ArticleNature communications2025
Genome-wide profiling of highly similar paralogous genes using HiFi sequencing.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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.
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Who cites it
11 citing papers in PubMed.
- Sequencing approaches in hereditary cancer testing: strengths, limitations and future directions.European journal of human genetics : EJHG · 2026Review
- Near-perfect genome sequencing in medical genetics.Nature genetics · 2026Review
- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
- Sensitivity of HiFi long-read genome sequencing for difficult-to-detect pathogenic variants when applied to real-world clinical laboratory samples.American journal of human genetics · 2026Article
- Integrative analysis of in silico predictions and clinical evidence to delineate the capability of HiFi long-read sequencing in paralogous genes.NPJ genomic medicine · 2026Article
- Analyses of contiguous reference genomes of Amaranthus tuberculatus highlight the landscape of the sex-associated region and PEBP gene family diversity.BMC genomics · 2025Article
- GREGoR: accelerating genomics for rare diseases.Nature · 2025Article
- Multi-platform framework for mapping somatic retrotransposition in human tissues.bioRxiv : the preprint server for biology · 2025Article
- Long and Accurate: How HiFi Sequencing is Transforming Genomics.Genomics, proteomics & bioinformatics · 2025Review
- The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases.Genome research · 2025Review
- GREGoR: Accelerating Genomics for Rare Diseases.ArXiv · 2024Article
Corrections and comments
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Authors and funding
23 authors.
Funding
Abstract
Variant calling is hindered in segmental duplications by sequence homology. We developed Paraphase, a HiFi-based informatics method that resolves highly similar genes by phasing all haplotypes of paralogous genes together. We applied Paraphase to 160 long (>10 kb) segmental duplication regions across the human genome with high (>99%) sequence similarity, encoding 316 genes. Analysis across five ancestral populations revealed highly variable copy numbers of these regions. We identified 23 paralog groups with exceptionally low within-group diversity, where extensive gene conversion and unequal crossing over contribute to highly similar gene copies. Furthermore, our analysis of 36 trios identified 7 de novo SNVs and 4 de novo gene conversion events, 2 of which are non-allelic. Finally, we summarized extensive genetic diversity in 9 medically relevant genes previously considered challenging to genotype. Paraphase provides a framework for resolving gene paralogs, enabling accurate testing in medically relevant genes and population-wide studies of previously inaccessible genes.
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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.