Searching journal content for articles similar to Song et al. 33 (6): 923.

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  1. Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
    • Ying Zhou,
    • Li Song,
    • and Heng Li
    Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
    ...sequence (Robinson et al. 2018).High-throughput sequencing with short reads has become a common approach to typing HLA/KIR alleles, which enables the discovery of the connection between special gene groups and clinical outcomes in large cohorts (Sakaue et al. 2023). By searching the best combinations...
  2. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...variations in the noncoding regions that regulate RNA expression are not explored (Ramsuran et al. 2015). HLA typing on the PacBio platform was demonstrated by Albrecht et al. by combining highly accurate MiSeq data with lower accuracy full-length RS II data to sequence a long HLA amplicon. The full...
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  3. Research: Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
    • Taishan Hu,
    • Timothy L. Mosbruger,
    • Nikolaos G. Tairis,
    • Amalia Dinou,
    • Pushkala Jayaraman,
    • Mahdi Sarmady,
    • Kingham Brewster,
    • Yang Li,
    • Tristan J. Hayeck,
    • Jamie L. Duke,
    • and Dimitri S. Monos
    Genome Res. October 2024 34: 1500-1513; Published in Advance September 26, 2024, doi:10.1101/gr.278588.123
    ...the accuracy of the assembly could not be measured in the same way as the previous samples. Instead, we compared the final assemblies of the two haplotypes to (1) the Bionano optical maps, (2) the independently genotyped HLA gene sequences, and (3) the SNP array genotyping data of the sample.Both haplotype...
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  4. Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
    • Tsung-Kai Hung,
    • Wan-Chi Liu,
    • Sheng-Kai Lai,
    • Hui-Wen Chuang,
    • Yi-Che Lee,
    • Hong-Ye Lin,
    • Chia-Lang Hsu,
    • Chien-Yu Chen,
    • Ya-Chien Yang,
    • Jacob Shujui Hsu,
    • and Pei-Lung Chen
    Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
    ...for interacting with human leukocyte antigens (HLAs) on target cells to regulate host innate and adaptive immunity (Martin et al. 2002; Vilches and Parham 2002; Pollock et al. 2022). The KIR complex comprises 15 genes with diverse inhibitory and activating domains, although not all are essential for healthy...
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  5. Resource: Assembly and analysis of 100 full MHC haplotypes from the Danish population
    • Jacob M. Jensen,
    • Palle Villesen,
    • Rune M. Friborg,
    • The Danish Pan-Genome Consortium,
    • Thomas Mailund,
    • Søren Besenbacher,
    • and Mikkel H. Schierup
    Genome Res. September 2017 27: 1597-1607; Published in Advance August 3, 2017, doi:10.1101/gr.218891.116
    ...number of studies. A recent advance in inference in the MHC region is the construction of population reference graphs (Dilthey et al. 2015). Population reference graphs tie together variant sequence such as MHC alleles from the IMGT/HLA database and variants from The 1000 Genomes Project (The 1000...
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  6. Method: A comprehensively molecular haplotype-resolved genome of a European individual
    • Eun-Kyung Suk,
    • Gayle K. McEwen,
    • Jorge Duitama,
    • Katja Nowick,
    • Sabrina Schulz,
    • Stefanie Palczewski,
    • Stefan Schreiber,
    • Dustin T. Holloway,
    • Stephen McLaughlin,
    • Heather Peckham,
    • Clarence Lee,
    • Thomas Huebsch,
    • and Margret R. Hoehe
    Genome Res. October 2011 21: 1672-1685; Published in Advance August 3, 2011, doi:10.1101/gr.125047.111
    ...is critically impacted by the specific combination, or phase, of multiple HLA alleles; nonmatching long-range MHC haplotypes significantly increased the risk for severe graft-versus-host-disease (GvHD) (Petersdorf et al. 2007). Thus, accurate phase information allows identification of donor-recipient matches...
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  7. Method: Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity
    • Brianna Chrisman,
    • Chloe He,
    • Jae-Yoon Jung,
    • Nate Stockham,
    • Kelley Paskov,
    • Peter Washington,
    • Juli Petereit,
    • and Dennis P. Wall
    Genome Res. October 2023 33: 1734-1746; Published in Advance October 25, 2023, doi:10.1101/gr.277175.122
    ...across the human population (Gourraud et al. 2014). These sequences were extracted from reads that did not align well to the primary reference or the decoy contigs; therefore, ASLAN is localizing HLA subsequences that are not well represented anywhere on GRCh38. Similarly, Chromosome 19 (around 54 Mb...
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