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Search: authors:"Jessica Nordlund"

7 papers found.
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Data quality of whole genome bisulfite sequencing on Illumina platforms

for Advanced Computational Science (UPPMAX). Author Contributions Conceptualization: Amanda Raine, Ulrika Liljedahl, Jessica Nordlund. Formal analysis: Amanda Raine, Jessica Nordlund. Investigation ... : Amanda Raine. Methodology: Amanda Raine, Jessica Nordlund. Resources: Ulrika Liljedahl. Visualization: Amanda Raine, Jessica Nordlund. Writing ± original draft: Amanda Raine, Ulrika Liljedahl, Jessica

DNA methylation holds prognostic information in relapsed precursor B-cell acute lymphoblastic leukemia

BackgroundFew biological markers are associated with survival after relapse of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). In pediatric T-cell ALL, we have identified promoter-associated methylation alterations that correlate with prognosis. Here, the prognostic relevance of CpG island methylation phenotype (CIMP) classification was investigated in pediatric BCP-ALL...

CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array

The Illumina Infinium HumanMethylation450 BeadChip (450k) is widely used for the evaluation of DNA methylation levels in large-scale datasets, particularly in cancer. The 450k design allows copy number variant (CNV) calling using existing bioinformatics tools. However, in cancer samples, numerous large-scale aberrations cause shifting in the probe intensities and thereby may...

Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment

Background Target enrichment and resequencing is a widely used approach for identification of cancer genes and genetic variants associated with diseases. Although cost effective compared to whole genome sequencing, analysis of many samples constitutes a significant cost, which could be reduced by pooling samples before capture. Another limitation to the number of cancer samples...

DNA Methylation Analysis of Bone Marrow Cells at Diagnosis of Acute Lymphoblastic Leukemia and at Remission

To detect genes with CpG sites that display methylation patterns that are characteristic of acute lymphoblastic leukemia (ALL) cells, we compared the methylation patterns of cells taken at diagnosis from 20 patients with pediatric ALL to the methylation patterns in mononuclear cells from bone marrow of the same patients during remission and in non-leukemic control cells from bone...

DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia

Background We present a method that utilizes DNA methylation profiling for prediction of the cytogenetic subtypes of acute lymphoblastic leukemia (ALL) cells from pediatric ALL patients. The primary aim of our study was to improve risk stratification of ALL patients into treatment groups using DNA methylation as a complement to current diagnostic methods. A secondary aim was to...

Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia

Background Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. The relationship between DNA methylation, cytogenetic background, drug resistance and relapse in ALL is poorly understood. Results We...