Published in Genome Res on January 31, 2007
Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol (2009) 2.88
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics (2008) 2.66
Retracted Simultaneous recovery of DNA and RNA from formalin-fixed paraffin-embedded tissue and application in epidemiologic studies. Cancer Epidemiol Biomarkers Prev (2010) 2.16
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics (2009) 1.83
Prognostic and predictive biomarkers in resected colon cancer: current status and future perspectives for integrating genomics into biomarker discovery. Oncologist (2010) 1.72
Single nucleotide polymorphism-based genome-wide chromosome copy change, loss of heterozygosity, and aneuploidy in Barrett's esophagus neoplastic progression. Cancer Prev Res (Phila) (2008) 1.43
High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays. BMC Med Genomics (2009) 1.29
Genome haploidisation with chromosome 7 retention in oncocytic follicular thyroid carcinoma. PLoS One (2012) 0.92
High quality and quantity Genome-wide germline genotypes from FFPE normal tissue. BMC Res Notes (2011) 0.91
Opening the archives for state of the art tumour genetic research: sample processing for array-CGH using decalcified, formalin-fixed, paraffin-embedded tissue-derived DNA samples. BMC Res Notes (2011) 0.89
Genomic changes in gliomas detected using single nucleotide polymorphism array in formalin-fixed, paraffin-embedded tissue: superior results compared with microsatellite analysis. J Mol Diagn (2011) 0.88
Genome-wide copy neutral LOH is infrequent in familial and sporadic microsatellite unstable carcinomas. Fam Cancer (2008) 0.88
Translation of an STR-based biomarker into a clinically compatible SNP-based platform for loss of heterozygosity. Cancer Biomark (2009) 0.87
Cervical carcinoma-associated fibroblasts are DNA diploid and do not show evidence for somatic genetic alterations. Cell Oncol (Dordr) (2011) 0.87
Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas. Acta Neuropathol (2010) 0.87
Molecular information obtained from radiobiological tissue archives: achievements of the past and visions of the future. Radiat Environ Biophys (2007) 0.86
Molecular biology: the key to personalised treatment in radiation oncology? Br J Radiol (2010) 0.84
High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix Cytoscan HD chip. PLoS One (2014) 0.80
Data analysis issues for allele-specific expression using Illumina's GoldenGate assay. BMC Bioinformatics (2010) 0.79
Loss of heterozygosity and copy number alterations in flow-sorted bulky cervical cancer. PLoS One (2013) 0.78
Copy number alterations and allelic ratio in relation to recurrence of rectal cancer. BMC Genomics (2015) 0.77
The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. Int J Genomics (2017) 0.75
Targeted next-generation sequencing at copy-number breakpoints for personalized analysis of rearranged ends in solid tumors. PLoS One (2014) 0.75
Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study. BMC Genomics (2017) 0.75
A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res (1988) 77.80
High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet (1998) 21.52
Normalization of cDNA microarray data. Methods (2003) 18.69
Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature (2005) 15.28
Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet (1999) 14.96
A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res (2005) 11.02
Large-scale genotyping of complex DNA. Nat Biotechnol (2003) 10.00
Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol (2003) 9.10
An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res (2004) 8.86
dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics (2004) 6.78
Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics (2005) 6.44
BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques (2002) 5.98
Aneuploidy and cancer. Nature (2004) 5.61
Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res (2004) 5.59
High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res (2004) 5.24
Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat Biotechnol (2000) 4.10
High-throughput SNP genotyping on universal bead arrays. Mutat Res (2005) 3.78
Breakpoint identification and smoothing of array comparative genomic hybridization data. Bioinformatics (2004) 2.85
Quantile smoothing of array CGH data. Bioinformatics (2004) 2.51
Comparative genomic hybridization. Annu Rev Genomics Hum Genet (2005) 2.34
Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. Semin Cancer Biol (1993) 2.09
Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP. Cancer Res (2003) 1.99
Genome-wide detection of LOH in prostate cancer using human SNP microarray technology. Genomics (2003) 1.80
Allelic dosage analysis with genotyping microarrays. Biochem Biophys Res Commun (2005) 1.78
High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines. Oncogene (2004) 1.69
Microsatellite instability, immunohistochemistry, and additional PMS2 staining in suspected hereditary nonpolyposis colorectal cancer. Clin Cancer Res (2004) 1.68
The order of genetic events associated with colorectal cancer progression inferred from meta-analysis of copy number changes. Genes Chromosomes Cancer (2006) 1.67
Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10K SNP mapping array. Hum Genet (2004) 1.64
Loss of heterozygosity in childhood acute lymphoblastic leukemia detected by genome-wide microarray single nucleotide polymorphism analysis. Cancer Res (2005) 1.57
Allelic imbalances in human bladder cancer: genome-wide detection with high-density single-nucleotide polymorphism arrays. J Natl Cancer Inst (2002) 1.34
Insights from genomic microarrays into structural chromosome rearrangements. Am J Med Genet A (2005) 1.29
Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single nucleotide polymorphism arrays. Cancer Res (2005) 1.27
Inherited susceptibility to colorectal adenomas and carcinomas: evidence for a new predisposition gene on 15q14-q22. Gastroenterology (1999) 1.26
High-resolution analysis of chromosomal imbalances using the Affymetrix 10K SNP genotyping chip. Genomics (2005) 1.21
Whole genome SNP arrays using DNA derived from formalin-fixed, paraffin-embedded ovarian tumor tissue. Hum Mutat (2005) 1.15
Allelotype of uterine leiomyomas. Cancer Genet Cytogenet (1999) 1.06
Whole genome loss of heterozygosity profiling on oral squamous cell carcinoma by high-density single nucleotide polymorphic allele (SNP) array. Cancer Genet Cytogenet (2004) 0.96
Intratumoral heterogeneity of genetic changes in primary colorectal carcinomas with metastasis. Surg Today (2003) 0.81
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet (2010) 17.38
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet (2010) 16.96
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature (2012) 16.13
A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet (2006) 15.63
A variant in CDKAL1 influences insulin response and risk of type 2 diabetes. Nat Genet (2007) 13.28
Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. Nat Genet (2007) 12.65
Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study. Lancet (2012) 12.10
Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet (2010) 9.90
A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Nat Genet (2007) 8.50
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet (2011) 7.98
Shared and distinct genetic variants in type 1 diabetes and celiac disease. N Engl J Med (2008) 7.66
Newly identified genetic risk variants for celiac disease related to the immune response. Nat Genet (2008) 7.63
Multiple common variants for celiac disease influencing immune gene expression. Nat Genet (2010) 6.90
The same sequence variant on 9p21 associates with myocardial infarction, abdominal aortic aneurysm and intracranial aneurysm. Nat Genet (2008) 6.72
Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat Genet (2011) 6.36
A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3. Nat Genet (2008) 6.26
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet (2006) 6.10
Human dectin-1 deficiency and mucocutaneous fungal infections. N Engl J Med (2009) 5.27
Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility. Nat Genet (2008) 5.05
Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat Rev Genet (2009) 4.79
Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet (2010) 4.65
High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nat Genet (2012) 4.46
Pervasive sharing of genetic effects in autoimmune disease. PLoS Genet (2011) 4.42
Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis. Nat Genet (2012) 4.41
Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity. Nat Genet (2012) 4.13
Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. PLoS Genet (2011) 3.68
Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS Genet (2011) 3.65
Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction. Nat Genet (2010) 3.55
Gene expression signature to improve prognosis prediction of stage II and III colorectal cancer. J Clin Oncol (2010) 3.30
Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology. Cancer Res (2009) 3.22
Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. PLoS Genet (2012) 3.21
Genetic analysis of innate immunity in Crohn's disease and ulcerative colitis identifies two susceptibility loci harboring CARD9 and IL18RAP. Am J Hum Genet (2008) 3.11
Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. Nat Genet (2011) 3.03
Common variants associated with plasma triglycerides and risk for coronary artery disease. Nat Genet (2013) 2.92
Cancer risk in hereditary nonpolyposis colorectal cancer due to MSH6 mutations: impact on counseling and surveillance. Gastroenterology (2004) 2.90
Novel association in chromosome 4q27 region with rheumatoid arthritis and confirmation of type 1 diabetes point to a general risk locus for autoimmune diseases. Am J Hum Genet (2007) 2.89
ITPR2 as a susceptibility gene in sporadic amyotrophic lateral sclerosis: a genome-wide association study. Lancet Neurol (2007) 2.80
Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell hemangioma in Ollier disease and Maffucci syndrome. Nat Genet (2011) 2.74
Using genome-wide pathway analysis to unravel the etiology of complex diseases. Genet Epidemiol (2009) 2.72
Myosin IXB variant increases the risk of celiac disease and points toward a primary intestinal barrier defect. Nat Genet (2005) 2.71
Identification of PLOD2 as telopeptide lysyl hydroxylase, an important enzyme in fibrosis. J Biol Chem (2003) 2.63
Genetic variation in DPP6 is associated with susceptibility to amyotrophic lateral sclerosis. Nat Genet (2007) 2.63
The gene product Murr1 restricts HIV-1 replication in resting CD4+ lymphocytes. Nature (2003) 2.63
Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci. Am J Hum Genet (2012) 2.53
Randomized feeding intervention in infants at high risk for celiac disease. N Engl J Med (2014) 2.39
Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. PLoS Genet (2012) 2.29
Identification of a new copper metabolism gene by positional cloning in a purebred dog population. Hum Mol Genet (2002) 2.24
Common and different genetic background for rheumatoid arthritis and coeliac disease. Hum Mol Genet (2009) 2.15
Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height. Am J Hum Genet (2010) 2.15
Genetic variation in Toll-like receptors and disease susceptibility. Nat Immunol (2012) 2.09
Immune system and prognosis in colorectal cancer: a detailed immunohistochemical analysis. Lab Invest (2004) 2.05
Meta-analyses on suspected chronic obstructive pulmonary disease genes: a summary of 20 years' research. Am J Respir Crit Care Med (2009) 2.04
Wnt signaling and Dupuytren's disease. N Engl J Med (2011) 2.02
Ptprj is a candidate for the mouse colon-cancer susceptibility locus Scc1 and is frequently deleted in human cancers. Nat Genet (2002) 2.00
Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci. Am J Hum Genet (2012) 1.96
A novel role for XIAP in copper homeostasis through regulation of MURR1. EMBO J (2003) 1.90
Susceptibility loci for intracranial aneurysm in European and Japanese populations. Nat Genet (2008) 1.90
Obesity genes identified in genome-wide association studies are associated with adiposity measures and potentially with nutrient-specific food preference. Am J Clin Nutr (2009) 1.88
Genome-wide association study of intracranial aneurysm identifies three new risk loci. Nat Genet (2010) 1.86
Disruption of ROBO2 is associated with urinary tract anomalies and confers risk of vesicoureteral reflux. Am J Hum Genet (2007) 1.85
Meta-analysis in more than 17,900 cases of ischemic stroke reveals a novel association at 12q24.12. Neurology (2014) 1.85
Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies. Gastroenterology (2013) 1.83
Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis. Nat Genet (2013) 1.83
Molecular analysis of hereditary nonpolyposis colorectal cancer in the United States: high mutation detection rate among clinically selected families and characterization of an American founder genomic deletion of the MSH2 gene. Am J Hum Genet (2003) 1.80
Genome-wide study of percent emphysema on computed tomography in the general population. The Multi-Ethnic Study of Atherosclerosis Lung/SNP Health Association Resource Study. Am J Respir Crit Care Med (2014) 1.80
Genome-wide association study identifies a sequence variant within the DAB2IP gene conferring susceptibility to abdominal aortic aneurysm. Nat Genet (2010) 1.79
Chromosome 8q23.3 and 11q23.1 variants modify colorectal cancer risk in Lynch syndrome. Gastroenterology (2008) 1.79
Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease. Hum Mol Genet (2010) 1.78
Beneficial effects of sorafenib on tumor progression, but not on radioiodine uptake, in patients with differentiated thyroid carcinoma. Eur J Endocrinol (2009) 1.78
Rapid KRAS, EGFR, BRAF and PIK3CA mutation analysis of fine needle aspirates from non-small-cell lung cancer using allele-specific qPCR. PLoS One (2011) 1.78
A novel t(6;14)(q25-q27;q32) in acute myelocytic leukemia involves the BCL11B gene. Cancer Genet Cytogenet (2004) 1.77
New Dutch reference curves for birthweight by gestational age. Early Hum Dev (2009) 1.73
Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders. Nat Genet (2013) 1.72
Prognostic and predictive biomarkers in resected colon cancer: current status and future perspectives for integrating genomics into biomarker discovery. Oncologist (2010) 1.72
A genome-wide association search for type 2 diabetes genes in African Americans. PLoS One (2012) 1.72
Evolutionary and functional analysis of celiac risk loci reveals SH2B3 as a protective factor against bacterial infection. Am J Hum Genet (2010) 1.71
Mutations in potassium channel kcnd3 cause spinocerebellar ataxia type 19. Ann Neurol (2012) 1.70
A major non-HLA locus in celiac disease maps to chromosome 19. Gastroenterology (2003) 1.69
Genome-wide association study of coronary and aortic calcification implicates risk loci for coronary artery disease and myocardial infarction. Atherosclerosis (2013) 1.69
Genome-wide association analysis in primary sclerosing cholangitis. Gastroenterology (2009) 1.69
Microsatellite instability, immunohistochemistry, and additional PMS2 staining in suspected hereditary nonpolyposis colorectal cancer. Clin Cancer Res (2004) 1.68
Loss-of-function variants in the filaggrin gene are a significant risk factor for peanut allergy. J Allergy Clin Immunol (2011) 1.68
Conventional and tissue microarray immunohistochemical expression analysis of mismatch repair in hereditary colorectal tumors. Am J Pathol (2003) 1.67
Heterogeneity of rhythmic suprachiasmatic nucleus neurons: Implications for circadian waveform and photoperiodic encoding. Proc Natl Acad Sci U S A (2003) 1.65
Complex nature of SNP genotype effects on gene expression in primary human leucocytes. BMC Med Genomics (2009) 1.64
Effective detection of human leukocyte antigen risk alleles in celiac disease using tag single nucleotide polymorphisms. PLoS One (2008) 1.64
The bone morphogenetic protein pathway is inactivated in the majority of sporadic colorectal cancers. Gastroenterology (2008) 1.61
The carcinoma-stromal ratio of colon carcinoma is an independent factor for survival compared to lymph node status and tumor stage. Cell Oncol (2007) 1.61
MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects. Bioinformatics (2011) 1.60
Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1. Am J Hum Genet (2011) 1.60
Human disease-associated genetic variation impacts large intergenic non-coding RNA expression. PLoS Genet (2013) 1.59
ATG16L1 and IL23R are associated with inflammatory bowel diseases but not with celiac disease in the Netherlands. Am J Gastroenterol (2007) 1.58
ImmunoChip study implicates antigen presentation to T cells in narcolepsy. PLoS Genet (2013) 1.55
Multiplex ligation-dependent probe amplification for the detection of 1p and 19q chromosomal loss in oligodendroglial tumors. Brain Pathol (2005) 1.54
A meta-analysis of genome-wide association scans identifies IL18RAP, PTPN2, TAGAP, and PUS10 as shared risk loci for Crohn's disease and celiac disease. PLoS Genet (2011) 1.54