GENOTYPE AND COPY NUMBER CALLING
基因型和拷贝数检测
基本信息
- 批准号:8171736
- 负责人:
- 金额:$ 0.49万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2010
- 资助国家:美国
- 起止时间:2010-08-01 至 2011-07-31
- 项目状态:已结题
- 来源:
- 关键词:AddressAffectAffinityAllelesAttentionBindingCell LineComputer Retrieval of Information on Scientific Projects DatabaseCopy Number PolymorphismDNA copy numberDataFree EnergyFundingGenotypeGrantInstitutionLaboratoriesMethodsModelingNucleotidesRegression AnalysisResearchResearch PersonnelResourcesSamplingSingle Nucleotide PolymorphismSourceStructureUnited States National Institutes of Health
项目摘要
This subproject is one of many research subprojects utilizing the
resources provided by a Center grant funded by NIH/NCRR. The subproject and
investigator (PI) may have received primary funding from another NIH source,
and thus could be represented in other CRISP entries. The institution listed is
for the Center, which is not necessarily the institution for the investigator.
Affymetrix SNP arrays have been widely used for single-nucleotide polymorphism (SNP) genotype calling and DNA copy number variation inference. Although numerous methods have achieved high accuracy in these fields, most studies have paid little attention to the modeling of hybridization of probes to off-target allele sequences, which can affect the accuracy greatly. In this study, we address this issue and demonstrate that hybridization with mismatch nucleotides (HWMMN) occurs in all SNP probe-sets and has a critical effect on the estimation of allelic concentrations (ACs). We study sequence binding through binding free energy and then binding affinity, and develop a probe intensity composite representation (PICR) model. The PICR model allows the estimation of ACs at a given SNP through statistical regression. Furthermore, we demonstrate with cell-line data of known true copy numbers that the PICR model can achieve reasonable accuracy in copy number estimation at a single SNP locus, by using the ratio of the estimated AC of each sample to that of the reference sample, and can reveal subtle genotype structure of SNPs at abnormal loci. We also demonstrate with HapMap data that the PICR model yields accurate SNP genotype calls consistently across samples, laboratories and even across array platforms.
这个子项目是众多研究子项目之一
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Robert C. Elston其他文献
Aerosol bronchodilator delivery methods. Relative impact on pulmonary function and cost of respiratory care.
气雾剂支气管扩张剂输送方法。
- DOI:
- 发表时间:
1989 - 期刊:
- 影响因子:0
- 作者:
Warren R. Summer;Robert C. Elston;Linda Tharpe;Steve Nelson;E. Haponik - 通讯作者:
E. Haponik
AUGMENTATION OF THE ANTIBODY RESPONSE BY HAPTEN HELP
HAPTEN HELP 增强抗体反应
- DOI:
- 发表时间:
1985 - 期刊:
- 影响因子:0
- 作者:
Stephen H. Leech;Christopher F. Bryan;Robert C. Elston - 通讯作者:
Robert C. Elston
A non-parametric method finds genetic etiology of nicotine dependence differs in males and females
- DOI:
10.1016/j.drugalcdep.2015.07.372 - 发表时间:
2015-11-01 - 期刊:
- 影响因子:
- 作者:
Qing Lu;Changshuai Wei;Robert C. Elston;Olga Vsevolozhskaya - 通讯作者:
Olga Vsevolozhskaya
Measures of observer agreement when binomial data are collected in free operant situations
- DOI:
10.1007/bf01341225 - 发表时间:
1982-12-01 - 期刊:
- 影响因子:1.700
- 作者:
Robert C. Elston;Stephen R. Schroeder;Johannes Rojahn - 通讯作者:
Johannes Rojahn
Genetic analysis of von Willebrand's disease in two large pedigrees: a multivariate approach.
两个大家系中冯维勒布兰德病的遗传分析:多变量方法。
- DOI:
- 发表时间:
1980 - 期刊:
- 影响因子:0
- 作者:
Lynn R. Goldin;Robert C. Elston;J. B. Graham;Connie H. Miller;Edmond A. Murphy - 通讯作者:
Edmond A. Murphy
Robert C. Elston的其他文献
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{{ truncateString('Robert C. Elston', 18)}}的其他基金
SERVICE TO GENETIC EPIDEMIOLOGISTS AND USERS OF SAGE
为遗传流行病学家和 SAGE 用户提供服务
- 批准号:
8171714 - 财政年份:2010
- 资助金额:
$ 0.49万 - 项目类别:
DEVELOPMENT OF PORTABLE COMPUTER PROGRAMS FOR HUMAN GENETIC ANALYSIS
用于人类遗传分析的便携式计算机程序的开发
- 批准号:
8171710 - 财政年份:2010
- 资助金额:
$ 0.49万 - 项目类别:
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