Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker Density
ABSTRACT: Objective: Analyze the information contained in homozygous haplotypes detected with high density genotyping. Methods: We analyze the genotypes of ∼2,500 markers on chr 22 in 12 population samples, each including 200 individuals. We develop a measure of disequilibrium based on haplotype hom...
- Autores:
-
Bedoya Berrío, Gabriel de Jesús
Lin, Chia-Ho
Service, Susan
Chen, Yuguo
Freimer, Nelson
Sabatti, Chiara
Wang, Hui
Ospina Duque, Jorge
- Tipo de recurso:
- Article of investigation
- Fecha de publicación:
- 2006
- Institución:
- Universidad de Antioquia
- Repositorio:
- Repositorio UdeA
- Idioma:
- eng
- OAI Identifier:
- oai:bibliotecadigital.udea.edu.co:10495/41530
- Acceso en línea:
- https://hdl.handle.net/10495/41530
- Palabra clave:
- Consanguinidad
Consanguinity
Cromosomas Humanos Par 22
Chromosomes, Human, Pair 22
Frecuencia de los Genes
Gene Frequency
Marcadores Genéticos
Genetic Markers
Cadenas de Markov
Markov Chains
Homocigoto
Homozygote
https://id.nlm.nih.gov/mesh/D003241
https://id.nlm.nih.gov/mesh/D002892
https://id.nlm.nih.gov/mesh/D005787
https://id.nlm.nih.gov/mesh/D005819
https://id.nlm.nih.gov/mesh/D008390
https://id.nlm.nih.gov/mesh/D006720
- Rights
- openAccess
- License
- https://creativecommons.org/licenses/by-nc/4.0/
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Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker Density |
| title |
Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker Density |
| spellingShingle |
Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker Density Consanguinidad Consanguinity Cromosomas Humanos Par 22 Chromosomes, Human, Pair 22 Frecuencia de los Genes Gene Frequency Marcadores Genéticos Genetic Markers Cadenas de Markov Markov Chains Homocigoto Homozygote https://id.nlm.nih.gov/mesh/D003241 https://id.nlm.nih.gov/mesh/D002892 https://id.nlm.nih.gov/mesh/D005787 https://id.nlm.nih.gov/mesh/D005819 https://id.nlm.nih.gov/mesh/D008390 https://id.nlm.nih.gov/mesh/D006720 |
| title_short |
Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker Density |
| title_full |
Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker Density |
| title_fullStr |
Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker Density |
| title_full_unstemmed |
Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker Density |
| title_sort |
Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker Density |
| dc.creator.fl_str_mv |
Bedoya Berrío, Gabriel de Jesús Lin, Chia-Ho Service, Susan Chen, Yuguo Freimer, Nelson Sabatti, Chiara Wang, Hui Ospina Duque, Jorge |
| dc.contributor.author.none.fl_str_mv |
Bedoya Berrío, Gabriel de Jesús Lin, Chia-Ho Service, Susan Chen, Yuguo Freimer, Nelson Sabatti, Chiara Wang, Hui Ospina Duque, Jorge |
| dc.contributor.researchgroup.spa.fl_str_mv |
Genética Molecular (GENMOL) Grupo de Investigación en Psiquiatría GIPSI |
| dc.subject.decs.none.fl_str_mv |
Consanguinidad Consanguinity Cromosomas Humanos Par 22 Chromosomes, Human, Pair 22 Frecuencia de los Genes Gene Frequency Marcadores Genéticos Genetic Markers Cadenas de Markov Markov Chains Homocigoto Homozygote |
| topic |
Consanguinidad Consanguinity Cromosomas Humanos Par 22 Chromosomes, Human, Pair 22 Frecuencia de los Genes Gene Frequency Marcadores Genéticos Genetic Markers Cadenas de Markov Markov Chains Homocigoto Homozygote https://id.nlm.nih.gov/mesh/D003241 https://id.nlm.nih.gov/mesh/D002892 https://id.nlm.nih.gov/mesh/D005787 https://id.nlm.nih.gov/mesh/D005819 https://id.nlm.nih.gov/mesh/D008390 https://id.nlm.nih.gov/mesh/D006720 |
| dc.subject.meshuri.none.fl_str_mv |
https://id.nlm.nih.gov/mesh/D003241 https://id.nlm.nih.gov/mesh/D002892 https://id.nlm.nih.gov/mesh/D005787 https://id.nlm.nih.gov/mesh/D005819 https://id.nlm.nih.gov/mesh/D008390 https://id.nlm.nih.gov/mesh/D006720 |
| description |
ABSTRACT: Objective: Analyze the information contained in homozygous haplotypes detected with high density genotyping. Methods: We analyze the genotypes of ∼2,500 markers on chr 22 in 12 population samples, each including 200 individuals. We develop a measure of disequilibrium based on haplotype homozygosity and an algorithm to identify genomic segments characterized by non-random homozygosity (NRH), taking into account allele frequencies, missing data, genotyping error, and linkage disequilibrium. Results: We show how our measure of linkage disequilibrium based on homozygosity leads to results comparable to those of R2, as well as the importance of correcting for small sample variation when evaluating D′. We observe that the regions that harbor NRH segments tend to be consistent across populations, are gene rich, and are characterized by lower recombination. Conclusions: It is crucial to take into account LD patterns when interpreting long stretches of homozygous markers. |
| publishDate |
2006 |
| dc.date.issued.none.fl_str_mv |
2006 |
| dc.date.accessioned.none.fl_str_mv |
2024-08-28T01:01:59Z |
| dc.date.available.none.fl_str_mv |
2024-08-28T01:01:59Z |
| dc.type.spa.fl_str_mv |
Artículo de investigación |
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http://purl.org/coar/resource_type/c_2df8fbb1 |
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https://purl.org/redcol/resource_type/ART |
| dc.type.coarversion.spa.fl_str_mv |
http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.driver.spa.fl_str_mv |
info:eu-repo/semantics/article |
| dc.type.version.spa.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
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http://purl.org/coar/resource_type/c_2df8fbb1 |
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publishedVersion |
| dc.identifier.issn.none.fl_str_mv |
0001-5652 |
| dc.identifier.uri.none.fl_str_mv |
https://hdl.handle.net/10495/41530 |
| dc.identifier.doi.none.fl_str_mv |
10.1159/000096599 |
| dc.identifier.eissn.none.fl_str_mv |
1423-0062 |
| identifier_str_mv |
0001-5652 10.1159/000096599 1423-0062 |
| url |
https://hdl.handle.net/10495/41530 |
| dc.language.iso.spa.fl_str_mv |
eng |
| language |
eng |
| dc.relation.ispartofjournalabbrev.spa.fl_str_mv |
Hum. Hered. |
| dc.relation.citationendpage.spa.fl_str_mv |
189 |
| dc.relation.citationstartpage.spa.fl_str_mv |
175 |
| dc.relation.citationvolume.spa.fl_str_mv |
62 |
| dc.relation.ispartofjournal.spa.fl_str_mv |
Human Heredity |
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https://creativecommons.org/licenses/by-nc/4.0/ |
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http://creativecommons.org/licenses/by-nc/2.5/co/ |
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info:eu-repo/semantics/openAccess |
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https://creativecommons.org/licenses/by-nc/4.0/ http://creativecommons.org/licenses/by-nc/2.5/co/ http://purl.org/coar/access_right/c_abf2 |
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openAccess |
| dc.format.extent.spa.fl_str_mv |
15 páginas |
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application/pdf |
| dc.publisher.spa.fl_str_mv |
Karger |
| dc.publisher.place.spa.fl_str_mv |
Basilea, Suiza |
| institution |
Universidad de Antioquia |
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Bedoya Berrío, Gabriel de JesúsLin, Chia-HoService, SusanChen, YuguoFreimer, NelsonSabatti, ChiaraWang, HuiOspina Duque, JorgeGenética Molecular (GENMOL)Grupo de Investigación en Psiquiatría GIPSI2024-08-28T01:01:59Z2024-08-28T01:01:59Z20060001-5652https://hdl.handle.net/10495/4153010.1159/0000965991423-0062ABSTRACT: Objective: Analyze the information contained in homozygous haplotypes detected with high density genotyping. Methods: We analyze the genotypes of ∼2,500 markers on chr 22 in 12 population samples, each including 200 individuals. We develop a measure of disequilibrium based on haplotype homozygosity and an algorithm to identify genomic segments characterized by non-random homozygosity (NRH), taking into account allele frequencies, missing data, genotyping error, and linkage disequilibrium. Results: We show how our measure of linkage disequilibrium based on homozygosity leads to results comparable to those of R2, as well as the importance of correcting for small sample variation when evaluating D′. We observe that the regions that harbor NRH segments tend to be consistent across populations, are gene rich, and are characterized by lower recombination. Conclusions: It is crucial to take into account LD patterns when interpreting long stretches of homozygous markers.COL0006723COL002914715 páginasapplication/pdfengKargerBasilea, Suizahttps://creativecommons.org/licenses/by-nc/4.0/http://creativecommons.org/licenses/by-nc/2.5/co/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker DensityArtículo de investigaciónhttp://purl.org/coar/resource_type/c_2df8fbb1https://purl.org/redcol/resource_type/ARThttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionConsanguinidadConsanguinityCromosomas Humanos Par 22Chromosomes, Human, Pair 22Frecuencia de los GenesGene FrequencyMarcadores GenéticosGenetic MarkersCadenas de MarkovMarkov ChainsHomocigotoHomozygotehttps://id.nlm.nih.gov/mesh/D003241https://id.nlm.nih.gov/mesh/D002892https://id.nlm.nih.gov/mesh/D005787https://id.nlm.nih.gov/mesh/D005819https://id.nlm.nih.gov/mesh/D008390https://id.nlm.nih.gov/mesh/D006720Hum. 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