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A new method for long-range haplotype phasing with short-read sequencing data.

一种利用短读长测序数据进行长程单倍型定相的新方法。

基本信息

批准号：
9048335
负责人：
Marco Blanchette
金额：
$ 14.98万
依托单位：
DOVETAIL GENOMICS, LLC
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-07-05 至 2017-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9048335
关键词：
Base Pairing Cancer cell line Chromatin Chromosomes Clinic Clinical Complex Computer Simulation Computer software DNA DNA Sequence DNA Sequence Rearrangement Data Data Set Development Diploid Cells Disease Equilibrium Equipment Genes Genetic Counseling Genome Genomics Goals Haploidy Haplotypes Health Hereditary Disease Heterozygote High-Throughput Nucleotide Sequencing Human Genome In Vitro Individual Libraries Link Malignant Neoplasms Medicine Methods Molecular Biology Molecular Weight Outcome Phase Process Reading Reagent Reference Standards Sampling Scheme Staging Structure Techniques Technology Testing Variant Work base clinical application commercial application cost crosslink genetic disorder diagnosis genetic pedigree genetic variant genomic data genomic variation human disease improved interest meetings method development new technology novel strategies public health relevance reconstitution reference genome restriction enzyme scale up whole genome

项目摘要

DESCRIPTION (provided by applicant): A key challenge to the integration of genomics into the clinical setting is the ability to link genomic variation within a chromosome, i.e., to separat and characterize the two copies of a genome present in a diploid cell. This linkage process, known as haplotype phasing, is difficult to accomplish using the shortread, highthroughput sequencing technologies in routine use today. Haplotype phasing is critical for many clinical genomics interests, including linking compound heterozygote variants within diseaseassociated genes and untangling complex genomic rearrangements frequently found in cancers. Attempts to circumvent the limitations of shortread sequencing in haplotype phasing by using longerread sequencing technology are in the early stages of development and years from routine use. Given the demand for haplotype phasing in the clinical setting, new approaches that can immediately leverage proven shortread sequencing technologies are needed. Dovetail Genomics has developed and generated preliminary feasibility data for a method that generates shortread sequencing libraries for phasing haplotypes. This technique promises more complete, contiguous, and accurate haplotype characterization than existing approaches, and does so simply and affordably. In order to successfully develop the concept and continue to demonstrate feasibly, the following two goals will be met: First computational models will be used to determine the parameters required for haplotype phasing with the method, and these parameters will be tested and adjusted. Second, the method's capacity to phase haplotypes and reconstruct reference genome standards at high accuracy and completeness will be tested. Successful demonstration of feasibility will permit further development of the method with the goal of developing a commercially viable kit and complementary software analysis suite for clinical genomics.