BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference
Abstract We introduce a Bayesian semi-supervised method for estimating cell counts from DNA methylation by leveraging an easily obtainable prior knowledge on the cell-type composition distribution of the studied tissue. We show mathematically and empirically that alternative methods which attempt to...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-09-01
|
| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-018-1513-2 |
| _version_ | 1818525333389836288 |
|---|---|
| author | Elior Rahmani Regev Schweiger Liat Shenhav Theodora Wingert Ira Hofer Eilon Gabel Eleazar Eskin Eran Halperin |
| author_facet | Elior Rahmani Regev Schweiger Liat Shenhav Theodora Wingert Ira Hofer Eilon Gabel Eleazar Eskin Eran Halperin |
| author_sort | Elior Rahmani |
| collection | DOAJ |
| description | Abstract We introduce a Bayesian semi-supervised method for estimating cell counts from DNA methylation by leveraging an easily obtainable prior knowledge on the cell-type composition distribution of the studied tissue. We show mathematically and empirically that alternative methods which attempt to infer cell counts without methylation reference only capture linear combinations of cell counts rather than provide one component per cell type. Our approach allows the construction of components such that each component corresponds to a single cell type, and provides a new opportunity to investigate cell compositions in genomic studies of tissues for which it was not possible before. |
| first_indexed | 2024-12-11T06:08:01Z |
| format | Article |
| id | doaj.art-f30ce8e98b92451bafd99e6a60756424 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-11T06:08:01Z |
| publishDate | 2018-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-f30ce8e98b92451bafd99e6a607564242022-12-22T01:18:13ZengBMCGenome Biology1474-760X2018-09-0119111810.1186/s13059-018-1513-2BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation referenceElior Rahmani0Regev Schweiger1Liat Shenhav2Theodora Wingert3Ira Hofer4Eilon Gabel5Eleazar Eskin6Eran Halperin7Department of Computer Science, University of California Los AngelesBlavatnik School of Computer Science, Tel Aviv UniversityDepartment of Computer Science, University of California Los AngelesDepartment of Anesthesiology and Perioperative Medicine, University of California Los AngelesDepartment of Anesthesiology and Perioperative Medicine, University of California Los AngelesDepartment of Anesthesiology and Perioperative Medicine, University of California Los AngelesDepartment of Computer Science, University of California Los AngelesDepartment of Computer Science, University of California Los AngelesAbstract We introduce a Bayesian semi-supervised method for estimating cell counts from DNA methylation by leveraging an easily obtainable prior knowledge on the cell-type composition distribution of the studied tissue. We show mathematically and empirically that alternative methods which attempt to infer cell counts without methylation reference only capture linear combinations of cell counts rather than provide one component per cell type. Our approach allows the construction of components such that each component corresponds to a single cell type, and provides a new opportunity to investigate cell compositions in genomic studies of tissues for which it was not possible before.http://link.springer.com/article/10.1186/s13059-018-1513-2DNA methylationCell-type compositionTissue heterogeneityCell countsBayesian modelEpigenetics |
| spellingShingle | Elior Rahmani Regev Schweiger Liat Shenhav Theodora Wingert Ira Hofer Eilon Gabel Eleazar Eskin Eran Halperin BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference Genome Biology DNA methylation Cell-type composition Tissue heterogeneity Cell counts Bayesian model Epigenetics |
| title | BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference |
| title_full | BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference |
| title_fullStr | BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference |
| title_full_unstemmed | BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference |
| title_short | BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference |
| title_sort | bayescce a bayesian framework for estimating cell type composition from dna methylation without the need for methylation reference |
| topic | DNA methylation Cell-type composition Tissue heterogeneity Cell counts Bayesian model Epigenetics |
| url | http://link.springer.com/article/10.1186/s13059-018-1513-2 |
| work_keys_str_mv | AT eliorrahmani bayescceabayesianframeworkforestimatingcelltypecompositionfromdnamethylationwithouttheneedformethylationreference AT regevschweiger bayescceabayesianframeworkforestimatingcelltypecompositionfromdnamethylationwithouttheneedformethylationreference AT liatshenhav bayescceabayesianframeworkforestimatingcelltypecompositionfromdnamethylationwithouttheneedformethylationreference AT theodorawingert bayescceabayesianframeworkforestimatingcelltypecompositionfromdnamethylationwithouttheneedformethylationreference AT irahofer bayescceabayesianframeworkforestimatingcelltypecompositionfromdnamethylationwithouttheneedformethylationreference AT eilongabel bayescceabayesianframeworkforestimatingcelltypecompositionfromdnamethylationwithouttheneedformethylationreference AT eleazareskin bayescceabayesianframeworkforestimatingcelltypecompositionfromdnamethylationwithouttheneedformethylationreference AT eranhalperin bayescceabayesianframeworkforestimatingcelltypecompositionfromdnamethylationwithouttheneedformethylationreference |