@article{roe2020efficient,

title = {Efficient Sequencing, Assembly, and Annotation of Human KIR Haplotypes},

author = {David Roe and Jonathan Williams and Keyton Ivery and Jenny Brouckaert and Nick Downey and Chad Locklear and Rui Kuang and Martin Maiers},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7581912/},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in immunology},

volume = {11},

publisher = {Frontiers Media SA},

keywords = {KIR Haplotype Inference},

pubstate = {published},

tppubtype = {article}

}

@article{roe2020detailed,

title = {A Detailed View of KIR Haplotype Structures and Gene Families as Provided by a New Motif-based Multiple Sequence Alignment},

author = {David Roe and Cynthia Vierra-Green and Chul-Woo Pyo and Daniel E Geraghty and Stephen R Spellman and Martin Maiers and Rui Kuang},

url = {https://www.frontiersin.org/articles/10.3389/fimmu.2020.585731/full},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in immunology},

volume = {11},

publisher = {Frontiers Media SA},

keywords = {KIR Haplotype Inference},

pubstate = {published},

tppubtype = {article}

}

@article{roe2020accurate,

title = {Accurate and Efficient KIR Gene and Haplotype Inference from Genome Sequencing Reads with Novel K-mer Signatures},

author = {David Roe and Rui Kuang},

url = {https://www.frontiersin.org/articles/10.3389/fimmu.2020.583013/full},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in immunology},

volume = {11},

pages = {3102},

publisher = {Frontiers},

keywords = {KIR Haplotype Inference},

pubstate = {published},

tppubtype = {article}

}

@article{KIR2017,

title = {Revealing complete complex KIR haplotypes phased by long-read sequencing technology},

author = {David Roe and Cynthia Vierra-Green and C-W Pyo and K Eng and R Hall and Rui Kuang and Stephen Spellman and S Ranade and D E Geraghty and Martin Maiers},

url = {https://www.nature.com/gene/journal/vaop/ncurrent/full/gene201710a.html},

doi = {10.1038/gene.2017.10},

year  = {2017},

date = {2017-06-01},

journal = {Genes Immunity},

volume = {1-8},

abstract = {The killer cell immunoglobulin-like receptor (KIR) region of human chromosome 19 contains up to 16 genes for natural killer (NK) cell receptors that recognize human leukocyte antigen (HLA)/peptide complexes and other ligands. The KIR proteins fulfill functional roles in infections, pregnancy, autoimmune diseases and transplantation. However, their characterization remains a constant challenge. Not only are the genes highly homologous due to their recent evolution by tandem duplications, but the region is structurally dynamic due to frequent transposon-mediated recombination. A sequencing approach that precisely captures the complexity of KIR haplotypes for functional annotation is desirable. We present a unique approach to haplotype the KIR loci using single-molecule, real-time (SMRT) sequencing. Using this method, we have—for the first time—comprehensively sequenced and phased sixteen KIR haplotypes from eight individuals without imputation. The information revealed four novel haplotype structures, a novel gene-fusion allele, novel and confirmed insertion/deletion events, a homozygous individual, and overall diversity for the structural haplotypes and their alleles. These KIR haplotypes augment our existing knowledge by providing high-quality references, evolutionary informers, and source material for imputation. The haplotype sequences and gene annotations provide alternative loci for the KIR region in the human genome reference GrCh38.p8.},

keywords = {KIR Haplotype Inference},

pubstate = {published},

tppubtype = {article}

}

@article{vierra2016estimating,

title = {Estimating KIR Haplotype Frequencies on a Cohort of 10,000 Individuals: A Comprehensive Study on Population Variations, Typing Resolutions, and Reference Haplotypes},

author = {Cynthia Vierra-Green and David Roe and Jyothi Jayaraman and John Trowsdale and James Traherne and Rui Kuang and Stephen Spellman and Martin Maiers},

url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163973},

doi = {10.1371/journal.pone.0163973},

year  = {2016},

date = {2016-10-10},

journal = {PloS one},

volume = {11},

number = {10},

pages = {e0163973},

publisher = {Public Library of Science},

abstract = {The killer cell immunoglobulin-like receptors (KIR) mediate human natural killer (NK) cell cytotoxicity via activating or inhibiting signals. Although informative and functional haplotype patterns have been reported, most genotyping has been performed at resolutions that are structurally ambiguous. In order to leverage structural information given low-resolution genotypes, we performed experiments to quantify the effects of population variations, reference haplotypes, and genotyping resolutions on population-level haplotype frequency estimations as well as predictions of individual haplotypes. We genotyped 10,157 unrelated individuals in 5 populations (518 African American[AFA], 258 Asian or Pacific Islander[API], 8,245 European[EUR], 1,073 Hispanic[HIS], and 63 Native American[NAM]) for KIR gene presence/absence (PA), and additionally half of the AFA samples for KIR gene copy number variation (CNV). A custom EM algorithm was used to estimate haplotype frequencies for each population by interpretation in the context of three sets of reference haplotypes. The algorithm also assigns each individual the haplotype pairs of maximum likelihood. Generally, our haplotype frequency estimates agree with similar previous publications to within <5% difference for all haplotypes. The exception is that estimates for NAM from the U.S. showed higher frequency association of cB02 with tA01 (+14%) instead of tB01 (-8.5%) compared to a previous study of NAM from south of the U.S. The higher-resolution CNV genotyping on the AFA samples allowed unambiguous haplotype-pair assignments for the majority of individuals, resulting in a 22% higher median typing resolution score (TRS), which measures likelihood of self-match in the context of population-specific haplo- and geno-types. The use of TRS to quantify reduced ambiguity with CNV data clearly revealed the few individuals with ambiguous genotypes as outliers. It is observed that typing resolution and reference haplotype set influence haplotype frequency estimates. For example, PA resolution may be used with reference haplotype sets up to the point where certain haplotypes are gene-content subsets of others. At that point, CNV must be used for all genes.},

keywords = {KIR Haplotype Inference},

pubstate = {published},

tppubtype = {article}

}