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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
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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.
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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.
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Contributor(s) |
Nordlund J, Marincevic-Zuniga Y, Syvänen AC |
Citation(s) |
32054878 |
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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
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Organization name |
Uppsala University
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Department |
Medical Sciences
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Lab |
Molecular Medicine
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Street address |
Husargatan 3, BOX 1432, Biomedicinskt Centrum (BMC)
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City |
Uppsala |
ZIP/Postal code |
75144 |
Country |
Sweden |
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Platforms (1) |
GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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Samples (12)
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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 |
GSM3307310 |
genomic DNA at diagnosis from BCP-ALL patient ALL_402 |
GSM3307311 |
genomic DNA at diagnosis from BCP-ALL patient ALL_458 |
GSM3307312 |
genomic DNA at diagnosis from BCP-ALL patient ALL_501 |
GSM3307313 |
genomic DNA at diagnosis from T-ALL patient ALL_559 |
GSM3307314 |
genomic DNA at diagnosis from BCP-ALL patient ALL_604 |
GSM3307315 |
genomic DNA at diagnosis from BCP-ALL patient ALL_613 |
GSM3307316 |
genomic DNA at diagnosis from BCP-ALL patient ALL_689 |
GSM3307317 |
genomic DNA at diagnosis from BCP-ALL patient ALL_707 |
GSM3307318 |
genomic DNA at diagnosis from BCP-ALL patient ALL_47 |
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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 |
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Relations |
BioProject |
PRJNA482972 |