ArticleBioinformatics (Oxford, England)2012
optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers, 7 of them syntheses that pooled it.
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Who cites it
58 citing papers in PubMed, 7 syntheses or guidelines pooled it.
- Pooled it
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- An integrative genomics approach identifies KDM4 as a modulator of trained immunity.European journal of immunology · 2022Pooled it
- Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease.Nature genetics · 2017Pooled it
- Identification of an Association of TNFAIP3 Polymorphisms With Matrix Metalloproteinase Expression in Fibroblasts in an Integrative Study of Systemic Sclerosis-Associated Genetic and Environmental Factors.Arthritis & rheumatology (Hoboken, N.J.) · 2016Pooled it
- Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.Nature genetics · 2015Pooled it
- Enhanced meta-analysis and replication studies identify five new psoriasis susceptibility loci.Nature communications · 2015Pooled it
- A randomized controlled trial of precision bezlotoxumab treatment for Clostridioides difficile infection.Cell reports. Medicine · 2026Trial
- Sex-stratified genetic regulators of cytokine production in the Dutch and Tanzanian populations.HGG advances · 2026Article
- Primary biliary cirrhosis and rheumatoid arthritis: a comprehensive study combining genetics and transcriptomics.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Primary biliary cirrhosis and inflammatory bowel disease: a two-sample bidirectional Mendelian randomization study.Experimental biology and medicine (Maywood, N.J.) · 2026Article
- Low-cost generation of clinical-grade, layperson-friendly pharmacogenetic passports using oligonucleotide arrays.American journal of human genetics · 2025Article
- GenoTriplo: A SNP genotype calling method for triploids.PLoS computational biology · 2024Article
- A single-cell view on host immune transcriptional response to in vivo BCG-induced trained immunity.Cell reports · 2023Article
- Genome-Wide Association Study RevealsJournal of fungi (Basel, Switzerland) · 2023Article
- Article
- Differences in thrombin and plasmin generation potential between East African and Western European adults: The role of genetic and non-genetic factors.Journal of thrombosis and haemostasis : JTH · 2022Article
- A functional genomics approach in Tanzanian population identifies distinct genetic regulators of cytokine production compared to European population.American journal of human genetics · 2022Article
- Article
- Impact of Human Genetic Variation on C-Reactive Protein Concentrations and Acute Appendicitis.Frontiers in immunology · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationExisting microarray genotype-calling algorithms adopt either SNP-by-SNP (SNP-wise) or sample-by-sample (sample-wise) approaches to calling. We have developed a novel genotype-calling algorithm for the Illumina platform, optiCall, that uses both SNP-wise and sample-wise calling to more accurately ascertain genotypes at rare, low-frequency and common variants.
resultsUsing data from 4537 individuals from the 1958 British Birth Cohort genotyped on the Immunochip, we estimate the proportion of SNPs lost to downstream analysis due to false quality control failures, and rare variants misclassified as monomorphic, is only 1.38% with optiCall, in comparison to 3.87, 7.85 and 4.09% for Illuminus, GenoSNP and GenCall, respectively. We show that optiCall accurately captures rare variants and can correctly account for SNPs where probe intensity clouds are shifted from their expected positions. AVAILABILITY AND IMPLEMENTATION: optiCall is implemented in C++ for use on UNIX operating systems and is available for download at http://www.sanger.ac.uk/resources/software/opticall/.
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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.