当前位置:文档之家› McCarthy 等. - 2008 - Genome-wide association studies for complex traits

McCarthy 等. - 2008 - Genome-wide association studies for complex traits

McCarthy 等. - 2008 - Genome-wide association studies for complex traits
McCarthy 等. - 2008 - Genome-wide association studies for complex traits

The first wave of large-scale, high-density genome-wide association (GWA) studies has improved our understanding of the genetic basis of many complex traits 1. For several diseases, including type 1 (Refs 2,3) and type 2 diabetes 4–9, inflammatory bowel disease 10–14, prostate cancer 15–20 and breast cancer 21–23, there has been rapid expansion in the numbers of loci implicated in predisposition. For others, such as asthma 24, coronary heart disease 25–27 and atrial fibrillation 28, fewer novel loci have been found, although opportunities for mechanistic insights are equally prom-ising. Several common variants influencing important continuous traits, such as lipids 7,29–31, height 32–35 and fat mass 36–38, have also been found. An updated list of published GWA studies can be found at the National Cancer Institute (NCI)-National Human Genome Research Institute (NHGRI)’s catalog of published genome-wide association studies .

These findings are providing valuable clues to the allelic architecture of complex traits in general. At the same time, many methodological and technical issues that are relevant to the successful prosecution of large-scale association studies have been addressed. However, despite understandable celebration of these achieve-ments, sober reflection reveals many challenges ahead. Compelling signals have been found, often highlighting previously unsuspected biology, but, for most of the

traits studied, known variants explain only a fraction of observed familial aggregation 39, limiting the potential for early application to determine individual disease risk. Because current technology surveys only a lim-ited subset of potentially relevant sequence variation, this should come as no surprise. Much work remains to obtain a complete inventory of the variants at each locus that contribute to disease risk and to define the molecular mechanisms through which these variants operate. The ultimate objectives — full descriptions of the susceptibility architecture of major biomedical traits and translation of the findings into clinical practice — remain distant.

With completion of the initial wave of GW A scans, it is timely to consider the status of the field. This Review considers each major step in the implementation of a GW A scan, highlighting areas where there is an emerg-ing consensus over the ingredients for success, and those aspects for which considerable challenges remain.

Subject ascertainment and design

Although there is a growing focus on the application of GWA methodologies to population-based cohorts, most published GWA studies have featured case– control designs , which raise issues related to the optimal selection of both case and control samples.

*Wellcome T rust Centre for Human Genetics, University of Oxford, Oxford, UK. Correspondence to M.I.M e-mail: mark.mccarthy@https://www.doczj.com/doc/c67696718.html,

doi:10.1038/nrg2344

Published online 9 April 2008

Genome-wide association (GWA) studies

studies in which a dense array of genetic markers, which captures a substantial proportion of common

variation in genome sequence, is typed in a set of DNA

samples that are informative for a trait of interest. The aim is to map susceptibility effects through the detection of

associations between genotype frequency and trait status.

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

Mark I. McCarthy*?, Gon?alo R. Abecasis §, Lon R. Cardon*||, David B. Goldstein ?, Julian Little #, John P . A. Ioannidis**?? and Joel N. Hirschhorn §§||||??

Abstract | The past year has witnessed substantial advances in understanding the

genetic basis of many common phenotypes of biomedical importance. These advances have been the result of systematic, well-powered, genome-wide surveys exploring the relationships between common sequence variation and disease predisposition. This approach has revealed over 50 disease-susceptibility loci and has provided insights into the allelic architecture of multifactorial traits. At the same time, much has been learned about the successful prosecution of association studies on such a scale. This Review highlights the knowledge gained, defines areas of emerging consensus, and describes the challenges that remain as researchers seek to obtain more complete descriptions of the susceptibility architecture of biomedical traits of interest and to translate the information gathered into improvements in clinical management.

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Case–control design

An association study design in which the primary comparison is between a group of individuals (cases), ascertained for the phenotype of interest and that are presumed to have a high prevalence of susceptibility alleles for that trait, and a second group (controls), not ascertained for the phenotype and considered likely to have a lower prevalence of such alleles. Selection bias

Bias arising from the fact that the samples ascertained for the study (particularly controls) might not be representative of the wider population that they are purported to represent. Misclassification bias

Bias resulting from the failure to correctly assign individuals to the relevant group in a case–control study; for example, the presence of some individuals who meet the criteria for being cases in a population-based control sample.

Population stratification The presence in study samples of individuals with different ancestral and demographic histories: if cases and controls differ with respect to these features, markers that are informative for them might be confounded with disease status and lead to spurious associations.Case selection. The principal issues with regard to case

ascertainment revolve around the extent to which selec-

tion should be driven by manoeuvres that are designed

to improve study power through enrichment for spe-

cific disease-predisposing alleles. These include efforts

to minimize phenotypic heterogeneity or to focus on

extreme and/or familial cases (defined, for example,

by early age of onset or ascertainment from multiplex

pedigrees). Because the genetic architecture of most

complex traits remains poorly understood, the value of

such efforts is hard to predict. In most circumstances,

and particularly when the total GWA sample size has

financial or operational constraints, efforts to enrich

case selection are likely to improve power. However,

there are situations in which selection of familial

cases or extreme individuals might have the opposite

effect40,41.

Control selection. optimal selection of control samples

remains more controversial, although the accumulating

empirical data indicate that many commonly expressed

concerns have been overstated. The Wellcome Trust

Case Control Consortium (WTCCC) study was able

to demonstrate the effectiveness of a ‘common control’

design in which 3,000 uK controls were compared

with 2,000 cases from each of 7 different diseases1. The

WTCCC also assuaged concerns about the potential

for selection bias when using non-population-based

controls1. Comparison of the genome-wide genotypic

distributions from the two constituents of the WTCCC

common-control resource (one derived from a popula-

tion-based birth cohort, the other from opportunistic

sampling of blood donors) revealed no excess of sig-

nificant associations, indicating that ascertainment,

selection and survival biases were, in this situation at

least, having minimal impact on genotype distributions.

Although each prospective control sample must be

critically evaluated, these findings suggest that a broad

range of ascertainment schemes are compatible with

GW A analysis.

one consequence of the common-control design is

the potential loss of power that is associated with the

inability to exclude latent diagnoses of the phenotype

of interest through intensive screening of controls.

Fortunately, the consequences of misclassification bias are

modest unless the trait is common, and any loss of power

is recoverable by increasing the sample size (BOX 1).

For common traits, such as obesity and hypertension, in

which the effect of misclassification on power is great-

est1, one remedy involves adopting a more stringent case

definition, for example, based on early age of onset or

ascertainment of a more extreme phenotype, while

still excluding monogenic cases. Although the most

powerful strategy for a given fixed sample size involves

a ‘hypernormal’ control group, it might be difficult to

identify such individuals without introducing inadvert-

ent selection effects. For instance, selecting extremely

low-weight individuals as controls for a case–control

study of obesity could result in overrepresentation of

alleles primarily associated with chronic medical dis-

ease or nicotine addiction rather than weight regulation

per se.

Other case–control design issues. Four other issues loom

large in the design of case–control studies. The first is

sample size, and with this issue the consensus view

is clear: the more samples the better1,34,35,38. The initial

wave of GW A studies has shown that, with rare excep-

tions, the effect sizes resulting from common SNP

associations are modest, and that sample sizes in the

thousands are essential1.

The second issue relates to the propensity for latent

population substructure (population stratification and

cryptic relatedness) to inflate the type 1 error rate

and generate spurious claims of association around

variants that are informative for that substructure42,43.

The evidence emerging from GWA studies is reassur-

ing: as long as cases and controls are well matched for

broad ethnic background, and measures are taken to

identify and exclude individuals whose GWA data

reveal substantial differences in genetic background,

the impact of residual substructure on type 1 error

seems modest1. Several statistical tools exist to detect

and adjust for residual stratification42,44, and invento-

ries of markers that are informative for the detection of

ethnic substructure are a useful by-product of current

scans1,45–47. These approaches can be used to adjust for

substructure even in populations with quite diverse

antecedents (such as european-descent populations

in North America)46,47 and with negligible impact on

power48. Analysis in African-descent populations is

complicated by their greater haplotypic diversity and

fine-scale geographical structure49, and by the exten-

sive admixture demonstrated by African-descent

populations that are resident in europe and North

America. Furthermore, it is important to note that the

tools mentioned above (particularly genomic-control

approaches44) correct for ‘average’ genome-wide meas-

ures of ethnic admixture, and will not always eliminate

spurious associations immediately adjacent to markers

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Cryptic relatedness evidence — typically gained from analysis of GWA data — that, despite allowance for known family relationships,

The third issue concerns the relative merits of family-

based and case–control association methods. Although

family-based association methods provide a robust strategy

for dealing with stratification, this typically comes at

has become less persuasive. Nevertheless, there are many

valuable clinical resources (for example, isolates) for

which pedigree information can be usefully exploited.

one option for the efficient use of family data in such a

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Pleiotropy

The phenomenon whereby a single allele can affect several distinct aspects of the phenotype of an organism, often traits not previously thought to be mechanistically related.

Linkage disequilibrium (LD). The nonrandom allocation of alleles at nearby variants to individual chromosomes as a result of recent mutation, genetic drift or selection, manifest as correlations between genotypes at closely linked markers.

Copy number variant (CNV). A class of DNA sequence variant (including deletions and duplications) in which the result is a departure from the expected diploid representation of DNA sequence.

DnA pooling approaches Association studies that are conducted using estimates of allele frequencies derived from pools of DNA compiled from multiple subjects rather than individual DNA samples.genotyping in the remaining members to propagate

genotypes through the family51.

The fourth question relates to the potential to use

historical control genotypes to substitute for, or supple-

ment, newly typed controls in future GW A studies. The

risks associated with this (particularly inflation of the

type 1 error) will clearly depend on the extent to which

there are disparities between the new cases and historical

controls with respect to population origins, DNA format

(whole-genome amplified DNA versus native DNA as

well as storage conditions)52,53 and genotyping imple-

mentation (platform, genotyping centre, generation of

chip or allele-calling software). The limits of acceptable

divergence are not yet known, but it seems safest that

studies intending to use historical control data also

type a sample of ethnically matched controls (including

a subset of the historical control samples, if available)

using the same assay as for the newly defined cases. This

should allow the detection of systematic effects that are

attributable to non-disease-related differences between

the historical and new data. An alternative approach

would involve the re-genotyping of any interesting GW A

signals in all samples using a dedicated assay.

From case–control to cohort studies. Increasingly, the

GWA approach is being extended from analysis of

case–control samples to population-based cohorts54–56.

Although typically underpowered for dichotomous phe-

notypes (given limited cases for any given disease), such

cohorts often offer a rich tapestry of longitudinal meas-

ures for a wide range of quantitative traits, and lifestyle

and exposure data can enable an evaluation of the joint

effects of genes and environment. These studies promise

new insights into the genetic basis of continuous traits

and enhanced opportunities for revealing pleiotropy57,

although low power remains an issue — especially

for the detection of non-additive gene–environment

interactions58,59. Whereas GWA data meta-analysis is

the obvious solution to overcome restrictions of sam-

ple size, such procedures are often complicated by the

lack of standardization that characterizes the meas-

urement of many key continuous biological traits and

environmental exposures60.

Implementation

Marker selection and assay design. The debates about

marker selection that dominated early discussions of

GWA approaches have now boiled down to choices

between a limited range of commodity genome-wide

chips61,62. This is not the place for a detailed discussion

of the relative merits of specific array-designs other than

to point out that, genotype for genotype, designs that

take linkage disequilibrium (lD) structure into account

when defining content will achieve greater coverage,

in the index population at least. However, they will also

be more vulnerable to loss of coverage when assays fail,

or when typing samples whose genetic ancestry differs

from that of the reference panel or panels used to guide

marker selection61,62. Although greater feature density,

which allows more variants to be typed in a single array,

increases coverage, this does not necessarily equate to

greater power. When funding is limited, but the avail-

ability of samples is not, overall power might be maxi-

mized by typing more individuals with a less dense and

less costly array. In populations of non-African ancestry,

some of the drive towards ever-increasing array density

has been blunted by the capability to impute genotypes

at untyped loci (discussed later)63,64.

A new option in array selection comes with the inclu-

sion on contemporary commodity arrays of additional

probes that are designed to type copy number variants

(CNvs)65. However, because the global inventory of

CNvs remains incomplete66, and with limited empirical

data currently available, the extent to which the cur-

rent round of products (such as the Affymetrix 6.0 and

Illumina Human1M arrays) captures the structural vari-

ome remains unclear. However, their use should provide

early insights into the contribution such variants make to

common phenotypes of biomedical importance67.

For any given study, the final choice of array platform

is often a pragmatic one, based not only on the number

and ethnic origin of the samples, and the overall research

objectives, but also on factors such as cost, array delivery

schedules and available genotyping capacity.

DNA pooling. The costs of well-powered GWA stud-

ies have reignited interest in the value of DNA pooling

approaches as a means to conduct more economical

genome-wide surveys for association68. However, even

though several studies have been completed69, the falling

costs of commodity genotyping and the intrinsic limita-

tions of the pooling approach (reduced power, loss of

individual genotype data and difficulties ensuring equi-

molar representation of samples) mean that the future of

this approach, for GW A studies at least, is uncertain.

Obtaining robust genotype data. experience from the

first wave of GW A studies has demonstrated that scru-

pulous attention to detail is required throughout because

each stage is fraught with the potential for error and

bias1,52,53,70,71. Many of these errors and biases have the

potential to generate extreme values for the association

test statistic; if uncorrected, these can dominate the tails

of the distribution, such that interesting true associa-

tions become lost in a sea of spurious signals. efforts to

prevent, detect and eradicate sources of bias and error

therefore remain a high priority in GW A studies1, despite

continuing improvements in genotyping performance.

These efforts start with careful attention to the qual-

ity and accurate quantification of the starting DNA.

Differences in extraction methods between cases

and controls can be an important source of bias52,53.

Implementation of genotyping-performance metrics allows

poorly performing arrays to be targeted for re-analysis

and deficient samples to be selected for replacement1.

Given the scale of data generation, conversion of raw

experimental data into genotypes has necessitated the

development of automated methods. Indeed, the very

idea of assigning a discrete genotype call has increasingly

been replaced by measures of the posterior probability of

each possible genotype, given the observed data1. Several

algorithms have been developed for defining the three

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Informative missingness

If patterns of missing data are nonrandom with respect to both genotype and trait status, then analysis of the available genotypes can result in misleading associations where none truly exists.

Signal intensity (cluster) plots

Plots of raw intensity data for individual variants that are generated by the genotyping platform and represent the extent to which the various genotypes can be discriminated: these provide a useful visual diagnostic for the genotyping data quality. Hardy–Weinberg equilibrium

(HWe). A theoretical description of the relationship between genotype and allele frequencies that is based on expectation in a stable population undergoing random mating in the absence of selection, new mutations and gene flow: in the context of genetic studies, departures from equilibrium can be used to highlight genotyping errors. Quantile-quantile plot

(Q-Q plot). In the context of GWA studies, a Q-Q plot is a diagnostic plot that compares the distribution of observed test statistics with the distribution expected under the null.

Cochran–Armitage test

A genotype-based contingency-table test for association that is well suited to the detection of trends across ordinal categories

(in this case, genotypes). Frequentist

A school of statistics that uses p values and combines them with hypothesis testing to make inferences.genotype clusters at a given SNP, and for assigning geno-

type calls to each1,53,72–74, with each generation of soft-

ware heralding steady improvements in both accuracy

and call rate. This last point is crucial because there is

no room for complacency regarding SNPs that display

low call rates1,53. Case–control studies, in particular, are

vulnerable to informative missingness, whereby spurious

associations arise through differences in the patterns of

missing data with respect to genotype.

Considerations such as these have highlighted a

tension between stringency and call rate, which has pre-

vented the promulgation of quality-control thresholds

with a universal value for defining the set of ‘clean’ geno-

types for analysis. If researchers aim to maximize accu-

racy by setting the threshold for calling genotypes too

high, the consequence for many SNPs will be a low call

rate (such that some true signals are discarded) and/or

a rise in type 1 error (due to informative missingness).

However, if a lower threshold is favoured, as some groups

have done1, call rates will be preserved (and informative

missingness minimized) at the expense of accuracy. Those

who adopt this more liberal strategy accept that a non-

trivial number of poorly performing SNPs will survive the

quality-control process and might be disproportionately

represented among the most extreme association signals.

If resources are not to be wasted in fruitless validation

and replication studies, it becomes essential to subject

interesting signals to individual reviews of quality-control

parameters (especially visualization of the signal intensity

(cluster) plots) (BOX 2) before proceeding. one corollary is

that GW A data-sharing efforts should extend to the pro-

vision of raw signal data as well as ‘finished’ genotypes.

once armed with a set of called genotypes, the

final phase of quality control beckons. experience has

shown that most SNPs showing extreme departures

from Hardy–Weinberg equilibrium (HWe) in controls can

be safely discarded1, although lesser (but nevertheless

quite marked) departures are to be expected under the

null hypothesis, given the number of tests performed.

Appropriate thresholds for any given study will depend

on the sample size and overall data quality, and might best

be defined by using the observed distribution of HWe

statistics (the WTCCC used this approach to set a thresh-

old at an exact p < 5.7 x 10–7 in controls)1. In any event,

HWe is an imprecise tool for quality control purposes.

Tests of departure from HWe are underpowered for the

detection of genotyping error75,76, whereas overenthusi-

astic use of HWe as a quality criterion can prove to be

counterproductive given that modest disequilibrium (in

cases particularly) can be a signature of true association.

Recent studies have emphasized the importance of

detecting individuals whose GW A data reveal an ancestry

that is discrepant with self-described labels, allowing them

to be removed from consideration1 or analysed separately.

Similarly, sample integrity needs to be confirmed using

recorded gender or previously obtained genotypes.

Inadvertent sample duplication and swaps, cross-contami-

nation and cryptic relatedness43 are frequently revealed by

analysis of GW A data, and, if unresolved, would violate

assumptions of statistical independence and introduce

misclassification effects. It is straightforward to identify

first- and second-degree relatives at least and exclude

one member of each pair from analysis. In the presence

of more remote relationships, options include explicit

modelling of those relationships, or adjustment through

genomic-control approaches43,44.

This sequence of manoeuvres has proved challenging

enough for experienced groups given the size of the data

sets concerned. However, all groups working with such

data, whether generated themselves or downloaded from

the web, need to appreciate the intricacies of data quality

control if they are to avoid potential misinterpretation.

The comments above refer to the implementation of SNP-

based scans, but the task of converting intensity traces

and SNP-based data into multi-allelic CNv genotypes is

far more demanding and is only now being tackled65.

Analysis and interpretation

Diagnostic plots. A limited number of formats have

emerged as standard tools for representing the data

emerging from a GWA scan, with the quantile-quantile

plot (Q-Q plot) among the most widely used52,77(BOX 2).

These plots help to indicate whether the study has gener-

ated more significant results than expected by chance and

to put such findings in context. undetected population

stratification or cryptic relatedness result in deviation

from the null across the entire distribution, whereas

large-effect susceptibility loci generate deviations at the

highly significant end of the range.

Single-point analyses. In most situations, the most power-

ful tool for the analysis of GW A data has been a single-

point, one degree of freedom test of association, such as the

Cochran–Armitage test. Such tests allow comparison of

the genotype distributions of cases and controls at each

SNP in turn, and can be conducted with or without

adjustment for relevant covariates, such as the principal

components of population substructure42. Although the

Cochran–Armitage method directly tests only one of sev-

eral possible genetic models, it has the merit of being robust

to modest deviations from additivity on the logistic scale

(at least to those most likely to be biologically relevant).

Furthermore, in situations in which the true model at the

causal variant is non-additive, even modest departures

from perfect lD will result in greatly reduced power to

detect that non-additivity at nearby variants: in the GW A

context therefore, in situations when few causal variants

will be directly typed, the additive model is likely to per-

form well. Whereas the use of alternative models (general,

dominant or recessive) could result in enhanced detection

of some signals78, the use of multiple correlated tests also

complicates computation of type 1 error rates and can

reduce the efficiency of subsequent follow-up efforts.

Historically, interpretation of genetic association find-

ings has adopted the standard frequentist approach to the

evaluation of significance. From such a view-point, GW A

results are compared against a single criterion of genome-

wide significance. Although several benchmarks have

been proposed, in european-descent GW A studies opin-

ion is coalescing around the need to adjust for 1–2 million

independent tests, which results in a target α (p value)of

~5 x 10–8(Refs 49,79,80). However, such an approach fails

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Quantile-quantile (Q-Q) plots provide a visual summary of the distribution of the observed test statistics generated by a genome-wide association (GWA) study 52,77. Typically, a single test statistic (for case–control studies, plots based on ~200 genotypes. In panel e the three clusters are well defined and individual genotypes are accurately called (as shown by the three colours). In panel f the clusters are well defined, but an error in Nature Reviews | Genetics C h r 1

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Bayes’ factors

The Bayesian alternative to classical frequentist approaches to hypothesis testing, essentially equivalent to likelihood ratio tests: prior and posterior information are combined in a ratio that measures the strength of the evidence in favour of one model rather than the other. False-positive report probability

The probability that a reported association between a genetic variant and a trait of interest is not true.

Haplotype-based methods Association methods that rely on the relationship between the distribution of estimated haplotype frequencies and trait status, rather than each individual variant in turn. Imputation methods

A set of approaches for filling in missing genotype data using a sparse set of genotypes (for example, from a GWA scan) and a scaffold of linkage disequilibrium relationships (as provided by the HapMap).to account for factors such as the power of a study and the

number of likely true positives, which are important com-

ponents of any comprehensive evaluation of GW A find-

ings81. Consider a small case–control GW A performed

for a condition for which there is only weak evidence for

genetic involvement: any associations found are unlikely

to be genuine, whatever the p value obtained. Such

limitations have excited interest in Bayesian approaches,

which incorporate information on the likely number

of true associations, and the power of a given study to

detect associations of a given magnitude, into estimates of

credibility81,82. These methods, which generate measures

such as Bayes’ factors, or the false-positive report probability

rather than p values, avoid a single threshold for genome-

wide significance but depend on the ability to assign

plausible probabilities to each of the alternate hypoth-

eses (see Ref.1 for further discussion). Nevertheless,

both approaches conclude that only very low p values

equate to strong evidence for association (that is, are

associated with a low false-positive rate). Crucially, most

GW A signals that have attained such significance levels

have subsequently been confirmed by replication1.

Multi-marker analyses. As expected, given the incom-

plete coverage of common variation that is provided by

contemporary GWA platforms61,62, a modest boost to

power can be provided by computational approaches that

improve the detection of associations that are attribut-

able to variants that have not themselves been directly

typed83. Haplotype-based methods and imputation methods

are related but complementary approaches to achieve

this. In situations when haplotype-based analyses83,84

reveal evidence for association that exceeds that of any

directly typed SNP in the vicinity (after allowance for the

increased dimensionality), one can invoke either an effect

that is directly attributable to the haplotype (that is, inde-

pendent causal cis effects at multiple SNPs) or the expla-

nation that the haplotype tags more efficiently than any

individual genotyped SNP, an as yet untyped aetiological

variant. Imputation methods63,64 rely on information from

sets of resequenced and/or densely genotyped individuals

to infer missing genotypes at untyped variants. Because

data from the International HapMap Consortium49 are

typically used as the reference, imputation methods have

proved most powerful in recovering associations and

causal effects attributable to HapMap SNPs that are not

included on commercial arrays. Importantly, the use of

such methods is not restricted to samples drawn from

HapMap reference populations85.

Challenges. Immediate challenges in this area are numer-

ous. The imminent arrival of large-scale genome-wide

CNv data65 has focused attention on the development of

methods that are suited to the specific features of such

data (multiallelic, semi-quantitative and probably more

error prone) and methods that facilitate the integration of

CNv and SNP information. There is work to be done to

understand how best to incorporate the intrinsic uncer-

tainty that is associated with genotype calls derived from

both direct and, in particular, imputed data63,64, and in the

development of analysis tools that take account of, and/or

estimate, information on population history, which will

prove especially valuable for studies in genetic isolates86.

evaluation of the contribution of rare variants to com-

mon disease susceptibility raises issues related to detection

(rare variants are poorly captured by the standard GW A

arrays87) and functional assessment (the sheer number

of such variants and the limited power to test them for

association88). Finally, there is a need for improved meth-

ods to estimate the joint effects of multiple genes and/or

environmental exposures on disease predisposition. Such

analyses raise both computational and statistical issues,

related to the scale and complexity of the data and the

large number of hypotheses that could be addressed89.

Validation and replication

The importance of replication. The use of small sam-

ples, which are underpowered to detect loci of realistic

effect size, and over-liberal declarations of association

are the main reasons why so few of the complex-trait

associations that were claimed in the pre-GWA era

proved genuine81,90. This history, together with the high

dimensionality of GW A studies, their vulnerability to a

range of errors and biases, and the modest effect sizes

to be anticipated for most complex-trait susceptibility

alleles, help to explain the pre-eminent role of replication

in the evaluation of GW A findings91,92.

Terminology in this area can be confusing. Here,

we use ‘technical validation’ to refer specifically to the

reanalysis of original GWA samples using a second

genotyping platform. Technical validation allows early

detection of technical errors in typing or imputation that

might have generated a spurious association signal, and

is an important prelude to large-scale efforts to evalu-

ate selected signals in additional independent samples

(referred to here as ‘replication’).

Best practice. The aim of validation and replication is to

determine which of the findings arising from the primary

GW A reflect true reproducible associations. Accordingly,

the focus is not merely to provide additional evidence to

support or refute the original association, but also the

systematic appraisal of potential sources of error and bias

that could have been responsible. Hence, it is important

to use independent replication samples, and to use dis-

tinct genotyping assays to expose technical artefacts.

Credibility is increased when multiple investigative groups

find the same association in independent samples.

Claims of replication should be reserved for findings

involving the same allele or haplotype (or an established

proxy thereof), the same phenotype and the same genetic

model as the original signal. otherwise the risk of spurious

claims of association is increased by the testing of multiple

hypotheses. This has an important bearing on decisions

about the extent to which early replication efforts at a

given signal should focus exclusively on the index variant,

as opposed to including additional adjacent SNPs93. The

inclusion of adjacent SNPs runs the risk of generating a

profusion of apparent associations around spurious GW A

signals — complicating interpretation of the evidence

for replication — and can involve a substantial waste of

genotyping effort around the many false-positive signals.

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In most instances, therefore, it seems wise first to obtain definitive evidence of association at the index variant. So that failure to replicate can be meaningfully interpreted, the samples used in early rounds of replication should be broadly similar (with respect to ethnicity and ascertain-ment) to those of the original study. of course, as loci are validated as truly causal, extension into multiple ethnici-ties is highly desirable to test the generalizability and con-sistency of the proposed association, although such efforts will probably entail additional efforts at variant discovery given ethnic differences in lD.

Multi-stage designs. Several recent reports have empha-sized the potential advantages of multi-stage designs, in which signals from an initial, first-stage GW A are used to define a subset of SNPs that are retyped in additional second-stage samples94–96. Such designs have been seen as an effective way of retaining power while reducing geno-typing costs. However, the substantial price differential between commodity and custom genotyping means that those cost benefits can be less dramatic than comparisons of genotype numbers alone would suggest. In circum-stances in which the second-stage and GW A samples have similar provenance, so that the prospects for appreciable genetic heterogeneity between the stages are low, the best-powered analytical strategy involves a joint analysis (in which the distribution of test statistics across the data from both stages combined is considered), rather than the conventional replication design (which considers the second-stage results in isolation)94. Such considerations blur the boundaries of where exactly replication starts, but whichever analytical approach is taken, confirmation in many independent samples is important and it is the over-all strength of the evidence of association that matters.Power, sample size and heterogeneity. An appreciation of power and sample size is central to the design and interpre-tation of appropriate replication studies. Studies that lack the power to offer convincing support or refutation of the original finding can generate misleading inferences when considered in isolation, although combinations of such studies might be of value provided that all suitable studies have been included. Calculations of replication sample size need to consider the so-called ‘winner’s curse’ effect, whereby the original study will typically overestimate the true effect size97. Replication efforts that fail to make such allowance will probably be underpowered98,99.

If well-performed replication studies confirm the original findings, then the evidence in favour of associa-tion is enhanced (unless of course both the original and replication studies have succumbed to the same errors). Interpretation of a failure to replicate is more difficult. If it is clear that the replication studies were well powered and well performed, and that there is genuine divergence between the effect-size estimates (for example, no overlap of 95% confidence intervals), then there are two possible explanations. either the original finding was wrong, or the difference in findings is attributable to some source of heterogeneity100,101. The list of potential causes of hetero-geneity is long: it includes variable patterns of lD between the genotyped SNP and untyped causal alleles (although this is unlikely if the samples are of similar ancestry); dif-ferences in the distribution, frequency or effect size of the causal alleles at a given locus (due to, for example, drift or selection, or differences in case ascertainment); and the impact of non-additive interactions with other genetic variants or environmental exposures.

We should be wary of appealing to heterogeneity as a rationale for failure to replicate, as over-eagerness to deploy such an explanation would mean that no report of association could ever be refuted. Nevertheless, there are established instances in which the effects of proven associations can vary substantially across studies, so clearly circumstances exist where it can be justified. The role of variants in the fat mass and obesity associ-ated (FTO) gene on the risk of diabetes and obesity (BOX 3) provides one such example, illustrating how a clear case for heterogeneity can be made, especially when the initial association finding has been robustly replicated and the source of the heterogeneity is apparent1,5,36,37. Some sources of heterogeneity can be directly evaluated, including dif-ferences in lD structure between populations (particu-larly once the true causal allele has been identified), clear variation in case ascertainment that can be correlated with effect size or a highly significant interaction with a well-measured covariate. other sources of heterogeneity, such as an unmeasured or poorly defined environmental exposure, will be difficult or impossible to demonstrate. The number of associations for which heterogeneity has an important role cannot be reliably estimated from the evidence to date: because our inventory of ‘proven’ com-plex-trait associations is heavily biased towards variants that have shown consistent replication across studies (this being such an important factor in determining proof), there is likely to be a substantial under-representation

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heterogeneity 102. Moreover, estimation of between-study heterogeneity is highly imprecise when the number of studies is limited (less than 10) and/or their individual power is low. Systematic efforts to define the impact of gene–gene and gene–environment interactions, well-powered GW A studies in multiple ethnicities and com-prehensive exploration of variation around strong signals of association should all help to address this point.

Finding additional susceptibility genes

Meta-analysis. Individual GW As are underpowered to detect all but the biggest effects, and the susceptibility variants identified so far are probably only a subset of the loci that would be detectable using this approach if power were increased 39. Joint (meta) analysis of data

from comparable GWA scans 9,34,35,38,103 provides a low-cost approach to enhance power for both main and joint (gene–gene and gene–environment) effects, obtain in silico replication, inform SNP selection for subsequent replication efforts and explore potential sources of heter-ogeneity. In type 2 diabetes, joint analysis of three GW A scans (4,700 cases and 5,700 controls when combined)5–7,9 was central to the robust identification of several novel susceptibility variants, and allowed confirmation of the role of previously known susceptibility variants of modest effect size, such as those in KCNJ11 (potassium inwardly-rectifying channel, subfamily J, member 11) and PPARG (peroxisome proliferator-activated receptor gamma).

As increasingly large data sets are deployed to find signals for which smaller samples were underpowered, the average effect size of the novel variants that are dis-covered will decrease. For some purposes, such as pre-dictive diagnostics, this has implications for their likely translational impact. even so, it is worth remembering that owing to imperfect lD, a modest finding from the initial GWA might ultimately lead to fine mapping of variants with considerably larger effect sizes. When it comes to insights into disease pathogenesis, however, locus effect size is almost immaterial: even loci with modest effects, once they are established as genuine, can reveal novel causal mechanisms. Thus, discovery efforts are likely to continue to bear fruit as long as the clinical, logistical and financial resources are available to support them, and, as genotyping costs fall, ever larger studies will become possible.

The technical aspects of successful data combination have been widely discussed in the meta-analysis litera-ture 100,104. Clearly, researchers seeking to obtain an unbi-ased estimate of the significance of a given association are duty-bound to be as inclusive as possible 90. Although it might be tempting to exclude particular studies on the basis of some perceived failure of quality or potential het-erogeneity, any such decisions must be carefully justified. In the presence of heterogeneity, random-effects models provide more appropriate estimates of overall effect size, because heterogeneity violates the basic assumption of fixed-effects analysis 100. Although summary-level data will suffice for many meta-analysis purposes, access to primary individual-level data allows for more sophisti-cated reanalysis, including the capacity to undertake hap-lotype and conditional analyses, to perform imputation, to examine the joint effects of genes and environment, and to explore phenotypic heterogeneity.

Reintroducing biology. So far, most efforts at replication have concentrated, not unreasonably, on the signals for which the statistical evidence is strongest. However, the efficient identification of additional susceptibility loci with more modest effect sizes might benefit from the integration of statistical evidence with some assessment of functional candidacy. Several prioritization strategies for defining variant subsets with increased ‘prior’ odds for association can be envisaged, embracing aspects of bio-logical candidacy (for example, variants mapping to genes that interact with, or lie within the same pathways as, those

Box 4 | Strategies for resequencing within genome-wide association signals

Because genome-wide association (GWA) studies directly genotype only a small

proportion of the variants that segregate within the population examined, it is unlikely that the causal variant(s) will be among those for which genotype data are available. Imputation methods 63,64 allow association analysis to be extended to a larger set of variants (HapMap SNPs for which reliable imputation is possible), but this still comprises a minority of all common SNPs, and representation of rare variants is poorer still 87. Targeted resequencing allows recovery of a more complete inventory of sequence variation

within regions of interest, and enables systematic fine-mapping efforts to identify those putatively causal variants with the strongest effects on disease susceptibility.

For any given region, the extent and scope of resequencing efforts depends on the strategic goal. Consider the example of the fat mass and obesity associated (FTO ) region that is implicated in obesity and type 2 diabetes (see the figure)1,5,36. Association analysis using directly typed (black) and imputed (grey) SNPs localized the association signal to a 47 kb region (A–B) defined by flanking recombination hot spots (red trace), within intron 1 of the FTO gene. If the goal is to identify common causal variants that could underlie this index signal, it should suffice to resequence this ~50 kb interval in ~200 individuals (a total of ~10 Mb). If the aim is, instead, to identify all common variants contributing to regional susceptibility (including those independent of the index signal, so-far missed owing to incomplete coverage) then all sequence that is relevant to gene expression or function (arbitrarily, C–D) needs to be considered (~600 kb, hence a total of ~120 Mb). Should the aim extend to identification of rare variants with independent effects on disease risk, recovery of the full allelic spectrum of sequence variants will require deep resequencing in ~500–1000 individuals: in the first instance, such deep resequencing efforts might be preferentially targeted to exonic and conserved non-coding sequence. AKTIP , AKT interacting protein; CHD9, chromodomain helicase DNA binding protein 9; IRX3, iroquois homeobox 3; IRX5, iroquois homeobox 5; RBL2, retinoblastoma-like 2; RPGRIP1L , retinitis pigmentosa GTPase regulator interacting protein 1-like.

40800

5

10

15

2

4c M p e r M b

–l o g 10(P )

c M f r o m h i t S N P

Genes

51.5

52.0

52.5

53.0

53.5

Chromosomal position (Mb)

CHD9

AKTIP

IRX3

RPGRIP1L

FTO

RBL2

IRX5

AB C

D

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that were previously implicated in susceptibility to the dis-ease of interest) and genomic annotation (for example, all variants capturing variation in microRNA target sites).

Other populations. Among the GWA scans that have already been performed there has been a strong bias towards samples of North european origin1–38. There are excellent reasons for extending analyses to samples from populations with differing mutational and demo-graphical histories, including other major ethnic groups49 and population isolates86. each such sample offers new opportunities in terms of detectable susceptibility vari-ants, generating ethnic-specific patterns with respect to the identity of the loci themselves, the frequency and lD relationships of disease-susceptibility alleles, and the presence of additional genetic or environmental factors with which they might interact. Studies in other popula-tions are therefore capable of revealing novel suscepti-bility loci and aetiological pathways, as well as assisting with the fine-mapping of causal variants within those loci already confirmed105. Given the large sample sizes that are needed to achieve these ends, the ascertainment of GW A and replication sample sets from diverse ethnic groups is a priority.

Other sequence variants. Finally, it is worth reiterating that, so far, GW A scans have focused almost exclusively on the detection of effects that are attributable to com-mon SNPs. The first wave of GW A arrays offered limited power to capture structural variants106 and rare variants of any type87. The arrival of tools that are better-suited to the direct evaluation of these variant types is likely to provide the most immediate source of novel susceptibil-ity loci, although each brings its own set of technical and analytical challenges65.Following-up confirmed signals

The confirmed signals emerging from GWA scans and subsequent replication efforts are just that — associa-tion signals. The causal variants will only occasionally be among those that are directly typed in GWA scans, and the interval within which the aetiological variant(s) are expected to lie (typically defined in terms of flank-ing recombination hot spots) can be sizeable, often con-taining several genes1,24. even worse, because it seems likely that many complex-trait susceptibility effects are mediated through remote regulatory elements107, the coding exons of the susceptibility gene could lie well beyond the interval of maximal association.

Resequencing and fine mapping. The task of moving from confirmed association signal to complete enu-meration of the pattern of causal variants at a given locus poses significant challenges. on occasion, useful shortcuts to exhaustive fine mapping might be avail-able. The set of associated variants might include a number with particularly strong biological credentials — a non-synonymous coding SNP in a compelling bio-logical candidate, for example. Alternatively, clues can be gathered from expression studies108–110: the cluster of associated variants might display strong cis associations with expression of one of the nearby genes, transcript levels of which are themselves associated with the phe-notype of interest13,24. Although caution is warranted in placing weight on in silico or in vitro functional data (the concordance between epidemiological associa-tions and measurable functional effects has historically been poor111), such findings can provide a rapid route towards direct functional confirmation of the implicated molecular mechanisms.

In the absence of such insights, further progress will generally require exhaustive examination of the region, first, to generate a comprehensive inventory of regional variation, and second, to use fine-mapping approaches to define the signals with the strongest statistical claims112. Despite recent advances in sequencing and genotyping, both are daunting tasks.

Resequencing plans need to be tailored to the desired objective (BOX 4). Implementation raises a host of unanswered issues related to optimal study design and data interpretation. There are numerous choices to be made: first, about the samples to be resequenced, that is, the balance of HapMap individuals versus disease cases and whether to favour cases carrying the known susceptibility variant or haplotype; second, the depth of resequencing to be undertaken, which defines the allele spectrum recovered; and finally, the merits of extend-ing the search for rare variants beyond well-annotated sequence, given the difficulties associated with obtain-ing robust evidence for a statistical or functional effect for rare variants in unannotated sequence (BOX 4). Related challenges lie in the development of effi-cient strategies for fine mapping that take into account the desire both to discriminate between highly corre-lated variants (to determine which variants are causal) and to search for additional, independent signals. Given the relatively high price of custom genotyping,

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Mendelian randomization An analytical approach that allows one to test for a causal relationship between two phenotypes that show observational associations, but are subject to confounding: Mendelian randomization makes use of the random segregation of susceptibility alleles at meiosis to explore causality in a model that is freed from most sources of confounding.exhaustive fine-mapping efforts across multiple sig-

nals can cost far more than the original GWA scan.

Multi-stage approaches to fine mapping (homing

in on causal variants through successive rounds of

genotyping, whereby ever fewer SNPs are typed in

increasingly large samples) might seem efficient but

they can involve costly, time-consuming investment

in successive assay designs. Given inter-ethnic differ-

ences in patterns of lD and mutational histories (see

above), samples from other ethnicities (especially

those of African origin) should be extremely valuable

tools for fine mapping, and considerable effort is being

expended to identify samples on the scale required for

robust inference.

Function and translation. once all the statistical evi-

dence has been extracted and putative causal variants

are identified, substantial challenges remain (BOX 5).

Prominent among these is the need to obtain func-

tional confirmation that the variants implicated are

truly causal, and to reconstruct the molecular and

physiological mechanisms whereby they have an impact

on the phenotype of interest. Because many of the

complex-trait susceptibility variants so far identified map

to sequence of unknown function that is some distance

from the nearest coding sequence5–9,15,17,25–27, the design

of contextually appropriate functional assays is far from

straightforward. Improved tools for the functional anno-

tation of the genome (for example, from the eNCoDe

project)107 will be essential, but generating such annota-

tions for all tissues and/or cells of biomedical relevance

remains a monumental task.

It is also important to move beyond the selected

samples used in the discovery phase and evaluate the

impact of the variants on unbiased population sam-

ples. From an epidemiological perspective, consensus

guidelines have been proposed to grade the strength of

the epidemiological evidence for a given association113.

These take into account the extent of the evidence, the

consistency of the replication and the protection from

bias in the accumulated data. Population-based studies

will enable research to establish whether, using studies of

the joint effects of genes and environment and Mendelian

randomization approaches114, genetic discoveries can be

used to pinpoint modifiable environmental exposures.

Such analyses will require very large study samples for

which both genetic and environmental exposures are

accurately measured58,59.

Finally, the ultimate objective of genetic research

lies in the translation of the findings into advances in

clinical care (BOX 6). The mechanistic insights generated

by gene discovery might identify new therapeutic tar-

gets and lead to novel pharmaceutical and preventative

approaches. In addition, there is growing expectation

that individual patterns of genetic predisposition will

be of value in health-care delivery (personalized medi-

cine). For many, but not all115, diseases the modest effect

sizes of the variants emerging from GW A studies limits

the degree to which this is possible (BOX 7). Higher pen-

etrance, lower frequency variants that are not detected

by current GWA approaches but are amenable to new

high-throughput sequencing efforts might prove more

valuable in this respect116.

Reporting and deposition

Because wide availability of data is central to the success

of many of these endeavours, there has been substan-

tial investment in structures to support data-sharing

between investigators, such as the National Institutes

of Health (NIH)-supported dbGAP programme117, and

the european Bioinformatics Institute-based european

Genotyping Archive. Moreover, the NIH recently

announced a policy for sharing of data obtained in NIH

supported or conducted GW A studies. Although aggre-

gate or summary data (genotype frequencies and asso-

ciation p values by group as provided by the WTCCC

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and the National Cancer Institute Cancer Genetic Markers of Susceptibility (CGeMS) studies, for exam-ple 1,118) provide an excellent and convenient substrate for many data-sharing purposes, individual-level data (including raw signal-intensity information) provide a more valuable resource that supports a wider range of analyses (see above).

lack of transparency and incomplete reporting of both data and study methods have raised concerns in many health research fields 119–121, and poor reporting has been associated with biased estimates of effect 122. The importance of transparency was emphasized by the NCI-NHGRI Working Group on Replication in Association Studies 91. To help remedy this problem, some groups have advocated the development of evidence- based reporting guidelines similar to the consolidated standards of reporting trials (CoNSoRT) guidelines for the reporting of randomized clinical trials 123. In

have been identified, shedding light on the fundamental mechanisms that influence disease predisposition, and much is being learned about the complex relationships between changes in genome sequence and phenotypic variation.

However, we are far from the end of this particular voyage, and recent discoveries are nothing more than initial forays into the terra incognita of our genomes. We remain unable to explain more than a small proportion of observed familial clustering for most multifactorial traits, a fact that emphasizes the need to extend analy-sis to a more complete range of potential susceptibility variants, and to support more explicit modelling of the joint effects of genes and environment. Many of the greatest challenges to be faced in the years ahead lie not so much in the identification of the association signals themselves, but in defining the molecular mecha-nisms through which they influence disease risk and/or phenotypic expression.

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Acknowledgements

Preparation of this article was supported by funding from the

European Commission to the MolPAGE Consortium (LSHG-

CT-2004-512066: MMcC) and by research grants from the

national Institutes for Health (nHGRI and nHLBI; GRA). We

thank our colleagues — particularly P. Donnelly, J. Marchini,

J. Barrett, E. Zeggini, C. Lindgren, M. Boehnke, F. Collins,

C. Spencer and

D. Altshuler for discussions and the reviewers

for their comments.

Competing interests statement

The authors declare competing financial interests: see web

version for details.

NATuRe RevIeWS |genetics voluMe 9 | MAy 2008 |369

?2008Nature Publishing Group

2008年(下)自考试卷及答案

2008年(下)高等教育自学考试全国统一命题考试 财务管理学试卷及参考答案 第一部分选择题 一、单项选择题(本大题共20小题,每小题1分,共20分)在每小题列出的四个备选项中只有一个是符合题目要求的,请将其代码填写在题后的括号内。错选、多选或未选均无分。 1.企业资金运动的中心环节是 ( ) A.资金筹集 B.资金投放 C.资金耗费 D.资金分配 2.以股东财富最大化作为公司财务管理目标时,主要的评价指标是 ( ) A.每股市价 B.每股利润 C.每股股利 D.每股净资产 3.后付年金终值系数的倒数是 ( ) 丸资本回收系数 B.偿债基金系数 C.先付年金终值系数 D.后付年金现值系数 4.下列可用于衡量投资风险程度的指标是 ( ) A.概率 B.预期收益 C.标准离差率 D.风险价值系数 5.与商业信用筹资方式相配合的筹资渠道是 ( ) A.银行信贷资金 B.政府财政资金

C.其他企业单位资金 D.非银行金融机构资金 6.某企业发行债券,面值为1 000元,票面利率为10 010,每年年末付息一次,五年到期还本。若目前市场利率为8%,则该债券是 ( ) A.平价发行 B.溢价发行 C.折价发行 D.贴现发行 7.企业为满足支付动机所持有的现金余额主要取决的因素是 ( ) A.企业临时举债能力 B.现金收支的可靠程度 C.企业的销售水平 D.企业可承担风险的程度 8.利用存货模型计算最佳现金持有量时,需要考虑的成本是 ( ) A.持有成本与转换成本 B.短缺成本与持有成本 C.取得成本与短缺成本 D.短缺成本与转换成本 9.固定资产按使用情况所作的分类是 ( ) A.生产用固定资产和非生产用固定资产 B.经营用固定资产和管理用固定资产 C.自有固定资产和融资租入固定资产 D.使用中的固定资产、未使用的固定资产和不需用的固定资产 10.下列各项中,属于非贴现投资评价指标的是 ( ) A.净现值 B.获利指数 C.净现值率 D.平均报酬率

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成功的经典公关案例分析_经典危机公关案例分析 矛盾的80%来自与缺乏沟通,很多事只要能恰当的沟通都会顺利 解决。当企业发生公关危急时沟通就是最必要的工作之一。首先要 与企业全体员工进行沟通,让大家了解事件细节,以便配合进行危 机公关活动,比如保持一直的口径,一直的行为等。而后要马上与 受害者进行沟通,主动联系受害者,以平息其不满的情绪,比如开 通专线电话接听相关投诉,负责人亲自慰问与会见受害人等,最好 抢在媒体与当事人接触前先与当事人沟通。接下来就是与媒体进行 沟通,必须第一时间向媒体提供真实的事件情况及随时提供事件发 展情况,因为如果你不主动公布消息媒体和公众就会去猜测,而猜 测推断出的结论往往是负面的。这个时候消费者很敏感,信心也很 脆弱,看到负面的消息后很容易相信,甚至是放大这个消息的危害 程度。所以,这个时候必须及时坦诚的通过媒体向大众公布信息与 事件处理进展,这样可以有效填补此时舆论的“真空期”,因为这 个“真空期”你不去填补它,小道消息、猜测,甚至是竞争对手恶 意散布的消息会填满它。而后就是与政府及相关部门进行沟通,得 到政府的支持或谅解,甚至是帮助,对控制事态发展有很大的帮助。同时也要对企业的合作伙伴如供应商、经销商等进行沟通,以免引 起误解及不必要的恐慌,如前面提到的金正集团,因为缺乏与合作 伙伴的沟通,导致了各方的恐慌,使事态恶化。 案例: 点评: 及时的沟通,真诚的态度,使索尼轻松度过了这次危机,没有造成更大的负面影响,相信很多读者都没听过这个事件吧?这就证明索 尼此次的危机公关处理的十分成功,也没有影响到索尼与佳能等合 作伙伴的关系。全面快速的真诚沟通是此次事件圆满处理的最大功臣。

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