DECATUR, GA, United States
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Li W.,Xi'an Jiaotong University | Li W.,Morehouse School of Medicine | Fu G.,4Dgenome, Inc. | Rao W.,4Dgenome, Inc. | And 7 more authors.
Bioinformatics | Year: 2015

We present a software tool called GenomeLaser that determines the haplotypes of each person from unphased high-throughput genotypes in family pedigrees. This method features high accuracy, chromosome-range phasing distance, linear computing, flexible pedigree types and flexible genetic marker types. © The Author 2015. Published by Oxford University Press. All rights reserved.


Li W.,Xi'an Jiaotong University | Li W.,Morehouse School of Medicine | Xu W.,Morehouse School of Medicine | Fu G.,4Dgenome, Inc. | And 9 more authors.
Gene | Year: 2015

Enormously growing genomic datasets present a new challenge on missing data imputation, a notoriously resource-demanding task. Haplotype imputation requires ethnicity-matched references. However, to date, haplotype references are not available for the majority of populations in the world. We explored to use existing unphased genotype datasets as references; if it succeeds, it will cover almost all of the populations in the world. The results showed that our HiFi software successfully yields 99.43% accuracy with unphased genotype references. Our method provides a cost-effective solution to breakthrough the bottleneck of limited reference availability for haplotype imputation in the big data era. © 2015 Elsevier B.V..


Grant
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 218.56K | Year: 2014

DESCRIPTION (provided by applicant): Haplotype is fundamental genetic information; it provides essential information for deciphering the functional and etiological roles of genetic variants. Current sequencing and genotyping technologies deliver only halfof the genetic information of each individual. They cannot deliver the other half of the information; the structural conformations of alleles or the haplotypes. Existing haplotyping technologies cannot meet the market needs on cost, labor, throughput, accuracy, resolution, and phasing distance; therefore, haplotype information has been absent from all but a handful of genome studies. We propose a cost-efficient technology towards commercialization to meet the unmet market needs for experimental haplotype determination. The proposed research in this grant application is based on the single-chromosome isolation approach that we developed recently. The low-resolution caveat of the first version of this approach has been resolved by our recently published w


PubMed | Morehouse School of Medicine, Xi'an Jiaotong University and 4Dgenome, Inc.
Type: Journal Article | Journal: Bioinformatics (Oxford, England) | Year: 2015

We present a software tool called GenomeLaser that determines the haplotypes of each person from unphased high-throughput genotypes in family pedigrees. This method features high accuracy, chromosome-range phasing distance, linear computing, flexible pedigree types and flexible genetic marker types.http://www.4dgenome.com/software/genomelaser.html.


PubMed | Morehouse School of Medicine, Xi'an Jiaotong University and 4Dgenome, Inc.
Type: Journal Article | Journal: Gene | Year: 2015

Enormously growing genomic datasets present a new challenge on missing data imputation, a notoriously resource-demanding task. Haplotype imputation requires ethnicity-matched references. However, to date, haplotype references are not available for the majority of populations in the world. We explored to use existing unphased genotype datasets as references; if it succeeds, it will cover almost all of the populations in the world. The results showed that our HiFi software successfully yields 99.43% accuracy with unphased genotype references. Our method provides a cost-effective solution to breakthrough the bottleneck of limited reference availability for haplotype imputation in the big data era.


PubMed | Morehouse School of Medicine and 4Dgenome, Inc.
Type: | Journal: Methods in molecular biology (Clifton, N.J.) | Year: 2017

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.

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