Sample processing obscures cancer-specific alterations in leukemic transcriptomes

NOTCH2 and FLT3 gene mis-splicings are common events in patients with acute myeloid leukemia (AML): new potential targets in AML

(2014) S. Adamia et al.   BLOOD

RNA-seq: impact of RNA degradation on transcript quantification

(2014) Irene Gallego Romero et al.   BMC BIOLOGY

Detecting and correcting systematic variation in large-scale RNA sequencing data

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

(2013) P. G. Ferreira et al.   GENOME RESEARCH

Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia

(2013) Julia A Meyer et al.   NATURE GENETICS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Translational Research in Pediatrics II: Blood Collection, Processing, Shipping, and Storage

(2013) C. Gillio-Meina et al.   PEDIATRICS

RNA-Seq Reveals Spliceosome and Proteasome Genes as Most Consistent Transcripts in Human Cancer Cells

(2013) Tara MacRae et al.   PLoS One

Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia

(2013) Zeynep Kalender Atak et al.   PLoS Genetics

High expression of lymphoid enhancer-binding factor-1 (LEF1) is a novel favorable prognostic factor in cytogenetically normal acute myeloid leukemia

(2012) K. H. Metzeler et al.   BLOOD

CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia

(2012) M. E. McNerney et al.   BLOOD

Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics

(2012) Roland Schmitz et al.   NATURE

Recurrent SETBP1 mutations in atypical chronic myeloid leukemia

(2012) Rocco Piazza et al.   NATURE GENETICS

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

New Fusion Transcripts Identified in Normal Karyotype Acute Myeloid Leukemia

(2012) Hongxiu Wen et al.   PLoS One

Overexpression of LEF1 predicts unfavorable outcome in adult patients with B-precursor acute lymphoblastic leukemia

(2011) A. Kuhnl et al.   BLOOD

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

(2011) Ryan D. Morin et al.   NATURE

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

(2011) Víctor Quesada et al.   NATURE GENETICS

Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods

(2011) Chao Chen et al.   PLoS One

Gene Expression Profiles from Peripheral Blood Mononuclear Cells Are Sensitive to Short Processing Delays

(2010) Michael G. Barnes et al.   BIOPRESERVATION AND BIOBANKING

A multilevel model to address batch effects in copy number estimation using SNP arrays

(2010) R. B. Scharpf et al.   BIOSTATISTICS

PTEN transcript variants caused by illegitimate splicing in “aged” blood samples and EBV-transformed cell lines

(2010) Yunying Liu et al.   HUMAN GENETICS

Nonsense-Mediated RNA Decay Regulation by Cellular Stress: Implications for Tumorigenesis

(2010) L. B. Gardner   MOLECULAR CANCER RESEARCH

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Levels of 5′ RNA tags in plasma and buffy coat from EDTA blood increase with time

(2008) F Salway et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Identification of genes with abnormal expression changes in acute myeloid leukemia

(2007) Derek L. Stirewalt et al.   GENES CHROMOSOMES & CANCER