ArticleBiostatistics (Oxford, England)2010
PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data.
Article in Biostatistics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers, 3 of them syntheses that pooled it.
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Who cites it
124 citing papers in PubMed, 3 syntheses or guidelines pooled it, 226 citations in OpenAlex.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor.Molecular systems biology · 2021Pooled it
- Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations.Nature genetics · 2016Pooled it
- Genomic landscape of metastatic colorectal cancer.Nature communications · 2014Trial
- A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data.Genome biology · 2024Article
- Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution.Nature communications · 2024Article
- Accurate prediction of quantitative traits with failed SNP calls in canola and maize.Frontiers in plant science · 2023Article
- A risk model of gene signatures for predicting platinum response and survival in ovarian cancer.Journal of ovarian research · 2022Article
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- Computational Drug Repurposing Based on a Recommendation System and Drug-Drug Functional Pathway Similarity.Molecules (Basel, Switzerland) · 2022Article
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- Pharmacogenomics characterization of the MDM2 inhibitor MI-773 reveals candidate tumours and predictive biomarkers.NPJ precision oncology · 2021Article
- Predicting breast cancer drug response using a multiple-layer cell line drug response network model.BMC cancer · 2021Article
- Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL.Nature biotechnology · 2021Article
- Impact of between-tissue differences on pan-cancer predictions of drug sensitivity.PLoS computational biology · 2021Article
- In Silico Inference of Synthetic Cytotoxic Interactions from Paclitaxel Responses.International journal of molecular sciences · 2021Article
- Fast mutual exclusivity algorithm nominates potential synthetic lethal gene pairs through brute force matrix product computations.Computational and structural biotechnology journal · 2021Article
- Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens.Patterns (New York, N.Y.) · 2020Article
- Evaluation of molecular subtypes and clonal selection during establishment of patient-derived tumor xenografts from gastric adenocarcinoma.Communications biology · 2020Article
- MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data.BMC medical genomics · 2020Article
64 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
12 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput oligonucleotide microarrays are commonly employed to investigate genetic disease, including cancer. The algorithms employed to extract genotypes and copy number variation function optimally for diploid genomes usually associated with inherited disease. However, cancer genomes are aneuploid in nature leading to systematic errors when using these techniques. We introduce a preprocessing transformation and hidden Markov model algorithm bespoke to cancer. This produces genotype classification, specification of regions of loss of heterozygosity, and absolute allelic copy number segmentation. Accurate prediction is demonstrated with a combination of independent experimental techniques. These methods are exemplified with affymetrix genome-wide SNP6.0 data from 755 cancer cell lines, enabling inference upon a number of features of biological interest. These data and the coded algorithm are freely available for download.
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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.