Population Genomic Architecture: Conserved Polymorphic Sequences (CPSs), Not Linkage Disequilibrium

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Background

Pedigree-based phasing of HLA and other regional alleles has shown that the major histocompatibility complex (MHC) on human chromosome 6p is characterized by high frequency long-range (1 to 4 Mb) polymorphic sequences known as conserved extended haplotypes (CEHs) or ancestral haplotypes (AHs), and their regional fragment blocks (50 to 200 kb). We introduce the term "conserved polymorphic sequence" (CPS) to encompass these genomic structures. Specific CPS frequencies show high variability both within and between sub-populations. Linkage disequilibrium (LD) and other expectation-maximization analyses of unrelated genotypes fail to detect such long-range population-level haplotypes in the MHC. Instead, LD detects relatively small blocks (5-200 kb; avg = 22 kb) of genetic fixity separated by hotspots of frequent meiotic crossing over. Although LD methodologies dominate the study of genomic architecture (and genetic analysis of complex traits), the technical explanation(s) for these radically different results are unresolved.

Although pedigree-based AH/CEH (CPS) analysis historically focused on the human MHC region and, to a lesser extent, the KIR region on human chromosome 19, much work remains throughout the human genome and in non-human genomes using phase-segregated observational techniques. We invite authors to explore the utility and significance of the CPS concept and methods in any diploid genome to address important medical and agricultural complex traits. Also, we seek reports addressing relatively unexplored questions such as comparisons of genomic architecture variation among ethnic groups and the effect of varying genetic marker type (e.g., SNP, indel, gene) and their polymorphic nature (e.g., minor allele frequency) on observed genomic architecture. We shall provide a forum for comparisons of and explanations for major differences in experimental observations obtained by different pedigree-based and unrelated genotype-based haplotype statistical methodologies. We shall consider four broad subcategories within the context of AH/CEH (CPS) research: 1: Background, history, implementation, and the future: use of pedigrees, model development, trait/disease association (with a focus on autoimmunity) and the way forward. 2: Genetic regulation, primate evolution and genomic duplication. 3: Reconciling CPS results with SNPs, bioinformatics, LD and homozygosity. 4: Applications other than trait/disease association (e.g., transplantation, diagnosis, forensics).

We welcome AH/CEH (CPS) Original Research, Review, and General Commentary manuscripts on any diploid species and any genomic region(s), including the MHC, related but not necessarily limited to:
• Pedigree-based or homozygous cell analyses of population-level haplotype genomic architecture (polymorphism) or genetic analysis.
• Effect of structural variant type (e.g., SNP, indel, gene/pseudogene allele, haplotype), polymorphism, or location (e.g., exon, intron/UTR, intergenic, chromosomal position) on population-level genomic architecture or genetic association.
• Comparison of pedigree-based single species' genomic architecture across subpopulation, trait, evolutionary, or human-selected breed groups.
• Using the same database(s), comparison of pedigree-phased haplotype results with those using LD or other statistically-based methods applied to unrelated genotypes.
• Comparison of pedigree-phased population-level haplotype genomic architecture either between species or between different genomic regions within a single species.
• Haplotype-based analytical bioinformatics or computational biology methods and software, including comparisons of such.
• Medical (with a focus on complex genetic disease) or agricultural applications.

Keywords: haplotype, genomic architecture, polymorphism, major histocompatibility complex, linkage disequilibrium

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