My NCBI Sign In
Jump to: Authorized Access | Attribution | Authorized Requests

Study Description

The UC San Diego Chronic Lymphocytic Leukemia Study is designed to identify genetic, epigenetic, and transcriptional changes important for CLL. This data release consists of samples collected to 1) identify genomic changes associated with CLL progression using serially collected tumor samples; 2) characterize the transcriptional consequences of SF3B1 mutation through RNA-seq; and 3) characterize the expression profiles of ROR1+ vs. ROR1- tumors. The samples were collected from participants at the University of California, San Diego Moores Cancer Center and the data was generated at UC San Diego or in collaboration with the BC Cancer Agency Genome Sciences Centre.

  • Study Type: Tumor vs. Matched-Normal
  • Number of study subjects that have individual level data available through Authorized Access: 49

Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Study Inclusion/Exclusion Criteria

Patient samples were chosen from patients treated at University of California, San Diego from the CLL Research Consortium. Patients in the progression study (1) were required to have an available tumor sample with about 1 yr of diagnosis and 1 yr prior to treatment. At least one of the tumor samples was required to be 80% tumor cells, as evidenced by the % of the cells that were cd5+/cd19+. Samples in the SF3B1 study (2) were selected for the presence of a mutation in SF3B1, as detected by targeted sequencing. Controls for this study overlap with those in the progression study. Samples in the ROR1 study (3) were selected based on their surface expression of ROR1, as assayed by FACS. Samples were considered ROR1- if they expressed ROR1 on <20% of their cells. ROR1+ samples overlap with those in the progression study.

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Whole Genome Genotyping Illumina HumanOmni2.5-4v1_B 2450000 1056550
Whole Genome Genotyping Illumina HumanOmni2.5-8 (Omni2.5) 2379855 N/A
Methylation Array Illumina Infinium HumanMethylation450 BeadChip N/A N/A
Target Capture Illumina TruSeq Custom Amplicon N/A N/A
Targeted Sequencing Illumina MiSeq N/A N/A
Exome Capture Agilent SureSelect Human All Exon 50Mb Target Enrichment Kit N/A N/A
Exome Sequencing Illumina HiSeq 2000 N/A N/A
cDNA Synthesis Clontech SMART cDNA Library Construction Kit N/A N/A
RNA Sequencing Illumina HiSeq 2000 N/A N/A
Selected publications
Diseases/Traits Related to Study (MESH terms)
Links to Related Resources
Authorized Data Access Requests
Study Attribution