Abstract:
:Understanding the nature of the genetic regulation of gene expression promises to advance our understanding of the genetic basis of disease. However, the methodological impact of the use of local ancestry on high-dimensional omics analyses, including, most prominently, expression quantitative trait loci (eQTL) mapping and trait heritability estimation, in admixed populations remains critically underexplored. Here, we develop a statistical framework that characterizes the relationships among the determinants of the genetic architecture of an important class of molecular traits. We provide a computationally efficient approach to local ancestry analysis in eQTL mapping while increasing control of type I and type II error over traditional approaches. Applying our method to National Institute of General Medical Sciences (NIGMS) and Genotype-Tissue Expression (GTEx) datasets, we show that the use of local ancestry can improve eQTL mapping in admixed and multiethnic populations, respectively. We estimate the trait variance explained by ancestry by using local admixture relatedness between individuals. By using simulations of diverse genetic architectures and degrees of confounding, we show improved accuracy in estimating heritability when accounting for local ancestry similarity. Furthermore, we characterize the sparse versus polygenic components of gene expression in admixed individuals. Our study has important methodological implications for genetic analysis of omics traits across a range of genomic contexts, from a single variant to a prioritized region to the entire genome. Our findings highlight the importance of using local ancestry to better characterize the heritability of complex traits and to more accurately map genetic associations.
journal_name
Am J Hum Genetjournal_title
American journal of human geneticsauthors
Zhong Y,Perera MA,Gamazon ERdoi
10.1016/j.ajhg.2019.04.009subject
Has Abstractpub_date
2019-06-06 00:00:00pages
1097-1115issue
6eissn
0002-9297issn
1537-6605pii
S0002-9297(19)30155-7journal_volume
104pub_type
杂志文章abstract::The Asian-specific 9-bp deletion between the genes for mitochondrial cytochrome oxidase II and lysine transfer RNA has been used to trace aboriginal human movements out of Southeast Asia and into portions of the South Pacific. Although it has been used to estimate the number of independent lineages that occur in the N...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1992-04-01 00:00:00
abstract::Renal stone formation is a common multifactorial disorder, of unknown etiology, with an established genetic contribution. Lifetime risk for nephrolithiasis is approximately 10% in Western populations, and uric acid stones account for 5%-10% of all stones, depending on climatic, dietary, and ethnic differences. We stud...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1086/320105
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abstract::Treacher Collins syndrome (TCS) is an autosomal dominant disorder of craniofacial development, the features of which include conductive hearing loss and cleft palate. We have studied 12 unrelated TCS families with multiple affected individuals for linkage to five chromosome 5 markers. There is strong evidence demonstr...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1991-07-01 00:00:00
abstract::Joubert syndrome is a rare developmental defect of the cerebellar vermis, with autosomal recessive inheritance. The phenotype is highly variable and may include episodic hyperpnea, abnormal eye movements, hypotonia, ataxia, developmental delay, and mental retardation. Even within sibships the phenotype may vary, makin...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1086/302655
更新日期:1999-12-01 00:00:00
abstract::Intellectual disability (ID) is a highly heterogeneous disorder involving at least 600 genes, yet a genetic diagnosis remains elusive in ∼35%-40% of individuals with moderate to severe ID. Recent meta-analyses statistically analyzing de novo mutations in >7,000 individuals with neurodevelopmental disorders highlighted...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1016/j.ajhg.2017.02.005
更新日期:2017-04-06 00:00:00
abstract::Otopalatodigital syndrome type 1 (OPD1) is an X-linked semidominant condition characterized by malformations of the skeleton, auditory apparatus, and palate. Previous studies have established linkage to a 16-cM region of Xq27-q28. A proposed allelic variant of OPD1, termed "OPD2," is associated with a more severe, fre...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1086/321280
更新日期:2001-07-01 00:00:00
abstract::On the basis of the known amino acid sequence of statherin, a human salivary protein, mixed synthetic oligonucleotides were synthesized and used to screen a cDNA library constructed from human parotid-gland mRNA. A cDNA clone coding for statherin was isolated from this library and has been completely sequenced. The cD...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1987-12-01 00:00:00
abstract::In Williams syndrome (WS), a deletion of approximately 1.5 Mb on one copy of chromosome 7 causes specific physical, cognitive, and behavioral abnormalities. Molecular dissection of the phenotype may be a route to identification of genes important in human cognition and behavior. Among the genes known to be deleted in ...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1086/302214
更新日期:1999-01-01 00:00:00
abstract::Aplastic anemia (AA) and myelodysplasia (MDS) are forms of bone marrow failure that are often part of the same progressive underlying disorder. While most cases are simplex and idiopathic, some show a clear pattern of inheritance; therefore, elucidating the underlying genetic cause could lead to a greater understandin...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1016/j.ajhg.2012.03.020
更新日期:2012-05-04 00:00:00
abstract::We report the physical linkage of the gene encoding one of the subunits of the GABAA receptor (GABRA3) to the polymorphic locus DXS374 on the human X chromosome at Xq28. X-linked manic depression and other psychiatric disorders have been mapped to this region, and thus GABRA3 is a potential candidate gene for these di...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1989-12-01 00:00:00
abstract::Using sequence-tagged sites we have performed deletion mapping of the Y chromosome in sex-reversed female patients with a Y chromosome and gonadoblastoma. The GBY gene (gonadoblastoma locus on the Y chromosome) was sublocalized to a small region near the centromere of the Y chromosome. We estimate the size of the GBY ...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1995-12-01 00:00:00
abstract::An elevated level of erythrocyte sodium-lithium (Na-Li) countertransport has been suggested as a predictor of predisposition to essential hypertension. In order to evaluate whether a single genetic or environmental factor with large effects explains the mixture of distributions in Na-Li countertransport in the general...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1991-06-01 00:00:00
abstract::We devised a rapid PCR-based method to screen for an A----G transition at nucleotide 8344 of the human mitochondrial tRNA(Lys) gene, which was recently reported, by Shoffner and co-workers, to be associated with myoclonus epilepsy and ragged-red fibers (MERRF), a maternally transmitted mitochondrial encephalomyopathy ...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1991-02-01 00:00:00
abstract::In spondylocostal dysostosis (SD), vertebral-segmentation defects are associated with rib anomalies. This results in short-trunk short stature, nonprogressive kyphoscoliosis, and radiological features of multiple hemivertebrae and rib fusions. SD can be familial, and both autosomal dominant and autosomal recessive (AR...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1086/302464
更新日期:1999-07-01 00:00:00
abstract::Despite the growing consensus on the importance of testing gene-gene interactions in genetic studies of complex diseases, the effect of gene-gene interactions has often been defined as a deviance from genetic additive effects, which is essentially treated as a residual term in genetic analysis and leads to low power i...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1086/508571
更新日期:2006-11-01 00:00:00
abstract::Idiopathic torsion dystonia (ITD) is characterized by involuntary twisting movements and postures. A gene for this disorder, DYT1, was mapped to chromosome 9q34 in 12 Ashkenazi Jewish (AJ) families and one large non-Jewish kindred. In the AJ population, strong linkage disequilibrium exists between DYT1 and adjacent ma...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1994-09-01 00:00:00
abstract::Allan-Herndon-Dudley syndrome was among the first of the X-linked mental retardation syndromes to be described (in 1944) and among the first to be regionally mapped on the X chromosome (in 1990). Six large families with the syndrome have been identified, and linkage studies have placed the gene locus in Xq13.2. Mutati...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1086/431313
更新日期:2005-07-01 00:00:00
abstract::Myotubular myopathy is a severe congenital disease inherited as an X-linked trait (MTM1; McKusick 31040). It has been mapped to the long arm of chromosome X, to the Xq27-28 region. Significant linkage has subsequently been established for the linkage group comprised of DXS304, DXS15, DXS52, and F8C in several studies....
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1995-07-01 00:00:00
abstract::Many disorders are associated with altered serum protein concentrations, including malnutrition, cancer, and cardiovascular, kidney, and inflammatory diseases. Although these protein concentrations are highly heritable, relatively little is known about their underlying genetic determinants. Through transethnic meta-an...
journal_title:American journal of human genetics
pub_type: 杂志文章,meta分析
doi:10.1016/j.ajhg.2012.08.021
更新日期:2012-10-05 00:00:00
abstract::SOX6 belongs to a family of 20 SRY-related HMG-box-containing (SOX) genes that encode transcription factors controlling cell fate and differentiation in many developmental and adult processes. For SOX6, these processes include, but are not limited to, neurogenesis and skeletogenesis. Variants in half of the SOX genes ...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1016/j.ajhg.2020.04.015
更新日期:2020-06-04 00:00:00
abstract::We report recessive mutations in the gene for the latent transforming growth factor-beta binding protein 4 (LTBP4) in four unrelated patients with a human syndrome disrupting pulmonary, gastrointestinal, urinary, musculoskeletal, craniofacial, and dermal development. All patients had severe respiratory distress, with ...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1016/j.ajhg.2009.09.013
更新日期:2009-11-01 00:00:00
abstract::The first hypervariable segment of the human mtDNA control region contains a homopolymeric tract of cytosines between nt 16184 and 16193, interrupted at position 16189 by a thymine, according to the Cambridge reference sequence. A variant commonly found in population screening is a T-to-C transition at nt 16189, resul...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1995-08-01 00:00:00
abstract::Bloom syndrome (BS) is an autosomal recessive disorder characterized by increases in the frequency of sister-chromatid exchange and in the incidence of malignancy. Chromosome-transfer studies have shown the BS locus to map to chromosome 15q. This report describes a subject with features of both BS and Prader-Willi syn...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1994-07-01 00:00:00
abstract::Accurate colorectal cancer (CRC) risk prediction models are critical for identifying individuals at low and high risk of developing CRC, as they can then be offered targeted screening and interventions to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and i...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1016/j.ajhg.2020.07.006
更新日期:2020-09-03 00:00:00
abstract::Loss-of-heterozygosity (LOH) studies have implicated one or more chromosome 11 tumor-suppressor gene(s) in the development of cutaneous melanoma as well as a variety of other forms of human cancer. In the present study, we have identified multiple independent critical regions on this chromosome by use of homozygosity ...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:10.1086/302999
更新日期:2000-08-01 00:00:00
abstract::Age at onset of motor symptoms was collected on 611 persons affected with Huntington disease (HD) among 3,201 persons "at risk" in 108 kindreds. Life-table estimates correcting for truncated intervals of observation (censoring) produced a median age at onset 5 years older than the observed mean. Risk estimates of HD o...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1988-11-01 00:00:00
abstract::We screened DNA from unrelated individuals for RFLPs in the muscle nicotinic acetylcholine receptor (AcChoR) genes. These RFLP markers can be used for genetic linkage and association studies to test the hypothesis that receptor structure or regulation is involved in the development of myasthenia gravis (MG). The cDNAs...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1989-04-01 00:00:00
abstract::A NotI-linking library was constructed from a radiation hybrid containing fragments of human chromosome 16. The clones were mapped on a panel of somatic cell hybrids, and 10 different NotI site-containing clones were localized close to and between genetic markers flanking the PKD1 locus. With pulsed-field gel analysis...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1991-02-01 00:00:00
abstract::The long-QT syndrome (LQT; Ward-Romano syndrome) is a cardiac disorder that is inherited as an autosomal dominant trait. Affected family members suffer from recurrent syncope and sudden death due to ventricular arrhythmias. Recently, we identified a DNA marker on the short arm of chromosome 11 (the Harvey ras-1 locus ...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1991-12-01 00:00:00
abstract::On the basis of accumulating evidence that obesity has a substantial genetic component, a genomewide search for linkages of DNA markers to percent body fat is ongoing in Pima Indians, a population with a very high prevalence of obesity. An initial screen of the genome (>600 markers in 874 individuals) has been complet...
journal_title:American journal of human genetics
pub_type: 杂志文章
doi:
更新日期:1997-01-01 00:00:00