, Chen YJ, Wu SJ, Lin KI, Khoo KH, Angata T. Front Immunol 13: 2022 840388	15