Abstract：
:We present a full-likelihood method to infer polygenic adaptation from DNA sequence variation and GWAS summary statistics to quantify recent transient directional selection acting on a complex trait. Through simulations of polygenic trait architecture evolution and GWASs, we show the method substantially improves power over current methods. We examine the robustness of the method under stratification, uncertainty and bias in marginal effects, uncertainty in the causal SNPs, allelic heterogeneity, negative selection, and low GWAS sample size. The method can quantify selection acting on correlated traits, controlling for pleiotropy even among traits with strong genetic correlation (|rg|=80%) while retaining high power to attribute selection to the causal trait. When the causal trait is excluded from analysis, selection is attributed to its closest proxy. We discuss limitations of the method, cautioning against strongly causal interpretations of the results, and the possibility of undetectable gene-by-environment (GxE) interactions. We apply the method to 56 human polygenic traits, revealing signals of directional selection on pigmentation, life history, glycated hemoglobin (HbA1c), and other traits. We also conduct joint testing of 137 pairs of genetically correlated traits, revealing widespread correlated response acting on these traits (2.6-fold enrichment, p = 1.5 × 10-7). Signs of selection on some traits previously reported as adaptive (e.g., educational attainment and hair color) are largely attributable to correlated response (p = 2.9 × 10-6 and 1.7 × 10-4, respectively). Lastly, our joint test shows antagonistic selection has increased type 2 diabetes risk and decrease HbA1c (p = 1.5 × 10-5).
journal_name
Am J Hum Genetjournal_title
American journal of human geneticsauthors
Stern AJ,Speidel L,Zaitlen NA,Nielsen Rdoi
10.1016/j.ajhg.2020.12.005subject
Has Abstractpub_date
2021-01-08 00:00:00eissn
0002-9297issn
1537-6605pii
S0002-9297(20)30441-9pub_type
杂志文章abstract：:Premature ovarian failure (POF) is characterized by elevated gonadotropins and amenorrhea in women aged <40 years. In a Lebanese family with five sisters who received the diagnosis of POF, we established linkage to the long arm of the X chromosome (between Xq21.1 and Xq21.3.3), using whole-genome SNP typing and homozy...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/505406
更新日期：2006-07-01 00:00:00
abstract：:The fourth-year medical student elective in clinical genetics has been enhanced by the addition of a problem-solving project. The assignment requires students to pose and answer a practical question about a professionally relevant genetic problem. Exemplary questions and the details of the exercise are given. Six of 1...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1991-08-01 00:00:00
abstract：:Leri-Weill dyschondrosteosis (LWD) is a pseudoautosomal dominant disorder characterized by disproportionate short stature and a characteristic curving of the radius, known as the "Madelung deformity." SHOX mutations resulting in SHOX haploinsufficiency have been found in LWD and in a variable proportion of patients wi...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/449313
更新日期：2005-10-01 00:00:00
abstract：:Linkage analyses were performed in 11 families with X-linked Menkes disease. In each family more than one affected patient had been diagnosed. Forty informative meioses were tested using 11 polymorphic DNA markers. From two-point linkage analyses high lod scores are seen for DXS146 (pTAK-8; maximal lod score 3.16 at r...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1992-05-01 00:00:00
abstract：:Each year at the annual meeting of The American Society of Human Genetics (ASHG), addresses are given in honor of the Society and a number of award winners. A summary of each of these is provided below. On the following pages, we have printed the Presidential Address as well as the addresses for the William Allan Awar...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1016/j.ajhg.2019.02.019
更新日期：2019-03-07 00:00:00
abstract：:The gene that is involved in juvenile neuronal ceroid lipofuscinosis (JNCL), or Batten disease--CLN3--has been localized to 16p12, and the mutation shows a strong association with alleles of microsatellite markers D16S298, D16S299, and D16S288. Recently, haplotype analysis of a Batten patient from a consanguineous rel...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1995-03-01 00:00:00
abstract：:We report the transmission of HLA haplotypes and Gm allotypes in 97 members of a single kindred containing 257 individuals, 45 of whom were determined by clinical examination, autopsy, or historical data to have had Alzheimer disease (AD). Extensive inbreeding suggests that more than one gene may contribute to suscept...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1983-05-01 00:00:00
abstract：:We analyzed mutations and defined the chromosomal haplotype in 127 patients and Mediterranean descent who were affected by Wilson disease (WD), 39 Sardinians, 49 Italians, 33 Turks, and 6 Albanians. Haplotypes were derived by use of the microsatellite markers D13S301, D13S296, D13S297, and D13S298, which are linked to...
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：:We have previously shown that intracellular trafficking and extracellular assembly of tropoelastin into elastic fibers is facilitated by the 67-kD elastin-binding protein identical to an enzymatically inactive, alternatively spliced variant of beta-galactosidase (S-Gal). In the present study, we investigated elastic-f...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/302968
更新日期：2000-07-01 00:00:00
abstract：:The distribution of HLA antigens in a sample of 124 Chagas serologically positive Chilean individuals was studied. The sample was subdivided according to the presence or absence of chagasic cardiomyopathy, in order to search for genetic differences associated with this pathological condition. The frequency of antigen ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1988-11-01 00:00:00
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journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1989-09-01 00:00:00
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journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/339766
更新日期：2002-04-01 00:00:00
abstract：:In linkage analysis, when the lod score is maximized over multiple genetic models, standard asymptotic approximation of the significance level does not apply. Monte Carlo methods can be used to estimate the p value, but procedures currently used are extremely inefficient. We propose a Monte Carlo procedure based on th...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1992-12-01 00:00:00
abstract：:We present the findings of a large linkage study of bipolar affective disorder (BPAD) that involved genomewide analysis of 52 families (448 genotyped individuals) of Spanish, Romany, and Bulgarian descent and further fine mapping of the 1p34-p36, 4q28-q31, and 6q15-q24 regions. An additional sample of 56 German famili...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/498619
更新日期：2005-12-01 00:00:00
abstract：:Two hundred subjects with insulin-dependent (type I) diabetes mellitus (IDDM) were typed for HLA-B, HLA-DR, and properdin factor B (Bf). HLA and Bf antigen and haplotype frequencies in subjects were compared with control frequencies derived from the 8th HLA Workshop. Frequencies of extended haplotypes (defined by B-Bf...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1984-09-01 00:00:00
abstract：:Recently the second gene for autosomal dominant polycystic kidney disease (ADPKD), located on chromosome 4q21-q22, has been cloned and characterized. The gene encodes an integral membrane protein, polycystin-2, that shows amino acid similarity to the PKD1 gene product and to the family of voltage-activated calcium (an...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/515497
更新日期：1997-09-01 00:00:00
abstract：:In the present study, we report a kindred with hearing loss, congenital heart defects, and posterior embryotoxon, segregating as autosomal dominant traits. Six of seven available affected patients manifested mild-to-severe combined hearing loss, predominantly affecting middle frequencies. Two patients were diagnosed w...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/341327
更新日期：2002-07-01 00:00:00
abstract：:A new polymorphic DNA marker U6.2, defining the locus DXS304, was recently isolated and mapped to the Xq27 region of the X chromosome. In the previous communication we describe a linkage study encompassing 16 fragile-X families and using U6.2 and five previously described polymorphic markers at Xq26-q28. One recombina...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1989-08-01 00:00:00
abstract：:The frequencies of the bromodeoxyuridine (BrdU)-requiring fragile site at 10q25 in 1,026 unselected neonates, 901 patients referred for chromosome studies, and 87 institutionalized retardates were not significantly different from each other. The gene frequency was .013, and the population was in Hardy-Weinberg equilib...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1982-09-01 00:00:00
abstract：:The hyper-IgE syndrome (HIES) is a rare primary immunodeficiency characterized by recurrent skin abscesses, pneumonia, and highly elevated levels of serum IgE. HIES is now recognized as a multisystem disorder, with nonimmunologic abnormalities of the dentition, bones, and connective tissue. HIES can be transmitted as ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/302547
更新日期：1999-09-01 00:00:00
abstract：:The Million Veteran Program (MVP), initiated by the Department of Veterans Affairs (VA), aims to collect biosamples with consent from at least one million veterans. Presently, blood samples have been collected from over 800,000 enrolled participants. The size and diversity of the MVP cohort, as well as the availabilit...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1016/j.ajhg.2020.03.004
更新日期：2020-04-02 00:00:00
abstract：:A cloned 2.2 Eco RI segment of interspersed repetitive DNA was hybridized to genomic DNA from a mentally retarded patient with an interstitial deletion in the long arm of one chromosome 12 (12q-). Under hybridization conditions of high stringency, one prominent 2.2-kilobase (kb) Eco RI fragment demonstrated reduced au...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1984-07-01 00:00:00
abstract：:Genetic testing has increased the number of variants identified in disease genes, but the diagnostic utility is limited by lack of understanding variant function. CARD11 encodes an adaptor protein that expresses dominant-negative and gain-of-function variants associated with distinct immunodeficiencies. Here, we used ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1016/j.ajhg.2020.10.015
更新日期：2020-12-03 00:00:00
abstract：:The gamete-competition model is an application of the Bradley-Terry model for ranking of sports teams. If allele i of a marker locus is assigned parameter taui>0, then the probability that a parent with heterozygous genotype i/j transmits allele i is Pr(i/j-->)=tau(i)/(tau(i) + tau(j). Mendelian segregation correspond...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/302826
更新日期：2000-03-01 00:00:00
abstract：:Genetic defects affecting motility of cilia and flagella cause chronic destructive airway disease, randomization of left-right body asymmetry, and, frequently, male infertility in primary ciliary dyskinesia (PCD). The most frequent defects involve outer and inner dynein arms (ODAs and IDAs) that are large multiprotein...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1016/j.ajhg.2009.10.018
更新日期：2009-12-01 00:00:00
abstract：:The gene for vimentin, an intermediate-filament protein, is growth regulated. We used Southern blot analysis and in situ chromosome hybridization to determine the location of the human vimentin gene. Our results show that there is only one copy of the vimentin gene and that it is located on the short arm of chromosome...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1987-10-01 00:00:00
abstract：:Patients with a strong family history of breast cancer are often counseled to receive genetic screening for BRCA1 and BRCA2 mutations, the strongest known predictors of breast cancer. A major limitation of genetic testing is the number of inconclusive results due to unclassified BRCA1 and BRCA2 sequence variants. Many...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/342192
更新日期：2002-09-01 00:00:00
abstract：:Association studies offer an exciting approach to finding underlying genetic variants of complex human diseases. However, identification of genetic variants still includes difficult challenges, and it is important to develop powerful new statistical methods. Currently, association methods may depend on single-locus an...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/511312
更新日期：2007-02-01 00:00:00
abstract：:Wolfram syndrome (MIM 222300) is characterized by optic atrophy, diabetes mellitus, diabetes insipidus, neurosensory hearing loss, urinary tract abnormalities, and neurological dysfunction. The association of clinical manifestations in tissues and organs unrelated functionally or embryologically suggested the possibil...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1996-05-01 00:00:00
abstract：:Mutations in the MCOLN1 gene cause mucolipidosis type IV (MLIV), a severely debilitating, autosomal recessive, lysosomal storage disorder. Approximately 80% of patients with MLIV are of Ashkenazi Jewish (AJ) descent, and two mutations, IVS3-2A-->G and 511del6434, account for >95% of the mutant alleles in this populati...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/339519
更新日期：2002-04-01 00:00:00
