Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds

Nina Bosch, Geòrgia Escaramís, Josep M. Mercader, Lluís Armengol, Xavier P. Estivill

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Copy number variants contribute extensively to inter-individual genomic differences, but little is known about their inter-population variability and diversity. In a previous study (Bosch et al., 2007; 16:2572-2582), we reported that the primate-specific gene family FAM90A, which accounts for as many as 25 members in the human reference assembly, has expanded the number of FAM90A clusters across the hominoid lineage. Here we examined the copy number variability of FAM90A genes in 260 HapMap samples of European, African, and Asian ancestry, and showed significant inter-population differences (p < 0.0001). Based on the recent study of Stranger et al. (2007; 315:848-853), we also explored the correlation between copy number variability and expression levels of the FAM90A gene family. Despite the high genomic variability, we found a low correlation between FAM90A copy number and expression levels, which could be due to the action of independent trans-acting factors. Our results show that FAM90A is highly variable in copy number between individuals and between populations. However, this variability has little impact on gene expression levels, thus highlighting the importance of genomic variability for genes located in regions containing segmental duplications.

Original languageEnglish
Pages (from-to)113-117
Number of pages5
JournalGene
Volume420
Issue number2
DOIs
Publication statusPublished - 1 Sep 2008
Externally publishedYes

Fingerprint

Genes
Genomic Segmental Duplications
HapMap Project
Population
Trans-Activators
Individuality
Primates
Gene Expression

Keywords

  • FAM90A (family with sequence similarity 90, GenBank: NM_018088)
  • Inter-population variability
  • Real-time PCR

ASJC Scopus subject areas

  • Medicine(all)
  • Genetics

Cite this

Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds. / Bosch, Nina; Escaramís, Geòrgia; Mercader, Josep M.; Armengol, Lluís; Estivill, Xavier P.

In: Gene, Vol. 420, No. 2, 01.09.2008, p. 113-117.

Research output: Contribution to journalArticle

Bosch, Nina ; Escaramís, Geòrgia ; Mercader, Josep M. ; Armengol, Lluís ; Estivill, Xavier P. / Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds. In: Gene. 2008 ; Vol. 420, No. 2. pp. 113-117.
@article{3a1f817e62ee4becb0618a66c4937fdb,
title = "Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds",
abstract = "Copy number variants contribute extensively to inter-individual genomic differences, but little is known about their inter-population variability and diversity. In a previous study (Bosch et al., 2007; 16:2572-2582), we reported that the primate-specific gene family FAM90A, which accounts for as many as 25 members in the human reference assembly, has expanded the number of FAM90A clusters across the hominoid lineage. Here we examined the copy number variability of FAM90A genes in 260 HapMap samples of European, African, and Asian ancestry, and showed significant inter-population differences (p < 0.0001). Based on the recent study of Stranger et al. (2007; 315:848-853), we also explored the correlation between copy number variability and expression levels of the FAM90A gene family. Despite the high genomic variability, we found a low correlation between FAM90A copy number and expression levels, which could be due to the action of independent trans-acting factors. Our results show that FAM90A is highly variable in copy number between individuals and between populations. However, this variability has little impact on gene expression levels, thus highlighting the importance of genomic variability for genes located in regions containing segmental duplications.",
keywords = "FAM90A (family with sequence similarity 90, GenBank: NM_018088), Inter-population variability, Real-time PCR",
author = "Nina Bosch and Ge{\`o}rgia Escaram{\'i}s and Mercader, {Josep M.} and Llu{\'i}s Armengol and Estivill, {Xavier P.}",
year = "2008",
month = "9",
day = "1",
doi = "10.1016/j.gene.2008.05.003",
language = "English",
volume = "420",
pages = "113--117",
journal = "Gene",
issn = "0378-1119",
publisher = "Elsevier",
number = "2",

}

TY - JOUR

T1 - Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds

AU - Bosch, Nina

AU - Escaramís, Geòrgia

AU - Mercader, Josep M.

AU - Armengol, Lluís

AU - Estivill, Xavier P.

PY - 2008/9/1

Y1 - 2008/9/1

N2 - Copy number variants contribute extensively to inter-individual genomic differences, but little is known about their inter-population variability and diversity. In a previous study (Bosch et al., 2007; 16:2572-2582), we reported that the primate-specific gene family FAM90A, which accounts for as many as 25 members in the human reference assembly, has expanded the number of FAM90A clusters across the hominoid lineage. Here we examined the copy number variability of FAM90A genes in 260 HapMap samples of European, African, and Asian ancestry, and showed significant inter-population differences (p < 0.0001). Based on the recent study of Stranger et al. (2007; 315:848-853), we also explored the correlation between copy number variability and expression levels of the FAM90A gene family. Despite the high genomic variability, we found a low correlation between FAM90A copy number and expression levels, which could be due to the action of independent trans-acting factors. Our results show that FAM90A is highly variable in copy number between individuals and between populations. However, this variability has little impact on gene expression levels, thus highlighting the importance of genomic variability for genes located in regions containing segmental duplications.

AB - Copy number variants contribute extensively to inter-individual genomic differences, but little is known about their inter-population variability and diversity. In a previous study (Bosch et al., 2007; 16:2572-2582), we reported that the primate-specific gene family FAM90A, which accounts for as many as 25 members in the human reference assembly, has expanded the number of FAM90A clusters across the hominoid lineage. Here we examined the copy number variability of FAM90A genes in 260 HapMap samples of European, African, and Asian ancestry, and showed significant inter-population differences (p < 0.0001). Based on the recent study of Stranger et al. (2007; 315:848-853), we also explored the correlation between copy number variability and expression levels of the FAM90A gene family. Despite the high genomic variability, we found a low correlation between FAM90A copy number and expression levels, which could be due to the action of independent trans-acting factors. Our results show that FAM90A is highly variable in copy number between individuals and between populations. However, this variability has little impact on gene expression levels, thus highlighting the importance of genomic variability for genes located in regions containing segmental duplications.

KW - FAM90A (family with sequence similarity 90, GenBank: NM_018088)

KW - Inter-population variability

KW - Real-time PCR

UR - http://www.scopus.com/inward/record.url?scp=47149114158&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=47149114158&partnerID=8YFLogxK

U2 - 10.1016/j.gene.2008.05.003

DO - 10.1016/j.gene.2008.05.003

M3 - Article

VL - 420

SP - 113

EP - 117

JO - Gene

JF - Gene

SN - 0378-1119

IS - 2

ER -