Estimation of allele frequency and association mapping using next-generation sequencing data

Su Yeon Kim; Kirk E Lohmueller; Anders Albrechtsen; Yingrui Li; Thorfinn Korneliussen; Geng Tian; Niels Grarup; Tao Jiang; Gitte Andersen; Daniel Rinse Witte; Torben Jorgensen; Torben Hansen; Oluf Pedersen; Jun Wang; Rasmus Nielsen

doi:10.1186/1471-2105-12-231

Estimation of allele frequency and association mapping using next-generation sequencing data

Su Yeon Kim, Kirk E Lohmueller, Anders Albrechtsen, Yingrui Li, Thorfinn Korneliussen, Geng Tian, Niels Grarup, Tao Jiang, Gitte Andersen, Daniel Rinse Witte, Torben Jorgensen, Torben Hansen, Oluf Pedersen, Jun Wang, Rasmus Nielsen

147 Citations (Scopus)

Abstract

Estimation of allele frequency is of fundamental importance in population genetic analyses and in association mapping. In most studies using next-generation sequencing, a cost effective approach is to use medium or low-coverage data (e.g., <15X). However, SNP calling and allele frequency estimation in such studies is associated with substantial statistical uncertainty because of varying coverage and high error rates.

Original language	English
Journal	B M C Bioinformatics
Volume	12
Pages (from-to)	231
ISSN	1471-2105
DOIs	https://doi.org/10.1186/1471-2105-12-231
Publication status	Published - 2011

Keywords

Gene Frequency
Genetics, Population
Genotype
High-Throughput Nucleotide Sequencing
Humans
Likelihood Functions
Polymorphism, Single Nucleotide
Sequence Analysis, DNA

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10.1186/1471-2105-12-231

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Kim, S. Y., Lohmueller, K. E., Albrechtsen, A., Li, Y., Korneliussen, T., Tian, G., Grarup, N., Jiang, T., Andersen, G., Witte, D. R., Jorgensen, T., Hansen, T., Pedersen, O., Wang, J., & Nielsen, R. (2011). Estimation of allele frequency and association mapping using next-generation sequencing data. B M C Bioinformatics, 12, 231. https://doi.org/10.1186/1471-2105-12-231

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title = "Estimation of allele frequency and association mapping using next-generation sequencing data",

abstract = "Estimation of allele frequency is of fundamental importance in population genetic analyses and in association mapping. In most studies using next-generation sequencing, a cost effective approach is to use medium or low-coverage data (e.g., <15X). However, SNP calling and allele frequency estimation in such studies is associated with substantial statistical uncertainty because of varying coverage and high error rates.",

keywords = "Gene Frequency, Genetics, Population, Genotype, High-Throughput Nucleotide Sequencing, Humans, Likelihood Functions, Polymorphism, Single Nucleotide, Sequence Analysis, DNA",

author = "Kim, {Su Yeon} and Lohmueller, {Kirk E} and Anders Albrechtsen and Yingrui Li and Thorfinn Korneliussen and Geng Tian and Niels Grarup and Tao Jiang and Gitte Andersen and Witte, {Daniel Rinse} and Torben Jorgensen and Torben Hansen and Oluf Pedersen and Jun Wang and Rasmus Nielsen",

year = "2011",

doi = "10.1186/1471-2105-12-231",

language = "English",

volume = "12",

pages = "231",

journal = "B M C Bioinformatics",

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T1 - Estimation of allele frequency and association mapping using next-generation sequencing data

AU - Kim, Su Yeon

AU - Lohmueller, Kirk E

AU - Albrechtsen, Anders

AU - Li, Yingrui

AU - Korneliussen, Thorfinn

AU - Tian, Geng

AU - Grarup, Niels

AU - Jiang, Tao

AU - Andersen, Gitte

AU - Witte, Daniel Rinse

AU - Jorgensen, Torben

AU - Hansen, Torben

AU - Pedersen, Oluf

AU - Wang, Jun

AU - Nielsen, Rasmus

PY - 2011

Y1 - 2011

N2 - Estimation of allele frequency is of fundamental importance in population genetic analyses and in association mapping. In most studies using next-generation sequencing, a cost effective approach is to use medium or low-coverage data (e.g., <15X). However, SNP calling and allele frequency estimation in such studies is associated with substantial statistical uncertainty because of varying coverage and high error rates.

AB - Estimation of allele frequency is of fundamental importance in population genetic analyses and in association mapping. In most studies using next-generation sequencing, a cost effective approach is to use medium or low-coverage data (e.g., <15X). However, SNP calling and allele frequency estimation in such studies is associated with substantial statistical uncertainty because of varying coverage and high error rates.

KW - Gene Frequency

KW - Genetics, Population

KW - Genotype

KW - High-Throughput Nucleotide Sequencing

KW - Humans

KW - Likelihood Functions

KW - Polymorphism, Single Nucleotide

KW - Sequence Analysis, DNA

U2 - 10.1186/1471-2105-12-231

DO - 10.1186/1471-2105-12-231

M3 - Journal article

C2 - 21663684

SN - 1471-2105

VL - 12

SP - 231

JO - B M C Bioinformatics

JF - B M C Bioinformatics

ER -

Estimation of allele frequency and association mapping using next-generation sequencing data

Abstract

Keywords

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