A simple and efficient algorithm for genome‐wide homozygosity analysis in disease
Abstract Here we propose a simple statistical algorithm for rapidly scoring loci associated with disease or traits due to recessive mutations or deletions using genome‐wide single nucleotide polymorphism genotyping case–control data in unrelated individuals. This algorithm identifies loci by definin...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2009-09-01
|
| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/msb.2009.53 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849225765070045184 |
|---|---|
| author | Wei Liu Jinhui Ding Jesse Raphael Gibbs Sue Jane Wang John Hardy Andrew Singleton |
| author_facet | Wei Liu Jinhui Ding Jesse Raphael Gibbs Sue Jane Wang John Hardy Andrew Singleton |
| author_sort | Wei Liu |
| collection | DOAJ |
| description | Abstract Here we propose a simple statistical algorithm for rapidly scoring loci associated with disease or traits due to recessive mutations or deletions using genome‐wide single nucleotide polymorphism genotyping case–control data in unrelated individuals. This algorithm identifies loci by defining homozygous segments of the genome present at significantly different frequencies between cases and controls. We found that false positive loci could be effectively removed from the output of this procedure by applying different physical size thresholds for the homozygous segments. This procedure is then conducted iteratively using random sub‐datasets until the number of selected loci converges. We demonstrate this method in a publicly available data set for Alzheimer's disease and identify 26 candidate risk loci in the 22 autosomes. In this data set, these loci can explain 75% of the genetic risk variability of the disease. |
| format | Article |
| id | doaj-art-5db228bb56624e238b2e949d2526c93e |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2009-09-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-5db228bb56624e238b2e949d2526c93e2025-08-24T11:59:19ZengSpringer NatureMolecular Systems Biology1744-42922009-09-01511610.1038/msb.2009.53A simple and efficient algorithm for genome‐wide homozygosity analysis in diseaseWei Liu0Jinhui Ding1Jesse Raphael Gibbs2Sue Jane Wang3John Hardy4Andrew Singleton5Laboratory of Neurogenetics, NIA, Porter Neuroscience Building, NIH Main CampusLaboratory of Neurogenetics, NIA, Porter Neuroscience Building, NIH Main CampusLaboratory of Neurogenetics, NIA, Porter Neuroscience Building, NIH Main CampusOffice of Biostatistics, OTS, Center for Drug Evaluation and Research, US Food and Drug AdministrationDepartment of Molecular Neuroscience and Reta Lila Weston Laboratories, Institute of Neurology, University College LondonLaboratory of Neurogenetics, NIA, Porter Neuroscience Building, NIH Main CampusAbstract Here we propose a simple statistical algorithm for rapidly scoring loci associated with disease or traits due to recessive mutations or deletions using genome‐wide single nucleotide polymorphism genotyping case–control data in unrelated individuals. This algorithm identifies loci by defining homozygous segments of the genome present at significantly different frequencies between cases and controls. We found that false positive loci could be effectively removed from the output of this procedure by applying different physical size thresholds for the homozygous segments. This procedure is then conducted iteratively using random sub‐datasets until the number of selected loci converges. We demonstrate this method in a publicly available data set for Alzheimer's disease and identify 26 candidate risk loci in the 22 autosomes. In this data set, these loci can explain 75% of the genetic risk variability of the disease.https://doi.org/10.1038/msb.2009.53disease networkhomozygous segmentsrisk locistatistical algorithmwhole‐genome screening |
| spellingShingle | Wei Liu Jinhui Ding Jesse Raphael Gibbs Sue Jane Wang John Hardy Andrew Singleton A simple and efficient algorithm for genome‐wide homozygosity analysis in disease Molecular Systems Biology disease network homozygous segments risk loci statistical algorithm whole‐genome screening |
| title | A simple and efficient algorithm for genome‐wide homozygosity analysis in disease |
| title_full | A simple and efficient algorithm for genome‐wide homozygosity analysis in disease |
| title_fullStr | A simple and efficient algorithm for genome‐wide homozygosity analysis in disease |
| title_full_unstemmed | A simple and efficient algorithm for genome‐wide homozygosity analysis in disease |
| title_short | A simple and efficient algorithm for genome‐wide homozygosity analysis in disease |
| title_sort | simple and efficient algorithm for genome wide homozygosity analysis in disease |
| topic | disease network homozygous segments risk loci statistical algorithm whole‐genome screening |
| url | https://doi.org/10.1038/msb.2009.53 |
| work_keys_str_mv | AT weiliu asimpleandefficientalgorithmforgenomewidehomozygosityanalysisindisease AT jinhuiding asimpleandefficientalgorithmforgenomewidehomozygosityanalysisindisease AT jesseraphaelgibbs asimpleandefficientalgorithmforgenomewidehomozygosityanalysisindisease AT suejanewang asimpleandefficientalgorithmforgenomewidehomozygosityanalysisindisease AT johnhardy asimpleandefficientalgorithmforgenomewidehomozygosityanalysisindisease AT andrewsingleton asimpleandefficientalgorithmforgenomewidehomozygosityanalysisindisease AT weiliu simpleandefficientalgorithmforgenomewidehomozygosityanalysisindisease AT jinhuiding simpleandefficientalgorithmforgenomewidehomozygosityanalysisindisease AT jesseraphaelgibbs simpleandefficientalgorithmforgenomewidehomozygosityanalysisindisease AT suejanewang simpleandefficientalgorithmforgenomewidehomozygosityanalysisindisease AT johnhardy simpleandefficientalgorithmforgenomewidehomozygosityanalysisindisease AT andrewsingleton simpleandefficientalgorithmforgenomewidehomozygosityanalysisindisease |