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Genome-wide association study of telomere length in individuals of Samoan ancestry

Authors
M. A. Taub, J. C. Carlson, H. Cheng, T. Naseri, M. Reupena, R. Deka, N. L. Hawley, S. T. McGarvey, D. E. Weeks, R. A. Mathias, R. L. Minster, TOPMed Hematology & Hemostasis and Structural Variation Working Groups
Name and Date of Professional Meeting
ASHG Conference (October 27, 2020)
Associated paper proposal(s)
Working Group(s)
Abstract Text
Telomere length (TL) is a proposed biomarker of biological age and is a risk factor for age-related diseases. Prior GWAS have identified numerous loci harboring genetic determinants of TL; several of these being implicated in human disease. However, studies have been limited to samples of European and Asian ancestry. We performed a GWAS of TL with 1,261 participants of Samoan ancestry. Whole-genome sequencing was conducted by the TOPMed Program, and TelSeq was used to compute TL from the sequences. We tested for association via linear mixed models as implemented in GENESIS, with age and sex as fixed effect covariates. We adjusted for relatedness and population stratification with values from PC-AiR and PC-Relate, respectively. There was one signal associated with TL at p<5×10⁻⁸ and two additional signals associated with TL at p<1×10⁻⁶. The peak variant is located on 14q12. This top signal (p=2.7×10⁻8) was rs4982872, an intronic variant in NEDD8, with the minor allele (MAF=0.26) associated with greater mean TL (0.12bp). This variant is in high LD (r²=1) with rs28372734, which is located in the 5′-UTR of TINF2, a gene that encodes for a member protein of the telosome/shelterin complex. Given that TINF2 has been reported to be associated with TL in people of Asian ancestry, we conditioned on rs28372734, to determine if there is more than one locus mapping to this region in our study. The association with rs4982872 is lost, suggesting that the peak variant (rs4982872) here, also maps to the previously reported TINF2 locus. Importantly, the MAF of the variants mapping to the TINF2 locus is quite different between Samoans and populations of continental ancestries. The MAF of rs28372734 is 23% in Samoans and is 9% in individuals of Asian ancestries but is ≤ 1% in individuals of African and European ancestries; in fact, TINF2 is completely missed in prior GWAS focused on European ancestries. Additionally, we observed novel association at p<1×10⁻6 of two variants in intergenic regions near PTPRG and AC005562.1 located on chromosomes 3 and 17, respectively. The minor alleles for both variants are rare in the Samoans (MAF= 0.006 and 0.008, respectively) and are not observed in populations of continental ancestries. These variants have not been reported to be associated with TL in any studies to date. Among participants of Samoan ancestry, we see the prior association with a high MAF variant in the TINF2 locus and identify two novel associations associated with TL. Additional work is necessary to replicate these novel associations and understand the biological mechanisms that may explain differences in TL associated with these variants.
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