ArticleGenome biology2020
Assembly and annotation of an Ashkenazi human reference genome.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 67 citations in OpenAlex.
- Article
- ChromoMapperWeb: evaluate genome alignments and track assembly steps within an interactive graphic environment.Nucleic acids research · 2026Article
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- A complete diploid human genome benchmark for personalized genomics.bioRxiv : the preprint server for biology · 2025Article
- Near-complete Middle Eastern genomes refine autozygosity and enhance disease-causing and population-specific variant discovery.Nature genetics · 2025Article
- RAmbler resolves complex repeats in human Chromosomes 8, 19, and X.Genome research · 2025Article
- Combining DNA and protein alignments to improve genome annotation with LiftOn.Genome research · 2025Article
- Upstream open reading frames may contain hundreds of novel human exons.PLoS computational biology · 2024Article
- The GIAB genomic stratifications resource for human reference genomes.Nature communications · 2024Article
- Limitations of current high-throughput sequencing technologies lead to biased expression estimates of endogenous retroviral elements.NAR genomics and bioinformatics · 2024Article
- Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.Cell · 2024Article
- Combining DNA and protein alignments to improve genome annotation with LiftOn.bioRxiv : the preprint server for biology · 2024Article
- Upstream open reading frames may contain hundreds of novel human exons.bioRxiv : the preprint server for biology · 2024Article
- Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles.Nucleic acids research · 2024Article
- Unlocking the mystery of the human Y chromosome.Nature reviews. Urology · 2024Article
- AsmMix: an efficient haplotype-resolved hybridFrontiers in genetics · 2024Article
- The status of the human gene catalogue.Nature · 2023Review
- The complete sequence of a human Y chromosome.Nature · 2023Article
- Variant calling and benchmarking in an era of complete human genome sequences.Nature reviews. Genetics · 2023Review
- SPUMONI 2: improved classification using a pangenome index of minimizer digests.Genome biology · 2023Article
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundThousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very small sample of the human population. There is a need for reference genomes from multiple human populations to avoid potential biases.
resultsHere, we describe the assembly and annotation of the genome of an Ashkenazi individual and the creation of a new, population-specific human reference genome. This genome is more contiguous and more complete than GRCh38, the latest version of the human reference genome, and is annotated with highly similar gene content. The Ashkenazi reference genome, Ash1, contains 2,973,118,650 nucleotides as compared to 2,937,639,212 in GRCh38. Annotation identified 20,157 protein-coding genes, of which 19,563 are > 99% identical to their counterparts on GRCh38. Most of the remaining genes have small differences. Forty of the protein-coding genes in GRCh38 are missing from Ash1; however, all of these genes are members of multi-gene families for which Ash1 contains other copies. Eleven genes appear on different chromosomes from their homologs in GRCh38. Alignment of DNA sequences from an unrelated Ashkenazi individual to Ash1 identified ~ 1 million fewer homozygous SNPs than alignment of those same sequences to the more-distant GRCh38 genome, illustrating one of the benefits of population-specific reference genomes.
conclusionsThe Ash1 genome is presented as a reference for any genetic studies involving Ashkenazi Jewish individuals.
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