Meta-analysis of loci associated with age at natural menopause in African-American women

Chen, Christina T. L.; Liu, Ching‐Ti; Chen, Gary K.; Andrews, Jeanette S.; Arnold, Alice M.; Dreyfus, Jill; Franceschini, Nora; García, Melissa; Kerr, Kathleen F.; Guo, Li; Lohman, Kurt; Musani, Solomon K.; Nalls, Michael A.; Raffel, Leslie J.; Smith, Jennifer A.; Ambrosone, Christine B.; Bandera, Elisa V.; Bernstein, Leslie; Britton, Angela; Brzyski, Robert G.; Cappola, Anne R.; Carlson, Christopher S.; Couper, David J.; Deming, Sandra L.; Goodarzi, Mark O.; Heiss, Gerardo; John, Esther M.; Lu, Xiaoning; Marchand, Loı̈c Le; Marciante, Kristin D.; McKnight, Barbara; Millikan, Robert C.; Nock, Nora L.; Olshan, Andrew F.; Press, Michael F.; Vaiyda, Dhananjay; Woods, Nancy Fúgate; Taylor, Herman A.; Zhao, Wei; Wang, Zheng; Evans, Michele K.; Harris, Tamara B.; Henderson, Brian E.; Kardia, Sharon L.R.; Kooperberg, Charles; Liu, Yongmei; Mosley, Thomas H.; Psaty, Bruce M.; Wellons, Melissa; Windham, B. Gwen; Zonderman, Alan B.; Cupples, L. Adrienne; Demerath, Ellen W.; Haiman, Christopher A.; Murabito, Joanne M.; Rajkovic, Aleksandar

doi:10.1093/hmg/ddu041

Cited by 54 publications

(43 citation statements)

References 75 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recent genome-wide association studies (GWASs) among women of European ancestry have identified at least 106 genetic loci for AM (He et al 2009;Ong et al 2009;Perry et al 2009;Sulem et al 2009;Elks et al 2010;Perry et al 2014) and 21 loci for ANM (He et al 2009;Stolk et al 2009;Stolk et al 2012). However, only 24 AM loci and 9 ANM loci have been replicated in women of either Asian or African ancestry and no novel loci have been identified in these non-European populations (Liu et al 2009;Chen et al 2012;Shen et al 2013;Spencer et al 2013;Tanikawa et al 2013;Delahanty et al 2013;Carty et al 2013;Demerath et al 2013;Pyun et al 2014;Chen et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Age at menarche and age at natural menopause in East Asian women: a genome-wide association study

Shi

Zhang

Choi

et al. 2016

AGE

View full text Add to dashboard Cite

Age at menarche (AM) and age at natural menopause (ANM) are complex traits with a high heritability. Abnormal timing of menarche or menopause is associated with a reduced span of fertility and risk for several age-related diseases including breast, endometrial and ovarian cancer, cardiovascular disease, and osteoporosis. To identify novel genetic loci for AM or ANM in East Asian women and to replicate previously identified loci primarily in women of European ancestry by genome-wide association studies (GWASs), we conducted a two-stage GWAS. Stage I aimed to discover promising novel AM and ANM loci using GWAS data of 8073 women from Shanghai, China. The Stage II replication study used the data from another Chinese GWAS (n = 1230 for AM and n = 1458 for ANM), a Korean GWAS (n = 4215 for AM and n = 1739 for ANM), and de novo genotyping of 2877 additional Chinese women. Previous GWAS-identified loci for AM and ANM were also AGE (2016) ) and rs1023935 at 4p15.1 (beta = −0.145 years, P = 4.9 × 10 −6) and one menopausal age locus tagged by rs3818134 at 22q12.2 (beta = −0.276 years, P = 8.8 × 10 −6). These suggestive loci warrant a further validation in independent populations. Although limited by low statistical power, we replicated 19 of the 98 menarche loci and 5 of the 20 menopause loci previously identified in women of European ancestry in East Asian women, suggesting a shared genetic architecture for these two traits across populations.

show abstract

Section: Introductionmentioning

confidence: 99%

Age at menarche and age at natural menopause in East Asian women: a genome-wide association study

Shi

Zhang

Choi

et al. 2016

AGE

View full text Add to dashboard Cite

show abstract

“…The standard practice for checking and correcting pedigrees and relationships within genetic data sets is to use pairwise prediction programs, [14][15][16][17][18] such as RELPAIR 19 and PREST (Pedigree Relationship Statistical Test), 20 to verify that the level of relatedness between every pair of individuals falls close to the expected level of relatedness from the reported pedigree. [21][22][23][24][25][26][27][28] Although using pairwise estimates to check relationships in pedigrees is sometimes sufficient, there are four major drawbacks that we illustrate in this manuscript. First, pairwise checking will not catch pedigree errors if there are multiple pedigree structures that fit the genetic data and if the reported pedigree structure is among the incorrect possibilities.…”

Section: Introductionmentioning

confidence: 99%

PRIMUS: Rapid Reconstruction of Pedigrees from Genome-wide Estimates of Identity by Descent

Staples

Qiao

Cho

et al. 2014

The American Journal of Human Genetics

150

162

View full text Add to dashboard Cite

Understanding and correctly utilizing relatedness among samples is essential for genetic analysis; however, managing sample records and pedigrees can often be error prone and incomplete. Data sets ascertained by random sampling often harbor cryptic relatedness that can be leveraged in genetic analyses for maximizing power. We have developed a method that uses genome-wide estimates of pairwise identity by descent to identify families and quickly reconstruct and score all possible pedigrees that fit the genetic data by using up to third-degree relatives, and we have included it in the software package PRIMUS (Pedigree Reconstruction and Identification of the Maximally Unrelated Set). Here, we validate its performance on simulated, clinical, and HapMap pedigrees. Among these samples, we demonstrate that PRIMUS can verify reported pedigree structures and identify cryptic relationships. Finally, we show that PRIMUS reconstructed pedigrees, all of which were previously unknown, for 203 families from a cohort collected in Starr County, TX (1,890 samples).

show abstract

“…In addition to WGS to identify rare variants, genomewide association studies to assess common variation are increasingly large, available, and able to identify genetic loci associated with more quantitative traits such as the onset of puberty (153) and menopause (154)(155)(156)(157), thereby offering new insights in the genetic complexity of reproductive disorders. Importantly, few loci associated with the age of menarche were mapped close to known IGD genes, and most genome-wide associations are either 1) localized at some distance from coding regions revealing possible long-range DNA interactions; 2) interrupt transcription factor binding with possible effects on downstream targets; or 3) interrupt noncoding RNA, which may play a role in the regulation of transcription and translation of target genes (158,159).…”

Section: A New Tools and Approaches For The Discovery Of Igd Genesmentioning

confidence: 99%

Discovering Genes Essential to the Hypothalamic Regulation of Human Reproduction Using a Human Disease Model: Adjusting to Life in the “-Omics” Era

2015

View full text Add to dashboard Cite

The neuroendocrine regulation of reproduction is an intricate process requiring the exquisite coordination of an assortment of cellular networks, all converging on the GnRH neurons. These neurons have a complex life history, migrating mainly from the olfactory placode into the hypothalamus, where GnRH is secreted and acts as the master regulator of the hypothalamicpituitary-gonadal axis. Much of what we know about the biology of the GnRH neurons has been aided by discoveries made using the human disease model of isolated GnRH deficiency (IGD), a family of rare Mendelian disorders that share a common failure of secretion and/or action of GnRH causing hypogonadotropic hypogonadism. Over the last 30 years, research groups around the world have been investigating the genetic basis of IGD using different strategies based on complex cases that harbor structural abnormalities or single pleiotropic genes, endogamous pedigrees, candidate gene approaches as well as pathway gene analyses. Although such traditional approaches, based on well-validated tools, have been critical to establish the field, new strategies, such as next-generation sequencing, are now providing speed and robustness, but also revealing a surprising number of variants in known IGD genes in both patients and healthy controls. Thus, before the field moves forward with new genetic tools and continues discovery efforts, we must reassess what we know about IGD genetics and prepare to hold our work to a different standard. The purpose of this review is to: 1) look back at the strategies used to discover the "known" genes implicated in the rare forms of IGD; 2) examine the strengths and weaknesses of the methodologies used to validate genetic variation; 3)substantiate the role of known genes in the pathophysiology of the disease; and 4) project forward as we embark upon a widening use of these new and powerful technologies for gene discovery.

show abstract

Meta-analysis of loci associated with age at natural menopause in African-American women

Cited by 54 publications

References 75 publications

Age at menarche and age at natural menopause in East Asian women: a genome-wide association study

Age at menarche and age at natural menopause in East Asian women: a genome-wide association study

PRIMUS: Rapid Reconstruction of Pedigrees from Genome-wide Estimates of Identity by Descent

Discovering Genes Essential to the Hypothalamic Regulation of Human Reproduction Using a Human Disease Model: Adjusting to Life in the “-Omics” Era

Contact Info

Product

Resources

About