Genome-wide association study identifies sequence variants on 6q21 associated with age at menarche

AbstractVertigo is the leading symptom of vestibular disorders and a major risk factor for falls. In a genome-wide association study of vertigo (Ncases = 48,072, Ncontrols = 894,541), we uncovered an association with six common sequence variants in individuals of European ancestry, including missense variants in ZNF91, OTOG, OTOGL, and TECTA, and a cis-eQTL for ARMC9. The association of variants in ZNF91, OTOGL, and OTOP1 was driven by an association with benign paroxysmal positional vertigo. Using previous reports of sequence variants associating with age-related hearing impairment and motion sickness, we found eight additional variants that associate with vertigo. Although disorders of the auditory and the vestibular system may co-occur, none of the six genome-wide significant vertigo variants were associated with hearing loss and only one was associated with age-related hearing impairment. Our results uncovered sequence variants associating with vertigo in a genome-wide association study and implicated genes with known roles in inner ear development, maintenance, and disease.

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Genome-wide association study of age at menarche in African-American women

Human Molecular Genetics ◽

10.1093/hmg/ddt181 ◽

2013 ◽

Vol 22 (16) ◽

pp. 3329-3346 ◽

Cited By ~ 28

Author(s):

E. W. Demerath ◽

C.-T. Liu ◽

N. Franceschini ◽

G. Chen ◽

J. R. Palmer ◽

...

Keyword(s):

African American ◽

Association Study ◽

African American Women ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Age At Menarche ◽

American Women ◽

Genome Wide

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A genome-wide association study of non-HPV-related head and neck squamous cell carcinoma identifies prognostic genetic sequence variants in the MAP-kinase and hormone pathways

Cancer Epidemiology ◽

10.1016/j.canep.2016.05.001 ◽

2016 ◽

Vol 42 ◽

pp. 173-180

Author(s):

Abul Kalam Azad ◽

Isabelle Bairati ◽

Xin Qiu ◽

Hala Girgis ◽

Lu Cheng ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Association Study ◽

Cell Carcinoma ◽

Head And Neck ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Sequence Variants ◽

Genetic Sequence ◽

Genome Wide ◽

A Genome

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Associations between age of menarche and genetic variation in women of African descent: genome-wide association study and polygenic score analysis

Journal of Epidemiology & Community Health ◽

10.1136/jech-2020-216000 ◽

2021 ◽

pp. jech-2020-216000

Author(s):

Molly Scannell Bryan ◽

Temidayo Ogundiran ◽

Oladosu Ojengbede ◽

Wei Zheng ◽

William Blot ◽

...

Keyword(s):

Genetic Variation ◽

Association Study ◽

Genome Wide Association Study ◽

African Ancestry ◽

Genome Wide Association ◽

Age At Menarche ◽

Polygenic Score ◽

Genome Wide ◽

A Genome ◽

The Usa

IntroductionMany diseases of adulthood are associated with a woman’s age at menarche. Genetic variation affects age at menarche, but it remains unclear whether in women of African ancestry the timing of menarche is regulated by genetic variants that were identified in predominantly European and East Asian populations.MethodsWe explored the genetic architecture of age at menarche in 3145 women of African ancestry who live in the USA, Barbados and Nigeria. We undertook a genome-wide association study, and evaluated the performance of previously identified variants.ResultsOne variant was associated with age at menarche, a deletion at chromosome 2 (chr2:207216165) (p=1.14×10−8). 349 genotyped variants overlapped with these identified in populations of non-African ancestry; these replicated weakly, with 51.9% having concordant directions of effect. However, collectively, a polygenic score constructed of those previous variants was suggestively associated with age at menarche (beta=0.288 years; p=0.041). Further, this association was strong in women enrolled in the USA and Barbados (beta=0.445 years, p=0.008), but not in Nigerian women (beta=0.052 years; p=0.83).DiscussionThis study suggests that in women of African ancestry the genetic drivers of age at menarche may differ from those identified in populations of non-African ancestry, and that these differences are more pronounced in women living in Nigeria, although some associated trait loci may be shared across populations. This highlights the need for well-powered ancestry-specific genetic studies to fully characterise the genetic influences of age at menarche.

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Genome-wide association study of multiple yield components in a diversity panel of polyploid sugarcane (Saccharum spp.)

10.1101/387001 ◽

2018 ◽

Cited By ~ 4

Author(s):

Xiping Yang ◽

Ziliang Luo ◽

James Todd ◽

Sushma Sood ◽

Jianping Wang

Keyword(s):

Association Study ◽

Yield Components ◽

Genome Wide Association Study ◽

Crop Improvement ◽

Dry Weight ◽

Genome Wide Association ◽

Sequence Variants ◽

Diversity Panel ◽

Fundamental Information ◽

Genome Wide

AbstractSugarcane (Saccharum spp.) is an important economic crop, contributes up to 80% of sugar and approximately 60% bio-fuel globally. To meet the increased demand for sugar and bio-fuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield components. Therefore, dissection of causal DNA sequence variants is of great importance by providing genetic resources and fundamental information for crop improvement. In this study, we evaluated and analyzed nine yield components in a sugarcane diversity panel consisting of 308 accessions primarily selected from the “world collection of sugarcane and related grasses”. By genotyping the diversity panel using target enrichment sequencing, we identified a large number of sequence variants. Genome-wide association study between the markers and traits were conducted with dosages and gene actions taken into consideration. In total, 217 non-redundant markers and 225 candidate genes were identified to be significantly associated with the yield components, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 ROHs, and found that the occurrence of ROH in the genome were non-random and probably under selection. ROHs were associated with total weight and dry weight, and high ROHs resulted in decrease of the two traits. This study approved that genomic inbreeding has led to negative impacts on sugarcane yield.

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