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Series GSE117692 Query DataSets for GSE117692
Status Public on Mar 02, 2020
Title Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing (ALL_450k)
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary We evaluated linked-read whole genome sequencing (WGS) for detection of structural chromosomal rearrangements in primary samples of varying DNA quality from 12 patients diagnosed with ALL. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements, aneuploidy assessment and gene deletions. Additional RNA-sequencing and copy number aberrations (CNA) data from Illumina Infinium arrays were also generated and assessed against the linked-read WGS data. RNA-sequencing data was used to support structural chromosomal rearrangements detected in the linked-read WGS data by detecting expressed fusion genes as a consequence of the rearrangements. Illumina Infinium arrays (450k array and/or SNP array) were used to assess CNA status to further support the findings in the linked-read WGS data. The processed CNA data from the primary ALL patient samples has been deposited to GEO. RNA-sequencing, linked-read WGS data, and raw SNP array data from the primary ALL patient samples will not be deposited because the patient/parent consent does not cover depositing data that may be used for large-scale determination of germline variants in a repository. The ALL samples were collected 10-20 years ago from pediatric patients aged 2-15 years, some whom have deceased. The linked-read WGS data and the RNA-sequencing data sets generated in the study are available upon reasonable request from the corresponding author Jessica.Nordlund@medsci.uu.se.
 
Overall design The Illumina Infinium HumanMethylation 450k BeadChip is based on the same biochemical principles as regular SNP genotyping arrays. Thus, the total raw fluorescence intensity from the 450k array can also be used to detect copy number variants in genomic DNA. We used the raw signal intensities from the 450k to assess copy number status of the ALL patient samples. LogR files with the extension ".cn" are submitted to GEO and can be visualized in IGV. This is a re-analysis of 12 ALL samples previously submitted in GSE49031.
 
Contributor(s) Nordlund J, Marincevic-Zuniga Y, Syvänen AC
Citation(s) 32054878
Submission date Jul 26, 2018
Last update date Mar 07, 2020
Contact name Yanara Marincevic-Zuniga
E-mail(s) yanara.marincevic_zuniga@medsci.uu.se
Organization name Uppsala University
Department Medical Sciences
Lab Molecular Medicine
Street address Husargatan 3, BOX 1432, Biomedicinskt Centrum (BMC)
City Uppsala
ZIP/Postal code 75144
Country Sweden
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (12)
GSM3307307 genomic DNA at diagnosis from BCP-ALL patient ALL_370
GSM3307308 genomic DNA at diagnosis from BCP-ALL patient ALL_390
GSM3307309 genomic DNA at diagnosis from BCP-ALL patient ALL_386
This SubSeries is part of SuperSeries:
GSE116057 Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing
Relations
BioProject PRJNA482972

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE117692_RAW.tar 379.4 Mb (http)(custom) TAR (of CN, IDAT)
Processed data provided as supplementary file

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