ArticleNucleic acids research2007
QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 380 papers, 5 of them syntheses that pooled it.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
380 citing papers in PubMed, 5 syntheses or guidelines pooled it.
- Genome-wide association meta-analysis and rare copy number variant analysis of treatment-resistant depression.Molecular psychiatry · 2025Pooled it
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Genome-wide Burden of Rare Short Deletions Is Enriched in Major Depressive Disorder in Four Cohorts.Biological psychiatry · 2019Pooled it
- Genome-wide meta-analysis of copy number variations with alcohol dependence.The pharmacogenomics journal · 2018Pooled it
- Copy Number Variants in Alzheimer's Disease.Journal of Alzheimer's disease : JAD · 2017Pooled it
- Genome-wide burden and association analyses implicate copy number variations in asthma risk among children and young adults from Latin America.Scientific reports · 2018Trial
- Comprehensive assessment showed no associations of variants at the SLC10A1 locus with susceptibility to persistent HBV infection among Southern Chinese.Scientific reports · 2017Trial
- Extensive load of somatic CNVs in the human placenta.Scientific reports · 2015Trial
- Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data.Circulation research · 2014Trial
- Common genetic variants are associated with increased likelihood of latent co-occurring neurodevelopmental and mental health factors among autistic individuals.Molecular psychiatry · 2026Article
- Determinants of functional burden pleiotropy and gene dosage responses across human traits.Nature communications · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- MarkerMatch: a proximity-based probe-matching algorithm for joint analysis of copy-number variants from different genotyping arrays.Bioinformatics (Oxford, England) · 2026Article
- Combinatorial effects of gene dosage, polygenic background and environment on complex traits.medRxiv : the preprint server for health sciences · 2026Article
- A pattern-learning algorithm associates copy number variations with brain structure and behavioural variables in an adolescent population cohort.Nature biomedical engineering · 2026Article
- Article
- CNValidatron: accurate and efficient validation of PennCNV calls using computer vision.BMC bioinformatics · 2026Article
- Copy Number Variant Duplications Associated with Essential Tremor.Tremor and other hyperkinetic movements (New York, N.Y.) · 2026Article
- Generation of Donor-Specific iPSC for Modelling Lysosomal Storage Disorders.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The hidden Markov model and its applications in bioinformatics analysis.Genes & diseases · 2026Review
320 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
10 authors.
Funding
Abstract
Array-based technologies have been used to detect chromosomal copy number changes (aneuploidies) in the human genome. Recent studies identified numerous copy number variants (CNV) and some are common polymorphisms that may contribute to disease susceptibility. We developed, and experimentally validated, a novel computational framework (QuantiSNP) for detecting regions of copy number variation from BeadArray SNP genotyping data using an Objective Bayes Hidden-Markov Model (OB-HMM). Objective Bayes measures are used to set certain hyperparameters in the priors using a novel re-sampling framework to calibrate the model to a fixed Type I (false positive) error rate. Other parameters are set via maximum marginal likelihood to prior training data of known structure. QuantiSNP provides probabilistic quantification of state classifications and significantly improves the accuracy of segmental aneuploidy identification and mapping, relative to existing analytical tools (Beadstudio, Illumina), as demonstrated by validation of breakpoint boundaries. QuantiSNP identified both novel and validated CNVs. QuantiSNP was developed using BeadArray SNP data but it can be adapted to other platforms and we believe that the OB-HMM framework has widespread applicability in genomic research. In conclusion, QuantiSNP is a novel algorithm for high-resolution CNV/aneuploidy detection with application to clinical genetics, cancer and disease association studies.
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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.