ArticleGenes2020
Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2.
Article in Genes, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
19 citing papers in PubMed, 31 citations in OpenAlex.
- LCPAN: efficient variation graph construction using locally consistent parsing.Genome biology · 2026Article
- Whole Genome Sequencing Reveals amedRxiv : the preprint server for health sciences · 2026Article
- Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes.Genome medicine · 2025Article
- CNPI: Rapid Analyses of Human Copy Number Data.Journal of molecular biology · 2025Article
- Article
- Human-specific gene expansions contribute to brain evolution.bioRxiv : the preprint server for biology · 2025Article
- mAutism research : official journal of the International Society for Autism Research · 2025Article
- The association between salivary amylase gene copy number and enzyme activity with type 2 diabetes status.PloS one · 2025Article
- Duplications and Retrogenes Are Numerous and Widespread in Modern Canine Genomic Assemblies.Genome biology and evolution · 2024Article
- Article
- GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads.Scientific reports · 2023Article
- Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.Genome biology · 2023Article
- Robust and accurate estimation of paralog-specific copy number for duplicated genes using whole-genome sequencing.Nature communications · 2022Article
- Article
- Diverse Molecular Mechanisms Contribute to Differential Expression of Human Duplicated Genes.Molecular biology and evolution · 2021Article
- Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism.Human genomics · 2021Article
- Special Issue: A Tale of Genes and Genomes.Genes · 2021Article
- Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper.PLoS computational biology · 2021Article
- Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications.Nucleic acids research · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Gene duplication is a major mechanism for the evolution of gene novelty, and copy-number variation makes a major contribution to inter-individual genetic diversity. However, most approaches for studying copy-number variation rely upon uniquely mapping reads to a genome reference and are unable to distinguish among duplicated sequences. Specialized approaches to interrogate specific paralogs are comparatively slow and have a high degree of computational complexity, limiting their effective application to emerging population-scale data sets. We present QuicK-mer2, a self-contained, mapping-free approach that enables the rapid construction of paralog-specific copy-number maps from short-read sequence data. This approach is based on the tabulation of unique k-mer sequences from short-read data sets, and is able to analyze a 20X coverage human genome in approximately 20 min. We applied our approach to newly released sequence data from the 1000 Genomes Project, constructed paralog-specific copy-number maps from 2457 unrelated individuals, and uncovered copy-number variation of paralogous genes. We identify nine genes where none of the analyzed samples have a copy number of two, 92 genes where the majority of samples have a copy number other than two, and describe rare copy number variation effecting multiple genes at the APOBEC3 locus.
Indexed as
Identifiers
What OpenQuestion holds
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.