Chromosome-Range Whole-Genome High-Throughput Experimental Haplotyping by Single-Chromosome Microdissection

Abstract

Haplotype is fundamental genetic information; it provides essential information for deciphering the functional and etiological roles of genetic variants. As haplotype information is closely related to the functional and etiological impact of genetic variants, it is widely anticipated that haplotype information will be extremely valuable in a wide spectra of applications, including academic research, clinical diagnosis of genetic disease and in the pharmaceutical industry. Haplotyping is essential for LD (linkage disequilibrium) mapping, functional studies on cis-interactions, big data imputation, association studies, population studies, and evolutionary studies. Unfortunately, current sequencing technologies and genotyping arrays do not routinely deliver this information for each individual, but yield only unphased genotypes. Here, we describe a high-throughput and cost-effective experimental protocol to obtain high-resolution chromosomal haplotypes of each individual diploid (including human) genome by the single-chromosome microdissection and sequencing approach.

Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

“…In addition to the already mentioned Bionano and fibre-FISH, several cytogenetic approaches have been used in interdependency with “orthodox” genomic studies (a changing concept, since genomic studies are progressively integrating research from all fields). These cytogenetic methodologies include chromosome microdissection [ 175 , 176 , 177 ], chromosome flow sorting [ 178 ], and assessment of chromatin interactions (e.g., Hi-C sequencing) [ 179 , 180 ]. Technologies like chromosome flow sorting, chromosome microdissection, and even magnetic bead capture offer an inventive, technical tackling of complex repetitive genomic regions, through the ability to isolate specific chromosomes/chromosomal regions [ 181 , 182 ].…”

Linkage Mapping and Discovery of Candidate Genes for Drought Tolerance in Rice During the Vegetative Growth Period

“…In contrast, haplotype analysis can more deeply analyze the combination of different genomic loci and their genetic characteristics in a single chromosome or a speci c chromosome region. This is particularly important for the study of heterosis and the discovery of ner allelic variation(Ma et al 2017). Haplotype analysis can reveal the genetic background of a trait by identifying the genetic markers associated with that trait.…”