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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...the full data sets for evaluation (coverage, 12.9× − 18.2×). We used the complete assemblies of five MHC haplotypes as ground truth to evaluate the accuracy of our estimated sequences. To quantify the accuracy, we measured edit distance between each estimated sequence and the corresponding ground...
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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
...are assigned a local haplotype if they intersect with variants in a phased block (pink segment = haplotype 1, blue segment = haplotype 2, gray segment = on both haplotypes). (H) Each locally phased block is oriented to the full MHC haplotype by intersecting with the reference-based haplotype scaffold (light...
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