Characterization of the Common Genetic Variation in the Spanish Population of Navarre

Alberto Maillo; Estefania Huergo; María Apellániz-Ruiz; Edurne Urrutia-Lafuente; María Miranda; Josefa Salgado; Sara Pasalodos-Sanchez; Luna Delgado-Mora; Óscar Teijido; Ibai Goicoechea; Rosario Carmona; Javier Perez-Florido; Virginia Aquino; Daniel Lopez-Lopez; María Peña-Chilet; Sergi Beltran; Joaquín Dopazo; Iñigo Lasa; Juan José Beloqui; Ángel Alonso; David Gomez-Cabrero

doi:10.3390/genes15050585

Characterization of the Common Genetic Variation in the Spanish Population of Navarre

Alberto Maillo, Estefania Huergo, María Apellániz-Ruiz, Edurne Urrutia-Lafuente, María Miranda, Josefa Salgado, Sara Pasalodos-Sanchez, Luna Delgado-Mora, Óscar Teijido, Ibai Goicoechea, Rosario Carmona, Javier Perez-Florido, Virginia Aquino, Daniel Lopez-Lopez, María Peña-Chilet, Sergi Beltran, Joaquín Dopazo, Iñigo Lasa, Juan José Beloqui, Ángel Alonso^*David Gomez-Cabrero^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

Large-scale genomic studies have significantly increased our knowledge of genetic variability across populations. Regional genetic profiling is essential for distinguishing common benign variants from disease-causing ones. To this end, we conducted a comprehensive characterization of exonic variants in the population of Navarre (Spain), utilizing whole genome sequencing data from 358 unrelated individuals of Spanish origin. Our analysis revealed 61,410 biallelic single nucleotide variants (SNV) within the Navarrese cohort, with 35% classified as common (MAF > 1%). By comparing allele frequency data from 1000 Genome Project (excluding the Iberian cohort of Spain, IBS), Genome Aggregation Database, and a Spanish cohort (including IBS individuals and data from Medical Genome Project), we identified 1069 SNVs common in Navarre but rare (MAF ≤ 1%) in all other populations. We further corroborated this observation with a second regional cohort of 239 unrelated exomes, which confirmed 676 of the 1069 SNVs as common in Navarre. In conclusion, this study highlights the importance of population-specific characterization of genetic variation to improve allele frequency filtering in sequencing data analysis to identify disease-causing variants.

Original language	English (US)
Article number	585
Journal	Genes
Volume	15
Issue number	5
DOIs	https://doi.org/10.3390/genes15050585
State	Published - May 2024

Bibliographical note

Publisher Copyright:
© 2024 by the authors.

Keywords

genetic variability
personalized medicine
population frequencies
single nucleotide variant SNV
whole exome sequencing WES
whole genome sequencing WGS

ASJC Scopus subject areas

Genetics
Genetics(clinical)

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10.3390/genes15050585

Cite this

Maillo, A., Huergo, E., Apellániz-Ruiz, M., Urrutia-Lafuente, E., Miranda, M., Salgado, J., Pasalodos-Sanchez, S., Delgado-Mora, L., Teijido, Ó., Goicoechea, I., Carmona, R., Perez-Florido, J., Aquino, V., Lopez-Lopez, D., Peña-Chilet, M., Beltran, S., Dopazo, J., Lasa, I., Beloqui, J. J., ... Gomez-Cabrero, D. (2024). Characterization of the Common Genetic Variation in the Spanish Population of Navarre. Genes, 15(5), Article 585. https://doi.org/10.3390/genes15050585

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title = "Characterization of the Common Genetic Variation in the Spanish Population of Navarre",

abstract = "Large-scale genomic studies have significantly increased our knowledge of genetic variability across populations. Regional genetic profiling is essential for distinguishing common benign variants from disease-causing ones. To this end, we conducted a comprehensive characterization of exonic variants in the population of Navarre (Spain), utilizing whole genome sequencing data from 358 unrelated individuals of Spanish origin. Our analysis revealed 61,410 biallelic single nucleotide variants (SNV) within the Navarrese cohort, with 35% classified as common (MAF > 1%). By comparing allele frequency data from 1000 Genome Project (excluding the Iberian cohort of Spain, IBS), Genome Aggregation Database, and a Spanish cohort (including IBS individuals and data from Medical Genome Project), we identified 1069 SNVs common in Navarre but rare (MAF ≤ 1%) in all other populations. We further corroborated this observation with a second regional cohort of 239 unrelated exomes, which confirmed 676 of the 1069 SNVs as common in Navarre. In conclusion, this study highlights the importance of population-specific characterization of genetic variation to improve allele frequency filtering in sequencing data analysis to identify disease-causing variants.",

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author = "Alberto Maillo and Estefania Huergo and Mar{\'i}a Apell{\'a}niz-Ruiz and Edurne Urrutia-Lafuente and Mar{\'i}a Miranda and Josefa Salgado and Sara Pasalodos-Sanchez and Luna Delgado-Mora and {\'O}scar Teijido and Ibai Goicoechea and Rosario Carmona and Javier Perez-Florido and Virginia Aquino and Daniel Lopez-Lopez and Mar{\'i}a Pe{\~n}a-Chilet and Sergi Beltran and Joaqu{\'i}n Dopazo and I{\~n}igo Lasa and Beloqui, {Juan Jos{\'e}} and {\'A}ngel Alonso and David Gomez-Cabrero",

note = "Publisher Copyright: {\textcopyright} 2024 by the authors.",

year = "2024",

month = may,

doi = "10.3390/genes15050585",

language = "English (US)",

volume = "15",

journal = "Genes",

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Maillo, A, Huergo, E, Apellániz-Ruiz, M, Urrutia-Lafuente, E, Miranda, M, Salgado, J, Pasalodos-Sanchez, S, Delgado-Mora, L, Teijido, Ó, Goicoechea, I, Carmona, R, Perez-Florido, J, Aquino, V, Lopez-Lopez, D, Peña-Chilet, M, Beltran, S, Dopazo, J, Lasa, I, Beloqui, JJ, Alonso, Á & Gomez-Cabrero, D 2024, 'Characterization of the Common Genetic Variation in the Spanish Population of Navarre', Genes, vol. 15, no. 5, 585. https://doi.org/10.3390/genes15050585

TY - JOUR

T1 - Characterization of the Common Genetic Variation in the Spanish Population of Navarre

AU - Maillo, Alberto

AU - Huergo, Estefania

AU - Apellániz-Ruiz, María

AU - Urrutia-Lafuente, Edurne

AU - Miranda, María

AU - Salgado, Josefa

AU - Pasalodos-Sanchez, Sara

AU - Delgado-Mora, Luna

AU - Teijido, Óscar

AU - Goicoechea, Ibai

AU - Carmona, Rosario

AU - Perez-Florido, Javier

AU - Aquino, Virginia

AU - Lopez-Lopez, Daniel

AU - Peña-Chilet, María

AU - Beltran, Sergi

AU - Dopazo, Joaquín

AU - Lasa, Iñigo

AU - Beloqui, Juan José

AU - Alonso, Ángel

AU - Gomez-Cabrero, David

PY - 2024/5

Y1 - 2024/5

N2 - Large-scale genomic studies have significantly increased our knowledge of genetic variability across populations. Regional genetic profiling is essential for distinguishing common benign variants from disease-causing ones. To this end, we conducted a comprehensive characterization of exonic variants in the population of Navarre (Spain), utilizing whole genome sequencing data from 358 unrelated individuals of Spanish origin. Our analysis revealed 61,410 biallelic single nucleotide variants (SNV) within the Navarrese cohort, with 35% classified as common (MAF > 1%). By comparing allele frequency data from 1000 Genome Project (excluding the Iberian cohort of Spain, IBS), Genome Aggregation Database, and a Spanish cohort (including IBS individuals and data from Medical Genome Project), we identified 1069 SNVs common in Navarre but rare (MAF ≤ 1%) in all other populations. We further corroborated this observation with a second regional cohort of 239 unrelated exomes, which confirmed 676 of the 1069 SNVs as common in Navarre. In conclusion, this study highlights the importance of population-specific characterization of genetic variation to improve allele frequency filtering in sequencing data analysis to identify disease-causing variants.

AB - Large-scale genomic studies have significantly increased our knowledge of genetic variability across populations. Regional genetic profiling is essential for distinguishing common benign variants from disease-causing ones. To this end, we conducted a comprehensive characterization of exonic variants in the population of Navarre (Spain), utilizing whole genome sequencing data from 358 unrelated individuals of Spanish origin. Our analysis revealed 61,410 biallelic single nucleotide variants (SNV) within the Navarrese cohort, with 35% classified as common (MAF > 1%). By comparing allele frequency data from 1000 Genome Project (excluding the Iberian cohort of Spain, IBS), Genome Aggregation Database, and a Spanish cohort (including IBS individuals and data from Medical Genome Project), we identified 1069 SNVs common in Navarre but rare (MAF ≤ 1%) in all other populations. We further corroborated this observation with a second regional cohort of 239 unrelated exomes, which confirmed 676 of the 1069 SNVs as common in Navarre. In conclusion, this study highlights the importance of population-specific characterization of genetic variation to improve allele frequency filtering in sequencing data analysis to identify disease-causing variants.

KW - genetic variability

KW - personalized medicine

KW - population frequencies

KW - single nucleotide variant SNV

KW - whole exome sequencing WES

KW - whole genome sequencing WGS

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U2 - 10.3390/genes15050585

DO - 10.3390/genes15050585

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C2 - 38790214

AN - SCOPUS:85194219512

SN - 2073-4425

VL - 15

JO - Genes

JF - Genes

IS - 5

M1 - 585

ER -

Characterization of the Common Genetic Variation in the Spanish Population of Navarre

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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