ArticlePLoS computational biology2006
Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays.
Article in PLoS computational biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
73 citing papers in PubMed, 159 citations in OpenAlex.
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- High-resolution genomic profiling and locus-specific FISH in subcutaneous and visceral adipose tissue of obese patients.Frontiers in genetics · 2023Article
- Ensemble of nucleic acid absolute quantitation modules for copy number variation detection and RNA profiling.Nature communications · 2022Article
- Liquid biopsy in pancreatic cancer: the beginning of a new era.Oncotarget · 2018Review
- Pancreatic Cancer Diagnosis and Management: Has the Time Come to Prick the Bubble?Frontiers in endocrinology · 2018Review
- Statistical Contributions to Bioinformatics: Design, Modeling, Structure Learning, and Integration.Statistical modelling · 2017Article
- Penalized weighted low-rank approximation for robust recovery of recurrent copy number variations.BMC bioinformatics · 2015Article
- Somatic mosaicism for copy-neutral loss of heterozygosity and DNA copy number variations in the human genome.BMC genomics · 2015Article
- Identification of two novel mutations in CDHR1 in consanguineous Spanish families with autosomal recessive retinal dystrophy.Scientific reports · 2015Article
- Emerging technologies in paediatric leukaemia.Translational pediatrics · 2015Review
- Allele-specific copy number profiling by next-generation DNA sequencing.Nucleic acids research · 2015Article
- Mitotic crossover--an evolutionary rudiment which promotes carcinogenesis of colorectal carcinoma.World journal of gastroenterology · 2014Review
- biomvRhsmm: genomic segmentation with hidden semi-Markov model.BioMed research international · 2014Article
- High frequency of CRB1 mutations as cause of Early-Onset Retinal Dystrophies in the Spanish population.Orphanet journal of rare diseases · 2013Article
- Haplotype-based profiling of subtle allelic imbalance with SNP arrays.Genome research · 2013Article
- Discovering subgroups of patients from DNA copy number data using NMF on compacted matrices.PloS one · 2013Article
- Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome.Clinical cancer research : an official journal of the American Association for Cancer Research · 2012Article
- Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer.Genome research · 2012Article
13 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 6 institutions in 1 country.
Funding
Abstract
Loss of heterozygosity (LOH) of chromosomal regions bearing tumor suppressors is a key event in the evolution of epithelial and mesenchymal tumors. Identification of these regions usually relies on genotyping tumor and counterpart normal DNA and noting regions where heterozygous alleles in the normal DNA become homozygous in the tumor. However, paired normal samples for tumors and cell lines are often not available. With the advent of oligonucleotide arrays that simultaneously assay thousands of single-nucleotide polymorphism (SNP) markers, genotyping can now be done at high enough resolution to allow identification of LOH events by the absence of heterozygous loci, without comparison to normal controls. Here we describe a hidden Markov model-based method to identify LOH from unpaired tumor samples, taking into account SNP intermarker distances, SNP-specific heterozygosity rates, and the haplotype structure of the human genome. When we applied the method to data genotyped on 100 K arrays, we correctly identified 99% of SNP markers as either retention or loss. We also correctly identified 81% of the regions of LOH, including 98% of regions greater than 3 megabases. By integrating copy number analysis into the method, we were able to distinguish LOH from allelic imbalance. Application of this method to data from a set of prostate samples without paired normals identified known regions of prevalent LOH. We have developed a method for analyzing high-density oligonucleotide SNP array data to accurately identify of regions of LOH and retention in tumors without the need for paired normal samples.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.