学术报告
题目：$1,000 Whole-Genome Haplotyping by Single-Chromosome Sequencing
报告人：马丽博士，亚特兰大的Morehouse医学院
时间：2014年6月17号下午3：00
地点：医学楼2400室
报告内容简介
Haplotype analysis is important for mapping disease genes, elucidating population histories, studying the evolutionary genetics and exploring cis interactions in the regulation of gene expression.Establishing a high-throughput way to detect chromosome-length haplotype is critical for understanding genetic functions and disease related genetic information. The objectives of this study are to (i) develop a high-throughput approach to detect chromosome length haplotype;(ii) integrate molecular haplotyping seeds with computer haplotyping to obtain complete whole genome haplotype; (iii) develop a low depth single chromosome next-generation sequencing to reduce the cost.
We microdissected single chromosomes using a computer-assisted Leica microdissection system. The microdissection harvests were subjected to whole genome amplification (WGA), and whole-genome genotyping with an Illumina (CNV370). Totally 24,245 heterozygous SNPs were haplotyped, among which 2,089 SNPs were phased by more than one microdissection harvests. 98.85% of these SNPs (2,065 SNPs) showed consistent results between different microdissection harvests.The technology provides the first high-throughput experimental method for determination of long-range haplotypes for large-scale and genome-wide studies. To solve the technical caveat inherited from single-molecule whole-genome amplificationin which 70% of loci were not amplified and phased in our pipeline, we developed a computational approach, which was coded in the software HiFi (haplotype imputation from incomplete data), to achieve thewhole-genome haplotyping. HiFi exhaustively seeks for non-ambiguous matches to the seed haplotypes and seed genotypes of a person among the reference haplotypes in each sliding window. We experimentally validated the HiFi accuracy by single-chromosome haplotyping. The accuracy of HiFi results was also observed to be 98.23% among imputed heterozygous loci. Finally, to reduce the cost of this experimental whole-genome haplotyping pipeline, we developed another approach employing the extremely low-depth single-chromosome sequencing strategy and computational imputation to achieve low-cost whole genome haplotyping. This approach has been coded into the software LowDepth. It can achieve a phasing accuracy of 98.13% with as low as 0.14x depth, with a cost of about $1,000 for whole-genome haplotype determination.
In summary, we have developed the first high-throughput and cost-efficient pipeline for whole-genome chromosome-length haplotype determination. It has solved the issue on haplotyping for genetic and genomic studies.