Integrating genomic analysis with the genetic basis of gene expression

Preliminary evidence of the identification of causal genes for cardiovascular and metabolic traits related to nutrition in Mexicans

Raúl A. Bastarrachea, Esther C. Gallegos-Cabriales, Edna J. Nava-González, Karin Haack, V. Saroja Voruganti, Jac Charlesworth, Hugo A. Laviada-Molina, Rosa A. Veloz-Garza, Velia Margarita Cardenas-Villarreal, Salvador B. Valdovinos-Chavez, Patricia Gomez-Aguilar, Guillermo Meléndez, Juan Carlos López-Alvarenga, Harald H H Göring, Shelley A. Cole, John Blangero, Anthony G. Comuzzie, Jack W. Kent

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Whole-transcriptome expression profiling provides novel phenotypes for analysis of complex traits. Gene expression measurements reflect quantitative variation in transcript-specific messenger RNA levels and represent phenotypes lying close to the action of genes. Understanding the genetic basis of gene expression will provide insight into the processes that connect genotype to clinically significant traits representing a central tenet of system biology. Synchronous in vivo expression profiles of lymphocytes, muscle, and subcutaneous fat were obtained from healthyMexican men. Most genes were expressed at detectable levels inmultiple tissues, and RNA levels were correlated between tissue types. A subset of transcripts with high reliability of expression across tissues (estimated by intraclass correlation coefficients) was enriched for cis-regulated genes, suggesting that proximal sequence variants may influence expression similarly in different cellular environments. This integrative global gene expression profiling approach is proving extremely useful for identifying genes and pathways that contribute to complex clinical traits. Clearly, the coincidence of clinical trait quantitative trait loci and expression quantitative trait loci can help in the prioritization of positional candidate genes. Such data will be crucial for the formal integration of positional and transcriptomic information characterized as genetical genomics.

Original languageEnglish (US)
JournalAdvances in Nutrition
Volume3
Issue number4
DOIs
StatePublished - Jul 2012
Externally publishedYes

Fingerprint

nutrition
genomics
Gene Expression
gene expression
Genes
Quantitative Trait Loci
Gene Expression Profiling
genes
quantitative trait loci
Phenotype
phenotype
Systems Biology
prioritization
Subcutaneous Fat
subcutaneous fat
messenger RNA
Genomics
transcriptomics
transcriptome
lymphocytes

ASJC Scopus subject areas

  • Food Science
  • Medicine (miscellaneous)
  • Nutrition and Dietetics
  • Medicine(all)

Cite this

Integrating genomic analysis with the genetic basis of gene expression : Preliminary evidence of the identification of causal genes for cardiovascular and metabolic traits related to nutrition in Mexicans. / Bastarrachea, Raúl A.; Gallegos-Cabriales, Esther C.; Nava-González, Edna J.; Haack, Karin; Voruganti, V. Saroja; Charlesworth, Jac; Laviada-Molina, Hugo A.; Veloz-Garza, Rosa A.; Cardenas-Villarreal, Velia Margarita; Valdovinos-Chavez, Salvador B.; Gomez-Aguilar, Patricia; Meléndez, Guillermo; López-Alvarenga, Juan Carlos; Göring, Harald H H; Cole, Shelley A.; Blangero, John; Comuzzie, Anthony G.; Kent, Jack W.

In: Advances in Nutrition, Vol. 3, No. 4, 07.2012.

Research output: Contribution to journalArticle

Bastarrachea, RA, Gallegos-Cabriales, EC, Nava-González, EJ, Haack, K, Voruganti, VS, Charlesworth, J, Laviada-Molina, HA, Veloz-Garza, RA, Cardenas-Villarreal, VM, Valdovinos-Chavez, SB, Gomez-Aguilar, P, Meléndez, G, López-Alvarenga, JC, Göring, HHH, Cole, SA, Blangero, J, Comuzzie, AG & Kent, JW 2012, 'Integrating genomic analysis with the genetic basis of gene expression: Preliminary evidence of the identification of causal genes for cardiovascular and metabolic traits related to nutrition in Mexicans', Advances in Nutrition, vol. 3, no. 4. https://doi.org/10.3945/an.112.001925
Bastarrachea, Raúl A. ; Gallegos-Cabriales, Esther C. ; Nava-González, Edna J. ; Haack, Karin ; Voruganti, V. Saroja ; Charlesworth, Jac ; Laviada-Molina, Hugo A. ; Veloz-Garza, Rosa A. ; Cardenas-Villarreal, Velia Margarita ; Valdovinos-Chavez, Salvador B. ; Gomez-Aguilar, Patricia ; Meléndez, Guillermo ; López-Alvarenga, Juan Carlos ; Göring, Harald H H ; Cole, Shelley A. ; Blangero, John ; Comuzzie, Anthony G. ; Kent, Jack W. / Integrating genomic analysis with the genetic basis of gene expression : Preliminary evidence of the identification of causal genes for cardiovascular and metabolic traits related to nutrition in Mexicans. In: Advances in Nutrition. 2012 ; Vol. 3, No. 4.
@article{356f2b73b9cd486b9fda5696d581f253,
title = "Integrating genomic analysis with the genetic basis of gene expression: Preliminary evidence of the identification of causal genes for cardiovascular and metabolic traits related to nutrition in Mexicans",
abstract = "Whole-transcriptome expression profiling provides novel phenotypes for analysis of complex traits. Gene expression measurements reflect quantitative variation in transcript-specific messenger RNA levels and represent phenotypes lying close to the action of genes. Understanding the genetic basis of gene expression will provide insight into the processes that connect genotype to clinically significant traits representing a central tenet of system biology. Synchronous in vivo expression profiles of lymphocytes, muscle, and subcutaneous fat were obtained from healthyMexican men. Most genes were expressed at detectable levels inmultiple tissues, and RNA levels were correlated between tissue types. A subset of transcripts with high reliability of expression across tissues (estimated by intraclass correlation coefficients) was enriched for cis-regulated genes, suggesting that proximal sequence variants may influence expression similarly in different cellular environments. This integrative global gene expression profiling approach is proving extremely useful for identifying genes and pathways that contribute to complex clinical traits. Clearly, the coincidence of clinical trait quantitative trait loci and expression quantitative trait loci can help in the prioritization of positional candidate genes. Such data will be crucial for the formal integration of positional and transcriptomic information characterized as genetical genomics.",
author = "Bastarrachea, {Ra{\'u}l A.} and Gallegos-Cabriales, {Esther C.} and Nava-Gonz{\'a}lez, {Edna J.} and Karin Haack and Voruganti, {V. Saroja} and Jac Charlesworth and Laviada-Molina, {Hugo A.} and Veloz-Garza, {Rosa A.} and Cardenas-Villarreal, {Velia Margarita} and Valdovinos-Chavez, {Salvador B.} and Patricia Gomez-Aguilar and Guillermo Mel{\'e}ndez and L{\'o}pez-Alvarenga, {Juan Carlos} and G{\"o}ring, {Harald H H} and Cole, {Shelley A.} and John Blangero and Comuzzie, {Anthony G.} and Kent, {Jack W.}",
year = "2012",
month = "7",
doi = "10.3945/an.112.001925",
language = "English (US)",
volume = "3",
journal = "Advances in nutrition (Bethesda, Md.)",
issn = "2161-8313",
publisher = "American Society for Nutrition",
number = "4",

}

TY - JOUR

T1 - Integrating genomic analysis with the genetic basis of gene expression

T2 - Preliminary evidence of the identification of causal genes for cardiovascular and metabolic traits related to nutrition in Mexicans

AU - Bastarrachea, Raúl A.

AU - Gallegos-Cabriales, Esther C.

AU - Nava-González, Edna J.

AU - Haack, Karin

AU - Voruganti, V. Saroja

AU - Charlesworth, Jac

AU - Laviada-Molina, Hugo A.

AU - Veloz-Garza, Rosa A.

AU - Cardenas-Villarreal, Velia Margarita

AU - Valdovinos-Chavez, Salvador B.

AU - Gomez-Aguilar, Patricia

AU - Meléndez, Guillermo

AU - López-Alvarenga, Juan Carlos

AU - Göring, Harald H H

AU - Cole, Shelley A.

AU - Blangero, John

AU - Comuzzie, Anthony G.

AU - Kent, Jack W.

PY - 2012/7

Y1 - 2012/7

N2 - Whole-transcriptome expression profiling provides novel phenotypes for analysis of complex traits. Gene expression measurements reflect quantitative variation in transcript-specific messenger RNA levels and represent phenotypes lying close to the action of genes. Understanding the genetic basis of gene expression will provide insight into the processes that connect genotype to clinically significant traits representing a central tenet of system biology. Synchronous in vivo expression profiles of lymphocytes, muscle, and subcutaneous fat were obtained from healthyMexican men. Most genes were expressed at detectable levels inmultiple tissues, and RNA levels were correlated between tissue types. A subset of transcripts with high reliability of expression across tissues (estimated by intraclass correlation coefficients) was enriched for cis-regulated genes, suggesting that proximal sequence variants may influence expression similarly in different cellular environments. This integrative global gene expression profiling approach is proving extremely useful for identifying genes and pathways that contribute to complex clinical traits. Clearly, the coincidence of clinical trait quantitative trait loci and expression quantitative trait loci can help in the prioritization of positional candidate genes. Such data will be crucial for the formal integration of positional and transcriptomic information characterized as genetical genomics.

AB - Whole-transcriptome expression profiling provides novel phenotypes for analysis of complex traits. Gene expression measurements reflect quantitative variation in transcript-specific messenger RNA levels and represent phenotypes lying close to the action of genes. Understanding the genetic basis of gene expression will provide insight into the processes that connect genotype to clinically significant traits representing a central tenet of system biology. Synchronous in vivo expression profiles of lymphocytes, muscle, and subcutaneous fat were obtained from healthyMexican men. Most genes were expressed at detectable levels inmultiple tissues, and RNA levels were correlated between tissue types. A subset of transcripts with high reliability of expression across tissues (estimated by intraclass correlation coefficients) was enriched for cis-regulated genes, suggesting that proximal sequence variants may influence expression similarly in different cellular environments. This integrative global gene expression profiling approach is proving extremely useful for identifying genes and pathways that contribute to complex clinical traits. Clearly, the coincidence of clinical trait quantitative trait loci and expression quantitative trait loci can help in the prioritization of positional candidate genes. Such data will be crucial for the formal integration of positional and transcriptomic information characterized as genetical genomics.

UR - http://www.scopus.com/inward/record.url?scp=84871869487&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84871869487&partnerID=8YFLogxK

U2 - 10.3945/an.112.001925

DO - 10.3945/an.112.001925

M3 - Article

VL - 3

JO - Advances in nutrition (Bethesda, Md.)

JF - Advances in nutrition (Bethesda, Md.)

SN - 2161-8313

IS - 4

ER -