Reviews

Opportunities and challenges for the

use of common controls in sequencing
studies
Genevieve L. Wojcik   1, Jessica Murphy2,3, Jacob L. Edelson   4, Christopher R. Gignoux2,5,6,
Alexander G. Ioannidis   7,8, Alisa Manning   9,10, Manuel A. Rivas4, Steven Buyske   11
and Audrey E. Hendricks   2,3,5,6 ✉
Abstract | Genome-​wide association studies using large-​scale genome and exome sequencing
data have become increasingly valuable in identifying associations between genetic variants and
disease, transforming basic research and translational medicine. However, this progress has not
been equally shared across all people and conditions, in part due to limited resources. Leveraging
publicly available sequencing data as external common controls, rather than sequencing new
controls for every study, can better allocate resources by augmenting control sample sizes or
providing controls where none existed. However, common control studies must be carefully
planned and executed as even small differences in sample ascertainment and processing can
result in substantial bias. Here, we discuss challenges and opportunities for the robust use
of common controls in high-​throughput sequencing studies, including study design, quality
control and statistical approaches. Thoughtful generation and use of large and valuable genetic
sequencing data sets will enable investigation of a broader and more representative set
of conditions, environments and genetic ancestries than otherwise possible.

Monogenic
A condition influenced by one
genetic locus.
Oligogenic
A condition influenced by a few
genetic loci.
Polygenic
A condition influenced by
a large number of genetic loci.
Allele frequencies
The rates of genetic variant
types in a specified population.
Common controls
Controls used for multiple
studies.
✉e-​mail: audrey.hendricks@
ucdenver.edu
https://doi.org/10.1038/
s41576-022-00487-4
High-​t hroughput genome and exome sequencing
has been foundational to advancing the understand-
ing of disease aetiology, precision medicine and drug
development1–7. From beginnings in rare diseases with
monogenic or oligogenic architecture, which studied
relatively small numbers of individuals or even single
families8–10, rare variant discovery research has more
recently encompassed common complex diseases, that
is, those with polygenic architectures, by using substantial
resources to recruit and analyse genomes at scale4,11–13.
Genome-​wide association studies (GWAS) for dichot-
omous outcomes use array-​based or high-​throughput
sequencing technology to scan and compare the
genomes of cases, recruited to have a certain condi-
tion, and controls, gathered for direct comparison.
Specifically, by comparing the allele frequencies of a var-
iant or the frequencies of rare alleles in a genetic region
of interest between the ascertained cases and controls,
GWAS aim to identify genetic variants or regions that
are associated with the phenotype of interest. However,
advances have not been equitably shared across ances-
tries, environments and conditions, exacerbating ineq-
uities in research, healthcare and drug development
and leading to poorer understanding of the complete
genomic landscape for all14–16. A multifaceted approach is
urgently required to address this gap, including advances
in sequencing technology to lower costs and enable
the generation of large, high-​quality studies of diverse
genetic ancestries and environments. In the meantime,
to extend the utility of existing and future large-​scale
sequencing studies, data can be leveraged to serve as a
community resource for comparison with sequenced
cases, an approach generally known as common controls.
Using common controls, rather than sequencing new
controls for every study, can boost power to detect gen-
otype–phenotype associations by increasing the sample
size or providing a control set where none existed. One
can distinguish between internal common controls,
which were ascertained and processed as part of a sin-
gle study that contains multiple case sets of different
phenotypes17, and the more frequent external common
controls, which were recruited as part of an unrelated
study. Although using external common controls as
the sole control group is more susceptible to bias and
confounding compared with using internal controls, as
described in more detail below, the practice is remark-
ably frequent18–36. Uses of external common controls
as the sole control group include data analysis of cases
recruited in a case-​only20,22,31,33,37 or family design for
rare diseases32,38, and to study germline associations in

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Very large case– The use of common controls can free resources

Polygenic
control studies for functional work, careful phenotyping of cases and
e.g. T2DM, autism, additional recruitment of cases from diverse ancestries
CHD, Alzheimer
and environments, helping to address a persistent lack

Genetic architecture
disease
of representation in genomic research45–48. Lack of rep-
Common controls
e.g. alopecia, vitiligo, resentation in sequencing studies is compounded in
medical or surgical conditions that are neither rare nor common. Given
outcomes, adverse
drug effects
their polygenic and complex architecture, these uncom-
mon conditions require large sample sizes but their
Small family studies relatively low prevalence (for example, 0.2–1.8% for
Mendelian

and case groups vitiligo)49 makes mobilizing the necessary resources dif-
e.g. Kabuki syndrome, ficult (Fig. 1). In these situations, even large-​scale biobanks
cystic fibrosis
and general population cohorts may not be adequately
Rare Uncommon Common powered for discovery, which can be worsened by chal-
Condition prevalence lenges in deriving precise phenotypes50–52 and stigma for
certain phenotypes53. For example, in the 500,000 UK
Fig. 1 | Where to use common controls? Optimal study
design for a particular condition is determined, in part, Biobank population cohort, only 2,000 cases of Crohn’s
by genetic architecture (y axis) and prevalence (x axis) of disease are available for genetic study, with disease
the condition. Small family studies and case groups are pheno­typing derived from a mixture of questionnaire
useful for rare, Mendelian conditions, whereas very large and hospital inpatient record data, whereas focused dis-
case–control studies can be used for common, polygenic ease case–control sequencing studies can gather more
conditions where sufficient resources can be garnered. than 30,000 cases and 80,000 shared controls36. Even
Uncommon conditions with low to moderate prevalence when feasible, gathering and sequencing controls for
are likely to be polygenic, necessitating large sample all conditions is not an optimal use of resources due to
sizes. However, low prevalence of the condition may make redundancy in control sets and limited recruitment from
recruiting sufficient sample sizes and resources difficult.
under-​represented populations.
Whereas common controls are useful across the genetic
architecture and prevalence spectrum, common controls Whereas common controls hold great potential in both
are particularly valuable for polygenic, uncommon conditions array-​based GWAS17 and sequencing studies34–36,54, their
where sufficient resources may be lacking. CHD, coronary robust use can pose challenges, with missteps caused by
heart disease; T2DM, type 2 diabetes mellitus. inadequate harmonization of batch effects30,31,55, mismatched
ancestries19,37,42,56, incorrect filtering19,21,22,26,28,29,37,57–59 and
Bias
cancer for cases originally recruited to identify somatic insufficient documentation of data and methods for
Systematic error (as opposed mutations 19,29,39–42. Large external common control reproducible results20,24,28,32,33,37,40,60. These missteps can
to error due to chance data have also been used for more common conditions result in biased and incorrect results, especially when
processes), whether caused such as coronary artery disease, obesity, osteoporosis using external common controls as the sole control set.
by statistical methods,
and schizophrenia18,34–36,43 and can be especially suc- Careful harmonization, analyses and quality control are
differences between sampled
individuals and the population cessful for the detection of rare, strong-​acting alleles. essential when employing external common controls,
they nominally represent, For example, studies using common controls have given the great potential for bias and confounding. Here,
differences between cases led to the detection of rare loss-​of-​function variants we discuss the data, study design, infrastructure and
and controls in ascertainment
in SETD1 associated with schizophrenia35 and mis- methods required to incorporate common controls in
or sample processing, or
other issues.
sense and protein-​truncating variants in ATG4C have rigorous rare variant analyses to advance human genetics
been associated with Crohn’s disease36, among other research. Throughout, we highlight two studies as exem-
findings34. Interest in common controls has increased plars of how to incorporate external common controls in
in fields outside genomic research as well, for example, a robust manner34,36 (Box 1). Although the focus here is on
for clinical trials44. high-​throughput sequencing studies, much of the con-
tent is also applicable to array-​based GWAS. Ultimately,
Author addresses careful use of common control data can be an important
1
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, tool for improving statistical power, addressing the lack of
Baltimore, MD, USA. data for understudied people or conditions and provid-
2
Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA. ing a more complete understanding of the entire human
3
Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA. genetics landscape.
4
Department of Biomedical Data Science, Stanford Medical School, Stanford, CA, USA.
5
Human Medical Genetics and Genomics Program, University of Colorado Anschutz Data and study design
Medical Campus, Aurora, CO, USA. The use of common controls in genetic studies is unique
6
Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical in that the researcher has already defined a specific
Campus, Aurora, CO, USA.
research question and ascertained cases. Selection of
7
Institute for Computational and Mathematical Engineering, Stanford University,
a common control set is therefore driven by case set
Stanford, CA, USA.
8
Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, characteristics, such as condition prevalence, genetic
MA, USA. ancestry, sequencing technology and sample process-
9
Metabolism Program, Broad Institute, Cambridge, MA, USA. ing. Selecting controls according to these considerations
10
Department of Medicine, Harvard Medical School, Boston, MA, USA. reduces the potential for confounding, both measured
11
Department of Statistics, Rutgers University, Piscataway, NJ, USA. and unmeasured. Beyond study characteristics, practical

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Confounding considerations such as accessibility, size and type of data
A spurious association or lack (individual level or summary level) may constrain the
of association caused by a utility of a common control data set. Below, we discuss
third variable that is related to aspects of the genetic data, participant demographics and
both the predictor variable (for
example, allele frequency) and
relevant confounders to support appropriate selection of
the outcome (for example, case common controls such as those provided in Table 1.
status).
Ascertainment of common controls
Internal controls
Common control data sets typically fall into one of three
Controls that were ascertained,
sequenced and processed
study designs: ascertained, convenience and population
together with the case sample. (Fig. 2). The relevant major difference among these designs
By contrast, external common is the expected prevalence of the outcome of interest
controls were recruited, or related conditions and its influence on findings,
sequenced and processed
separately, often using
which is expanded upon below.
different technology from the
case sample. Ascertained controls. Ascertained controls are gathered
to exclude individuals with specific condition(s); the
Biobanks
identification of a condition of interest occurs using, for
Collections of both biological
samples (particularly DNA) example, hospital records, questionnaire responses, dis-
and health information from ease diagnosis or family history of disease. Additionally,
individuals generally assembled controls should have had the opportunity to develop
from a region or a health the disease but did not, especially with respect to age
system.
(for late-​onset outcomes), sex (for outcomes dispropor-
Harmonization tionately affecting a specific sex)43 and location (such as
The formation of a single for geographic region-​specific outcomes). For example,
cohesive data set from two or in a genetic association study of heart disease, partic-
more separate data sets by
ipants ascertained to be ‘controls’ at age 55 years may
standardizing scales,
definitions, quality control and very well become ‘cases’ by age 65 years. However, in
other processing. this instance it is understood that differences in the age
of onset do not imply differences in genetic exposure but
Batch effects may result in a decrease in power to detect association.
Differences between groups
induced by processing over
A more extreme example is in studying host genetics
different times, places or responses to infectious disease, where it is optimal for
technologies unrelated to cases and controls to have similar exposure to the infec-
biological causes. tious agent61. Although ascertained controls are the ideal
comparison group due to the designed absence of the
Quality control
A process where low-​quality condition of interest, they are also the least available,
data or observations are especially for uncommon conditions for which deliberate
identified and improved or exclusion was not the priority.
removed from further analysis.
Statistical power
Convenience sampling. Controls gathered through con-
The probability of rejecting the venience sampling, such as from a biobank or a sam-
null hypothesis when it is false. ple ascertained for a different disease, are much more
Box 1 | Case studies for the exemplary use of common controls
Throughout this Review, we provide two case studies as examples of thoughtful and
robust use of common controls. Of note, both are samples of European ancestries.
As discussed comprehensively elsewhere48,120,160, broader representation of ancestries
is needed in genetic studies including in the creation of common control data sets.
Marenne et al.34 use the INTERVAL study and gnomAD data (Table 1) as common
controls for severe childhood-​onset obesity project cases from the UK10K project.
The UK10K project6 is an interesting example of a study where exome sequencing was
performed for cases (that is, obesity, neurodevelopment and rare diseases) without internal
controls, thus necessitating the use of external common controls34,35. The INTERVAL
sample was used as the primary common control set and gnomAD was used as a second
common control data set to complete partial replication of the top gene regions identified.
Sazonovs et al.36 used two case–control discovery samples and three case–control
follow-​up samples to identify rare variant genetic associations with Crohn’s disease.
External common control data from the Centers for Common Disease Genomics
(CCDG)151 were identified to match the sequencing technology and computational
pipeline of the discovery case samples, and INTERVAL83 and the UK Biobank85 were
used as external common controls for two of the follow-​up case samples.
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widely available, but may contain individuals with the
outcome of interest or relevant potential confounders.
An interesting example of this is the UK Biobank, which
contains healthier and wealthier individuals than the
general UK population, and thus may differ in related
features from case samples not drawn from the UK
Biobank62,63. Depending on the ascertained phenotype
of the convenience sample, both the cases and the con-
trols from the original study may be suitable as common
controls in a new study. The result of using a conveni-
ence sample ascertained for a different condition from
the cases is often not straightforward, with effect sizes
inflated or attenuated depending on allele frequency
deviations63,64. As such, identifying a reasonable and
unbiased model can be difficult.
Population controls. Population controls, namely individu-
als from the general population, are not ascertained with
respect to any particular outcome; they are easier and less
expensive to recruit compared with ascertained controls
but will often contain identified or unidentified cases.
The potential for misclassification as a control, when
in fact they are an unidentified case, will depend on the
prevalence of the condition. At one end of the spectrum,
conditions of low prevalence will have a small proportion
of unidentified cases in the control set, which is unlikely
to greatly affect the results of the study. For example, the
Marenne et al. study of severe childhood obesity used
INTERVAL, a population-​based cohort, as external
common controls34 (Box 1). Although it is likely that the
INTERVAL sample contained individuals who, when
they were children, met the criteria to be cases, the num-
ber is likely to be quite small given an estimated preva-
lence of severe childhood-​onset obesity of 0.15%65. As
the prevalence of conditions increases towards common
conditions (for example, prevalence >20%)66, the misclas-
sification of cases as population controls will increasingly
result in lower power and attenuated effect estimates67. In
rare variant association studies, the reduction of power
is likely to be more pronounced. Of course, the increase
in control sample size could make up for the inefficiency,
but not the bias of the effect estimates towards the null.
To reduce bias and increase power, using a control sam-
ple with fewer unascertained cases or case-​related traits
is preferable, particularly for common conditions.
Comparability of cases and common controls
Differences that are unaccounted for in sample char-
acteristics (for example, demographics such as age
and sex, genotyping or sequencing, genetic ancestries)
between cases and controls can result in substantial con-
founding and bias. For example, the Exome Sequencing
Project (ESP) used two sequencing centres and found
that differences in reagents and local analysis pipelines
resulted in unexpected batch effects68. An additional
classic example is a study of exceptional longevity, which
originally failed to fully correct for differences in geno-
typing platforms and found spurious associations55,69.
Whereas many association methods can adjust for some
differences, case attributes must be represented in the
common control data to be able to use these methods.
This is especially important for genetic ancestries.
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Table 1 | Resources for high-​throughput sequencing data sets that could be used as external common controls
Resourcea Sizeb Ancestries Datac Permissions Description
Individual-​level data d

1000 WGS/WES: 5 continental ancestries (African, – None Catalogue of human variation and
Genomes 2,504 East Asian, European, South genotype or sequencing data from
Project114 Asian and admixed American) self-​identified ‘healthy’ individuals
(AnVIL) and 26 populations
CCDG151 WES: 198,831 ~25% each of the African, – Permissions obtained Collection of case–control studies of
(AnVIL) admixed American and via dbGaP cardiovascular, neuropsychiatric and
WGS: 135,853
European continental ancestries immune-​mediated diseases
Estonian WES: 3,000 Estonian (83%), Russian (14%) Phenotypes Access form required Longitudinal, population-​based
Biobank81 and other (3%) cohort study of subjects recruited
WGS: 2,500
by general practitioners and hospital
physicians
H3Africa121 WGS: 581 African (50 ethnolinguistic Phenotypes Access form required Population-​based studies of
groups from 13 African common diseases in Africa, such as
WES: 314
countries) trypanosomiasis and paediatric HIV
HGDP115 WGS: 929 (828 54 populations – None WGS library of diverse indigenous
online) populations
INTERVAL83 WES: 4,502 ~91% white British individuals Phenotypes Permissions obtained Study of blood donation frequency
via EGA across England
WGS: 5,592
SGDP152 WGS: 300 142 populations (127 in publicly – Access form required Deep genome sequences from smaller
available data) for 21 genomes diverse populations
TOPMed84 WGS: ~155,000 41% European, 31% African, 15% Phenotypes, Permissions obtained More than 80 parent studies
(AnVIL, Hispanic/Latino, 9% Asian and ‘omics via dbGaP (prospective, case–control, family
BioData 4% other/unknown and case-​only) focusing on heart,
Catalyst) lung, blood and sleep disorders
UK WES: ~200,000 ~84% white British individuals Phenotypes Registration, data Prospective, population-​based cohort
Biobank85 WGS: ~300,000 application and fee study collected from volunteers across
required the UK
Summary-​level data
dbGaP WES: 29,931 12 populations – None Allele frequencies for variants in
ALFA153 dbGaP across approved unrestricted
WGS: 25,478
studies
FinnGen87 WGS: 3,775 Finnish Phenotypes Access form required A large public–private partnership
aiming to collect and analyse genome
and health data from 500,000
Finnish biobank participants
(10% of population)
gnomAD WES: 125,748 7 global and 7 subcontinental – None Exome and genome sequencing data
v2.189 WGS: 15,708 ancestries primarily from case–control studies of
common adult-​onset diseases
gnomAD WGS: 76,156 9 ancestries – None Genome sequencing data primarily
v3.189 from case–control studies of common
adult-​onset diseases
jMorp154 WGS: 8,380 Japanese ‘Omics Access form required Japanese reference panel of two
for genotype prospective cohort studies (a population-
frequency panel based adult cohort and a birth and
three-generation cohort)
SISu v4.1155 WES: 10,490 Finnish – None Finnish database of 13 cohorts with
population controls and cases/controls
from disease-​specific studies
Taiwan WGS: 1,517 Han Chinese Phenotypes None Taiwanese database of healthy controls
Biobank88 from cohort and case–control studies of
local diseases
TOPMed WGS: 132,345 Multiple – Google login required Variant browser for 705 million variants
BRAVO84 in TOPMed Freeze 8
Summary and individual-​level datad
All of Us103 WGS: 98,640 49% European, 23% African, 15% Phenotypes Individual: Effort to collect and study health data
(Researcher Latino/Admixed American, 9% registration required from a diverse and representative group
Workbench) Other, 2% East Asian, 1% South through the All of Us of people in the USA
Asian Research Program

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Table 1 (cont.) | Resources for high-​throughput sequencing data sets that could be used as external common controls
Resourcea Sizeb Ancestries Datac Permissions Description
Summary and individual-​level data (cont.)d

CSVS90 WGS/ Spanish Phenotypes Summary level: Crowdsourcing repository of Spanish

WES: 2,027 access form required; genetic variability
(individual: 267) individual level:
permissions obtained
via EGA
GenomeAsia WGS: 1,739 7 global regions (64 countries, – Individual level: WGS reference data set
100K116 219 population groups) with access form required
~80% Asian individuals
Data repositories of individual-​level data
dbGaP91 WES: ~500 Multiple Phenotypes NIH DAC application Database of studies that investigate
(AnVIL, studies required the interaction between genotypes
BioData and phenotypes in humans
WGS: ~300
Catalyst)
studies
EGA92 WES: ~1,200 Multiple Phenotypes DAC application Archive of genetic and phenotypic data,
studies required mostly of various types of cancer
WGS: ~1,050
studies
DAC, data access committee; dbGaP, database of Genotypes and Phenotypes; EGA, European Genome–Phenome Archive; NIH, National Institutes of Health; WES, whole-
exome sequencing; WGS, whole-​genome sequencing. aTable limited to resources that can be widely accessed by researchers globally. Future resources156–158 or other
potentially useful data sets that require consortia membership or collaboration159 are not included. AnVIL currently contains genomic data from eight consortia and
more than 280,000 participants, and BioData Catalyst from some 155,000 participants in TOPMed along with the parent studies. Resources currently available in AnVIL,
BioData Catalyst or Researcher Workbench are noted. bThe number of individuals with WGS and/or WES is provided unless otherwise noted. cAdditional data provided
including phenotypes or other ‘omics data. All resources provide sex and ancestry information. dAll individual-​level data resources, except for GenomeAsia100K and the
Collaborative Spanish Variability Server (CSVS), have FASTQ or BAM/CRAM files available for joint recalling. H3Africa and the UK Biobank also have gVCF files available.

Ascertained cases
Participants of a study who
are recruited to have a known
disease, outcome or condition
of interest.
Ascertained controls
Participants of a study who are
recruited to not have a known
disease, outcome or condition
of interest.
Convenience sample
A sample drawn from an easily
accessible, but often not
representative, cohort.
Population controls
A control group sampled from
a population but possibly
lacking information regarding
the condition of interest,
with the result that some of the
population controls will likely
have the condition of interest.
Admixed
A term to denote the mixture
of genetic ancestries from two
or more divergent groups.
Population stratification
The presence of
subpopulations with differing
allele frequencies in a study;
a source of confounding if
phenotypes also vary by
subpopulation.
For instance, although ancestry inference methods can be
used to adjust for differences among African American
admixed samples, there are limits to their applicability; an
African American sample cannot be robustly compared
with a sample with only European ancestries. A failure
to adequately match and adjust for genetic ancestry can
result in population stratification with an increase in both
false positives and false negatives due to genetic differ-
ences unrelated to disease risk. Classic examples of spu-
rious associations as a result of population stratification
include height with European ancestry70, type 2 diabetes
mellitus (T2DM) with Native American ancestry71,72 and
asthma with Indigenous ancestry in Latinx groups72,73,
among others70,72,74,75. Matching by fine-​scale ancestry in
addition to continental ancestry is especially important
for rare variants, which are more likely to segregate on
a geographically smaller scale76–78 (Fig. 3a–d). Similarly,
although rare variant methods have been developed to use
common control data sequenced and generated with dif-
ferent technology and computational pipelines (Table 2),
matching as closely as possible will reduce bias and
increase coverage of the genome (Fig. 3e,f). Both Marenne
et al. and Sazonovs et al. limit common controls to those
with European ancestries and match closely by sequenc-
ing technology (Box 1). Indeed, Sazonovs et al. identify
and use several common control data sets, including
INTERVAL, the Centers for Common Disease Genomics
(CCDG) and the UK Biobank, to match the technology
and sequencing centres for four Crohn’s disease case sets.
Curation of phenotypic data
Well-​curated and standardized phenotypic information,
which can enable optimal choice of common control data,
removal of cases and adjustment or assessment of envi-
ronmental factors, is key to supporting interoperability
and usefulness of common control data. Electronic
health record data, such as from biobanks, have stand-
ards for the translation of International Classification of
Disease (ICD) codes into standard codes, such as with the
Observational Medical Outcomes Partnership (OMOP)79
and the ICD-9/ICD-10-​compatible phecodes80. However,
many data harmonization efforts are focused on one or
a handful of conditions, whereas harmonization for
common control data must be broadly focused to enable
interoperability with various conditions. To enable broad
utility of common control data, information relating to
age, sex, ancestry and chronic conditions should be stand-
ard inclusions. In general, there are two main categories
of common control data: summary level (such as allele
frequencies) and individual level. For individual-​level
data, information should be included at the subject level,
whereas descriptive statistics (for example, five-​number
summary, mean, standard deviation) can be provided
for summary-​level data. Importantly, reporting of chronic
conditions enables cases or individuals with case-​related
traits to be removed from the common control data set.
A high degree of phenotypic metadata and study
detail is essential to ensure widespread interoperability
of common control data, not to mention an apprecia-
tion (for example, funding and incentives) for the efforts
needed to tailor and maintain common control data sets
for broad use (Box 2). Of note, the Estonian Biobank81,
H3Africa 82, INTERVAL 83, TOPMed 84 and the UK
Biobank85 are examples of individual-​level common con-
trol data sets that have well-​curated phenotypic data to
enable broad use as common controls. To better enable
easier identification of large-scale sequencing datasets
with deep phenotype information, Gutierrez-Sacristan
et al. provide a dynamic catalogue from which users can
identify data with desired characteristics86. Finngen87,

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False positives the Taiwan Biobank88, gnomAD89 and the Collaborative
Test results that are statistically Spanish Variability Server (CSVS)90 are summary-​level
significant even though common control data sets that provide summary sta-
there is no real association. tistics or grouping of age, sex, ancestry and common
By contrast, a false negative
is a test result that is not
conditions. For instance, gnomAD v2.1 provides a
statistically significant even ‘control’ subset where individuals recruited as cases are
though there is a real excluded, and the CSVS enables filtering to provide allele
association. frequency excluding selected conditions.
Accessibility and usability of common control data
Individual-​level data enable better harmonization and
analysis between cases and common controls. However,
individual-​level data often have more barriers to access,
Cases
+
a Ascertained controls (without condition) b Convenience sample
c Population controls (20% prevalence) d Population controls (1% prevalence)
Without condition With condition Other condition
Fig. 2 | Types of control samples. Three regularly used types of controls include ascer-
tained, convenience and population controls. a | Ascertained controls are specifically
collected to exclude the condition and conditions related to case status. b | Relative
ease of ascertainment or use is the defining factor of convenience samples. In human
genetics, convenience samples may have been ascertained for another condition related
to case status (blue people) and may also include unidentified cases (orange person).
c,d | Population controls are a random sample of controls from the general population that
often contain unidentified cases based on prevalence of the condition. Choosing which
controls to use as common controls should be based on the study design and research
question. For instance, population controls are appropriate for rare conditions (for example,
prevalence <1%) (part d) but not for common conditions (for example, prevalence >20%)
(part c), as the high proportion of unidentified cases for a common condition would affect
the study results including power. Ascertained controls are ideal, but more difficult and
expensive to collect compared with convenience sampling and population controls.
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in order to maintain participant privacy according
to existing consents, and require significantly more
resources to use than summary-​level data. Indeed,
although individual genetic data are often accessible
from a central database (for instance, the database of
Genotypes and Phenotypes (dbGaP)91 or the European
Genome–Phenome Archive (EGA)92), they can often
be missing important metadata, be in a less processed
state or be divided into sub-​data sets that can be dif-
ficult to combine. These aspects, combined with har-
monization and processing of individual-​level data,
necessitate a large amount of resources (for example,
person-​time, computing and data storage/transfer cost)
for appropriate use. Numerous common control data
sets are hosted on cloud computing environments to
minimize these hurdles (see Infrastructure). For exam-
ple, the UK Biobank Research Analysis Platform enables
researchers to access data from a centralized location
and although there are costs, they are tiered depending
on computational and financial needs, with discounted
rates for student researchers or those from low and
middle-​income countries93.
Conversely, summary-​level data are often readily
available for download, have undergone extensive qual-
ity control and processing, have few to no barriers to
access and require fewer resources for storage, transfer
and analysis. However, summary statistics, such as allele
frequencies, can mask heterogeneity and stratification
within and between samples, including population
structure, sample recruitment and processing. These
differences can cause severe batch effects between cases
and external common controls, resulting in biased
results. Additionally, adjusting for covariates is either
more difficult or impossible. Although some methods,
such as iECAT-​O94 and ProxECAT95 (Table  2), have
been developed to incorporate allele frequency data
while reducing the potential for bias94–98, more thorough
vali­dation and replication of results are necessary than
with individual-​level data. There are proposed inter-
mediate frameworks where case data are uploaded to
a central location and allele frequencies from matched
individual-level common control data by ancestry and
other covariates are returned; however, these frame-
works are not yet widely available99. The CSVS90 is an
especially interesting example of how to collect and dis-
tribute sequencing data. The CSVS crowdsourcing initi-
ative encourages genomic projects and consortia across
Spain to submit whole-​exome sequencing (WES) and
whole-genome sequencing (WGS) data, resulting in a
database of allele frequency information with the ability
to interactively exclude chronic disease subgroups90.
Lastly, when choosing a common control data set,
close attention should be paid to the consent type
of each contributing study. Only data labelled as no
restrictions (NRES), general research use (GRU) or
health, medical biomedicine use (HMB) can be used as
common controls for various phenotypes. (Studies with
disease-​specific consents can, of course, be used as com-
mon controls for the matching disease.) Because of this,
studies that obtain broad consents are far more useful
sources of common controls than those with narrower
consents (Box 2).
 Reviews

Ancestry

a b

0.005

Allele
frequency
maf 0.000

PC2
0.75 0.75

0.50 0.50
–0.005
0.25
0.25
–0.010

–0.008 –0.004 0.000 0.004

PC1

c d EUR
100
Mexico: 62.6–87.3%
South Korea: 68.9% Colombia: 55.8%
20 80
Japan: 77.6–82.1% Peru: 68.0% 40
China: 77.5–85.9% 60
60 40
Trinidad and Tobago: 25.0%
Pakistan: 54.55% Barbados: 10.9–20.9% 80
India: 54.2–61.8% 20
Puerto Rico: 36.9%
Bangladesh: 65.28% 100
AFR 20 40 60 80 100 AME

Coverage Processing
e Whole genome Whole genome Whole exome f Pipeline A Pipeline B Pipeline C
High depth Low depth High depth

Exon Intron Variant

Fig. 3 | Types of bias that could affect common control analyses.
Differences between cases and controls not due to case status, such as
differences in ancestry, coverage or processing, could result in confounding
and lead to inaccurate conclusions. a | Allele frequencies (here for
rs17578381) can differ greatly both between continental-​level regions and
within more fine-​scale regions, requiring careful matching or adjustment of
ancestry. b | Some of this matching can be conducted using principal
components (PCs). However, additional attention must be made beyond the
first PCs to ensure fine-​scale substructure is accounted for. c | This
substructure can occur within continental-​level groupings or self-​identified
racial categories, such as within Asia and even within East Asia.
d | Differences can also occur within a region due to admixture proportion
differences between groups, whether two-​way or three-​way admixture.
e | Coverage can differ in which part of the genome is sequenced (for
example, genome versus exome) and in number of sequencing reads
(for example, high depth or low depth). Type of coverage determines how
many and which variants are detected. f | Processing computational
pipelines can differ in number and type of steps such as the variant calling
algorithm, which can lead to differences in the variants detected in the
processed samples. To reduce ancestry, coverage or processing biases, cases
and external common controls should be harmonized prior to analysis.
AFR, Africa; AME, Americas; EUR, Europe.

Infrastructure workflow, researchers often use a combination of

Fine-​scale ancestry
Genetic differentiation
at a regional level (such as
subcontinental), as opposed
to continental-​level ancestry.
Metadata
A high-​level description of a
data set, often including details
of the cohort and of data
generation.
To ensure the broad, robust and equitable use of com-
mon controls, infrastructure must be secure, easy to use
and widely accessible. In addition to traditional infra-
structure, such as data storage, transfer and computing,
infrastructure to support educational training to use
common control resources is needed.
Common controls necessitate two primary areas
of computational infrastructure: storage and mainte-
nance of common control data sets in broadly acces-
sible locations; and environments and workflows to
bring together and analyse common control and case
data (Fig. 4). Depending on data permissions, size and
local and cloud computing. Cloud computing is an
increasingly widespread alternative to local computing,
ranging from a predefined, limited workspace where a
specific task is performed (for example, the TOPMed
Imputation Server)84,100 to flexible user environments
that store data and modifiable analysis pipelines, such
as the National Human Genome Research Institute’s
(NHGRI’s) AnVIL101, which includes data from the
CCDG, the National Heart, Lung, and Blood Institute’s
(NHLBI’s) BioData Catalyst102, which includes data from
TOPMed, and the National Institute of Health’s (NIH’s)
Researcher Workbench103.

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Table 2 | Case–control association methods or frameworks that incorporate preprocessed, the entire quality control process should
external common controls be well documented, including relevant variant-​level
and individual-​level quality control metadata, so that
Method Method type Internal Data type Covariates
controls users can assess and match the quality control per-
formed (Box 2). Here, we detail considerations for both
Individual-​level data sample-​level and variant-​level quality control, with
Chen and Lin128,a Single variant No Sequencing Yes current best practices for reducing bias.
iECAT Score test127 Single variant Yes Array Yes
Sample-​level harmonization and quality control.
Summary-​level data
Identical quality control filters should be applied to
iECAT-​O94,b Optimal combination Yes Array or No common controls and cases to ensure consistency
of burden and variance sequencing
component between data sets. This includes standard quality con-
trol procedures such as removing individuals with poor
ProxECAT95,c Burden No Sequencing No
sequencing quality, a low proportion of individuals
RV-​EXCALIBER 98
Harmonization framework No Sequencing No with a genotype call (that is, a low call rate) or high con-
for burden test tamination, among other well-​documented filters64,107.
TRAPD96 Filtering/harmonization No Sequencing No Covariates, and outcome definitions, where available,
framework for burden test should be defined and harmonized to ensure compa-
a
Requires variant depth and quality information. bOptimal in the presence of moderate to rability. In addition to choosing a common control data
large single-​variant confounding and requires the internal sample minor allele count to be
greater than two. cOptimal for very rare variants and can use variants with a minor allele count set that contains the genetic ancestries of the case data,
greater than zero. special consideration must be made to closely match
genetic ancestry at both a continental-​specific and
The advantage of the cloud in ‘bringing the user to region-​specific level to address fine-​scale substructure
the data’ can be especially useful for common control (Fig. 3a–d).
studies where large control data sets can be indexed and For individual-​level data, alignment of genome-​wide
stored in a central location that is available to author- (global) ancestry for cases and controls can be done with
ized users, avoiding redundancy as well as improving methods such as ADMIXTURE110, which estimates the
accessibility for groups lacking in-​house computational proportions of genetic ancestry in each individual, or
resources101,102,104,105. Users can upload their own data to through projection methods111,112, such as principal com-
integrate and analyse with common control data using ponent (PC) analysis113, with or without diverse ancestry
automated analysis workflows optimized for cloud envi- reference data sets such as the 1000 Genomes Project114,
ronments and made available in cloud repositories106. An the Human Genome Diversity Project (HGDP)115 and
alternative workflow uses the cloud environment for GenomeAsia116. As ADMIXTURE estimates the pro-
selecting common control data and local computing portion of the genome from a specific discretized ances-
for analysis. try, it is not able to provide insights beyond this often
continental-​level classification, such as subcontinental
Harmonization, quality control and association or subregional fine-​scale structure. Therefore, it may
analysis be ideal to closely match cases and controls using clas-
Following the selection of an appropriate common control sification methods that leverage continuous measures
data set, the next step is to implement and iteratively cal- of ancestry, such as the PCs that explain a substantial
ibrate a harmonization, quality control and analysis pipe- amount of variation. This strategy can also be used for
line (Fig. 4) to the specific case and common control data admixed populations as long as the PCs used for match-
sets. Although iterative pipeline optimization is useful for ing are informative for ancestry proportions. One clas-
any large-​scale genomic analysis with batches, it is espe- sic example of the importance of matching by ancestry
cially necessary when using external common controls. was demonstrated in a study of asthma in Latino par-
Without careful harmonization, analysis and quality con- ticipants, in which participants needed to be matched
trol, systematic differences (Fig. 3) can result in bias and an on both a subcontinental level (Mexican and Puerto
increased rate of both false positives and false negatives. Rican) and also by ancestry proportions within groups
to adequately control for population stratification and
Harmonization and quality control false positives73. For analyses that focus on a specific
To ensure that cases and controls are comparable with genomic region in admixed populations, local ancestry
one another, they must be harmonized prior to analy- can be estimated using methods such as RFMix117 or
sis with respect to both sample-​level and variant-​level Gnomix118. Estimation of ancestry in summary-​level
features. Case sample quality control can be performed data is less established and often limited to incomplete
before or during harmonization using well-​established matching of cases and common controls by reported
steps for genetic data64,107 and standard software such race, ethnicity and/or genetic ancestry, which can
as PLINK108,109. The level of harmonization needed result in removal of non-​homogeneous groups from
to reduce bias will depend on the extent of the differ- analysis or residual population stratification. More
ences in sequencing, such as scope (whole exome ver- recently, Summix119 enables genetic ancestry estima-
Local ancestry
The genetic ancestry of a
sus whole genome) or depth of coverage, processing tion and adjustment of allele frequencies requiring only
particular chromosomal region and recruitment between cases and external common summary-​level reference data, which is beginning to address
on a haplotype level. controls. If external common control data have been this limitation.

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Minor allele frequency
Using individual-​level data, both Marenne et al.
(MAF). For a genetic variant and Sazonovs et al. (Box 1) used PCs to assess concord-
with two alleles, the frequency, ance of genetic ancestry between cases and common
in a specified population, of controls34,36. Sazonovs et al. further used random forest
the less frequent allele.
on PCs generated from 1000 Genomes Phase 3 reference
data to classify UK Biobank samples into broad genetic
ancestry groups (Europe, Africa, South Asia, East Asia,
admixed). Samples classified as European ancestry were
retained.
Variant-​level harmonization and quality control. Large
differences in sequencing (or genotyping) technology
and processing (Fig. 3e,f) require a greater degree of
Box 2 | Considerations for the generation of new common control resources
Creation of broadly useful common control data sets and infrastructure to support their
use requires careful consideration. Here, we outline some guiding principles to consider
when establishing new common control resources.
• Metadata. There are resource and time costs in working with a new data set. Detailed
descriptions are valuable both in helping researchers decide whether to use a
particular data set and when harmonizing the chosen data. Helpful information
includes methods and procedures used in creating the data, sequencing technology,
coverage, variant calling algorithm, recruitment details, case definition, inclusion
criteria and ancestry description, among others.
• Variant-​level quality control metrics. Variant-​level quality control metrics enable
consistent quality control decisions across case data sets prior to harmonization with
the common control data set.
• Individual-​level quality control metrics. Similar to variant-​level quality control metrics,
individual-​level quality control metrics also enable consistent quality control decisions
between the common control data set and case data sets. For summary data, where
individual-​level metrics are not available, summary-​level information pertaining
to individual filters and distributions of quality control metrics should be provided.
• Rich phenotype and covariate data. Incorporating available phenotypes and
covariate information beyond just a few demographics can enable identification and
removal of cases or related conditions from the common control data set as well as
controlling for or evaluating the role of other conditions or environments. Age, sex,
ancestry and known chronic conditions should be standard variables in common
control data sets of individual-​level data. For summary data, descriptive statistics
of these variables should be provided and data should be grouped when possible
(for example, by ancestry or condition) to reduce heterogeneity in allele frequencies.
• Broad consent and sharing standards. Studies should seek broad consent, such as
no restrictions (NRES), general research use (GRU) or health, medical biomedicine
use (HMB), to allow their data to be readily used as common controls. Consents that
specify disease-​specific research, while not impeding the original investigators, make
the subsequent data of little use for common controls. Additional conditions, such as
letters of collaboration, add to research friction, particularly when investigators need
to combine several studies. Restrictions on who can use the data (for example, only
not-​for-​profit organizations) also reduce the value of the resource161.
• FAIR principles. FAIR principles state that data should be Findable, Accessible,
Interoperable and Reusable for both humans and machines162. These principles are
central to the utility of common control data, which must be useful for other researchers
and multiple case data sets.
• Intermediately processed data. When storage costs allow for it, inclusion of
intermediately processed data, such as gVCF files105, will allow for more efficient
joint recalling of cases and controls together, which can improve variant calls and
harmonization.
• Representation. Common control data sets and the researchers working to create
new data should be representative of the worldwide population. Such diversity
helps ensure that challenges relating to a broad set of conditions, environments
and ancestries are considered early on.
• Funding. Many of the recommendations listed above require additional time and
resources, often above and beyond a study’s primary mandate. As such, funding
and incentives are essential to support the creation and maintenance of high-​quality
common control data.
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harmonization and likely the use of analysis methods
developed explicitly for use with external common con-
trols (Table 2). Genetic variants or regions with poor or
differential sequencing quality between cases and con-
trols64,96 identified using variant quality metrics, such as
genotype quality, Hardy–Weinberg equilibrium (such
as PHWE < 10–4)120, variant quality score log-​odds, depth
of coverage and others64, should be removed. Removal of
genetic variants or regions can be performed with both
individual-​level and summary-​level data if adequate
variant quality control metrics are detailed.
A benefit of individual-​level data is the possibility
to improve variant calls through recalling cases and
common controls together34,35. Both Marenne et al.34
and Sazonovs et al.36 performed individual-​level inter-
mediate variant calling to produce gVCF files and then
performed joint variant calling across case and com-
mon control samples (Box 1). The feasibility of jointly
calling cases and common controls together depends
on the computational resources required and available.
Larger sample sizes and whole-​genome sequenced sam-
ples will require more resources, as will less processed
files. For instance, BAM files require more computa-
tional resources for storage and processing compared
with gVCF files. All individual-​level data resources pro-
vided in Table 1, except for GenomeAsia100K116 and the
CSVS90, have FASTQ or BAM/CRAM files available for
joint recalling. H3Africa121 and the UK Biobank85 also
have gVCF files available. For common, low-​frequency
and, increasingly, rare variants, variant calls can be
improved further with imputation of individual-​level
data using resources such as the TOPMed Imputation
Server84,100.
Filtering to rare alleles. Rare variant association tests
use filters or weights by minor allele frequency (MAF).
Although there are several appropriate filtering designs,
it is essential that the same criteria be applied to both
cases and controls64. For instance, filtering using only the
common control data set, but not the case data set, will
remove all variants above the MAF threshold in controls,
but not in cases, resulting in spurious associations64. The
ideal method for filtering to rare variants is to utilize
an independent, well-​matched (that is, by ancestry and
sequence technology and processing) external data set.
Importantly, some common control data sets contain
data that researchers might use to filter. For instance,
gnomAD contains 1000 Genomes Project114 and NHLBI
ESP122 data. As such, ideally, neither the 1000 Genomes
Project or the ESP should be used for filtering when gno-
mAD is used as the common control data set. When a
separate, well-​matched, external data set is not available,
filtering can be applied using both case and control data
by keeping only variants that are rare in both data sets95.
Marenne et al.34 used external data sets (1000 Genomes
Project and UK10K cohort reference panel) as well as the
case and common control data sets for filtering, whereas
Sazonovs et al.36 used an external, ancestry-​matched data
set (gnomAD Non-​Finnish European) (Box 1). Studies
of rare variant associations are also commonly limi­
ted to variants with predicted functional effects as a
way to improve power34,35, with multiple computational
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a Pre-analysis Research question(s) Example infrastructure

Internal case sample External common controls Account set-up and billing
• Individual vs summary
• Control type
• Case prevalence
• Ancestry
Processing pipeline • Processing pipeline
• Subject consent

Data access
Bring together e.g. AnVIL
Dataset Catalog

b Harmonization Harmonization
and analysis
• Depth of coverage Workflows
• Genotype quality
• Genome build
• Variant annotation
• MAF filtering

Analysis
8
Best practices Methods repository
–log10(P value)

6
Assess,
4 update
and
2
iterate
0
1

3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
20
22

Chromosome

Post-analysis quality control Interactive notebooks

8
–log10(observed)

6
• QQ plots
4 • Estimates of
2
polygenicity
0
0 1 3 4 5 5 6 7
–log10(expected)

c Results

Verification Interpretation Reproducibility and transparency

• In silico validation (e.g. • Contextualize findings
Open access Controlled access
depth, genotype quality) including limitations
• Partial replication (e.g. • Consider generalizability
allele frequencies in other to different ancestries,
common control data sets) ethnicities and environments

prediction tools (for example, FAVOR123, CADD124, Association methods

PolyPhen-2 (ref.125) and SIFT126) available that must Association methods have been explicitly developed to
be identically applied to cases and controls, as any robustly incorporate common controls while controlling
differences will introduce bias. for technology and processing differences between cases

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◀ Fig. 4 | Common control analysis workflow and example infrastructure with AnVIL.
a | Case–control analysis begins by identifying a research question and associated
condition of interest. Collection and processing of cases and potentially internal controls
are then conducted. Processing steps include sequencing, variant calling, imputation
and quality control. External common controls are chosen to match cases as closely as
possible on potential confounders. Internal and external data are then brought together
in a computing environment. If utilizing infrastructure such as AnVIL, accounts need to
be created for the Terra cloud computing platform and Gen3 data platform. Terra Billing
Project is created and linked to Google Billing Project or access to a specific billing
project is requested. Resources such as AnVIL Dataset Catalog or Gen3’s Data Explorer
can be used to search for common control data. Additionally, open (for example, 1000
Genomes), controlled (for example, database of Genotypes and Phenotypes (dbGaP))
or consortium access data can be requested and used. b | Cases and common controls
should be harmonized prior to analysis to reduce bias. Terra library or Dockstore, which
contains Broad Methods Repository and GATK Best Practices Toolkit, can be used to find
workflows. Analysis method, either single-​variant or region-​based, can be implemented
and post quality control performed. Jupyter Notebook can be created for interactive and
collaborative analysis using Python3 or R/Bioconductor, or a cloud environment can
be created for Galaxy. Harmonization, analysis and post-​quality control steps should
be iterated and updated until batch effects are no longer evident. c | Results are verified
and contextualized within limitations of a common control study. Reproducibility and
transparency supported by making the code and harmonization pipeline publicly available
(for example, on GitHub) and by citing methods and processing steps. Furthermore, data
and results (for example, test statistics) should be provided to the research community
through a publicly available portal such as the genome-​wide association studies (GWAS)
catalogue for open access and dbGaP or a consortia website for controlled access.
For more detailed tutorial on AnVIL infrastructure, see https://anvilproject.org/learn.
MAF, minor allele frequency; QQ, quantile–quantile. Logos reprinted with permission
from AnVIL (https://anvilproject.org/data); Dockstore (https://cancercollaboratory.org/
services-​dockstore); GATK (https://gatk.broadinstitute.org/hc/en-​us/categories/
360002310591); Terra (Geraldine Van der Auwera at the Broad Institute); Broad Institute
(https://www.broadinstitute.org/journalists/logos-​graphics); dbGaP (https://www.ncbi.
nlm.nih.gov/sra/docs/submitdbgap/); Bioconductor (https://www.bioconductor.org/
about/logo/); GWAS Catalogue (https://www.ebi.ac.uk/gwas/). Jupyter is reprinted with
permission from Jupyter (https://commons.wikimedia.org/wiki/File:Jupyter_logo.svg),
CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/).
improvement of the pipeline. After iteration of this pro-
cess until there is no longer any evidence of batch effects,
the study can progress to assessment and interpretation
of results. If there are unremovable batch effects, how-
ever, a different common control data set may be needed.
Starting with a subset of the data (for example, one chro-
mosome) and performing soundness checks (for exam-
ple, comparing distributions of quality control metrics
between cases and controls) at each stage of the process
enable facile assessment and updating of the pipeline.
The most common technique in a genome-​wide study
to assess a pipeline’s effectiveness is to use quantile–
quantile (QQ) plots to compare the observed distribu-
tion of test statistics with the expected distribution under
the null hypothesis of no association. Systematic bias will
manifest in a QQ plot with an inflated distribution of test
statistics at the median (that is, λGC > 1)96,107. Although
QQ plots can identify inflation of test statistics, they
cannot determine whether the inflation is due to popu­
lation structure or polygenicity130 using the single λGC
value. For WES, assessing inflation in rare variant test
statistics derived from synonymous variants can start to
disentangle bias from signal, as we expect less association
signal with synonymous variants96. For WGS, synony-
mous or a random subset of non-​coding variants may be
useful to identify residual bias. Additionally, the degree
to which a genetic marker tags local variability as esti-
mated using linkage disequilibrium score regression can
help distinguish polygenicity from population structure
effects131. Of note, careful attention to quality control,
filtering and association analysis is especially important
for candidate gene studies where bias cannot be assessed
through genome-​wide metrics, such as QQ plots.

In silico validation
Secondary quality control
analysis of genotype calls,
often of top association results,
that passed the initial
harmonization process to
ensure that differences in
processing do not drive
important association signals.
Partial replication
Repeating association analysis
reusing some data from the
discovery analysis (for example,
discovery cases and new
external common controls).
and controls (Table 2). The most computationally effi-
cient methods incorporate summary-​level common
control data. Methods such as iECAT can increase
power to detect rare variant genetic associations in an
existing case–control study by augmenting with com-
mon controls94, whereas ProxECAT95, TRAPD96 and
RV-​EXCALIBER98 enable the use of common controls
as the sole control set. Some common control data, such as
gnomAD, contain both exome and genome data. These
allele frequencies should be kept separate when using the
preceding methods, otherwise the methods will not be
able to adequately estimate and adjust for differences in
sequencing technology and processing. Other methods
incorporate individual common control data using only
variant calls127, using variant calls with other data such as
read depth128 or using different data, such as raw reads,
directly129. These methods can help alleviate residual dif-
ferences due to technology or computational pipelines
especially when jointly recalling cases and controls is
not feasible or does not fully alleviate bias. Importantly,
these methods do not inherently correct for differences
in ancestry and should be used along with ancestry
adjustment and matching discussed above.
Post-​analysis quality control
Post-​analysis quality control helps identify any remaining
systematic bias and issues in the harmonization and analy­
sis pipeline, which can then inform a recalibration and
Verification, follow-​up and reproducibility of results
When common controls are used, validation and rep-
lication of results are at the same time more important
and more difficult to implement than for traditional
case–control studies. The necessity of common con-
trols often follows from a scenario in which resources
are scarce; thus, gathering another independent and
sufficiently large replication sample of cases, let alone
cases and controls, may be difficult. In such a scenario,
in silico validation and partial replication can be per-
formed. In silico validation includes an in-​depth con-
firmation that top hits are not driven by subtle variant
quality issues. Partial replication, using other external
common control data sets or public databases, can be
used to cross-​reference genotype or allele frequencies
in the original common control data set or to complete
another association test with the discovery case sample.
Although these strategies do not comprise a traditional
external validation, they do provide additional support
for or against results from the primary analyses.
Sazonovs et al. and Marenne et al. both performed
replication using additional independent case and exter-
nal common control data34,36 (Box 1). Sazonovs et al. used
three follow-​up case–control studies for replication
including whole-​genome sequenced INTERVAL83 and
whole-​exome sequenced UK Biobank85 external com-
mon controls. Marenne et al. performed replication of
nine genes using targeted sequencing of independent

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severe childhood-​onset obesity cases and external com-
mon controls from the Fenland Study132. Additionally,
Marenne et al. performed partial replication of the
original severe childhood-​onset obesity samples with
gnomAD non-​Finnish European controls using the
association method ProxECAT95.
To ensure reproducibility of research with common
controls, code used for harmonization, quality control
and analysis should be publicly available, and common
control data used should be clearly identified including
version, access location and date accessed. Infrastructure
such as Dockstore133 for workflows and GitHub134 for
code are useful in supporting reproducibility.
Sharing of summary-​level results with sufficient
information for follow-​up is especially necessary for
common control studies. Standard recommenda-
tions exist for GWAS of common or low-​f requency
variants107,135 and are being developed for rare variant
analyses47. In addition to these standards, information
resulting from the harmonization process, such as allele
counts, frequencies before and after harmonization, and
study-​specific allele frequencies when multiple con-
trol sets are used, should be provided for common control
summary statistics. As summary statistics from analy­
ses using common controls become more prevalent,
the question of how to complete follow-​up analyses
from studies that utilize the same control set needs to
be addressed. Methods such as the Bayesian Multiple
Rare Variant and Phenotype framework harness corre-
lation, scale and/or direction of genetic effects to assess
summary statistics from a broad range of rare variant
association study designs including multiple diseases
and shared controls136.
Concluding perspectives
Foundational to the continued generation and use of
common control data are the urgency to better repre-
sent global populations in the data sets, the researchers
charged with generating new data sets and infrastruc-
ture, and users of the resources48,137,138. Deliberate atten-
tion to representation at every stage in the process
ensures that challenges are addressed prospectively
rather than as an afterthought or overlooked entirely139.
Importantly, the use of common control data should not
preclude the design and execution of large, high-​quality
studies of diverse genetic ancestries and environments.
Indeed, such large, diverse data sets are urgently needed
to increase representation of publicly available resources,
which may also serve as common controls.
Any development and maintenance of infrastructure
for the use of common controls, and data sharing in gen-
eral, must prioritize accessibility in terms of cost and ease
of use to close the resource gap, or else inequities regard-
ing who is able to conduct high-​quality research with
even ‘publicly available’107,140 data will persist. Structured
cloud computing and levelled cost structures, such as in
the UK Biobank, can help address disparities in access.
The need for broad representation and equity of access
for data resources does not necessarily mean that all data
should be publicly available. There is a balance between
open data and data sovereignty, especially for historically
marginalized groups, cultures and countries141. Although
676 | November 2022 | volume 23 www.nature.com/nrg
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broad consent from research participants is preferred for
common control data, as it allows the data to be more
widely used, consent must be obtained with respect,
accompanied by authentic community engagement and
trust building142. Efforts to ensure an equitable inclusion
of and partnership with people across environments,
ancestries and conditions must become the standard. As
such, structures for funding, publishing and rewarding
science must include expectations for representation,
equity and community engagement.
The generation and maintenance of rich phenotypic
data sets as well as ensuring representativeness require
funding and incentives. Current funding focuses on
the creation and analysis of individual data sets rather
than on broad interoperability among shared data sets.
Although there have been recent efforts by funding
agencies143 and organizations such as the Global Alliance
for Genomics and Health (GA4GH)144–147 to support
phenotype harmonization and data sharing standards,
such as common data elements and passports to enable
authentication and access, a commitment to continued
long-​term funding of these and other resources is needed.
The robust use of common controls requires careful
consideration and specialized training in how to access
data and complete robust analyses. Training programmes
currently exist for access and use of large-​scale genetic
data sets including the BioData Catalyst Fellowship
Program 148, AnVIL’s Massive Genome Informatics
in the Cloud (MaGIC) Jamboree149 and the GA4GH
starter kit150. Further integration of training into exist-
ing quantitative human genetics programmes through
institutions and professional societies would be benefi-
cial. Funding for time and travel is necessary to support
equity in training, especially for researchers who depend
on accessible public resources.
Genomic research requires an enormous amount of
resources, which can exacerbate disparities in research
and, ultimately, health outcomes for under-​represented
groups. With the increasing availability of genome
sequencing and low-​cost genotyping arrays, common
control data sets are an invaluable resource to the wider
research community in addressing these disparities.
Although common controls are and will likely continue to
be widely used in the future, there exist no comprehensive
guidelines and summary of the current resources to sup-
port robust use of common controls. As such, many stud-
ies have used common controls incorrectly (for example,
owing to improper filtering or mismatch of ancestry), and
quality control and analysis modifications would have
resulted in more robust studies. Importantly, the need
for appropriate calibration of test statistics when using
common control data sets is not eliminated by increas-
ing sample size; although this approach leads to reduced
variance of estimates and greater power for discoveries,
it can also open the door to additional batch effects and
other technical confounders. Thus, regardless of the size,
leveraging external data requires careful consideration.
Used rigorously, common controls hold the potential to
expand the impact of human genetics research across
a breadth of environments, conditions and populations.
Published online 17 May 2022

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Acknowledgements
This work was supported by the Genome Sequencing Program
(R35HG011293 to A.E.H. and C.R.G.; U01HG009080 to
A.E.H., A.G.I., C.R.G. and M.A.R.; and U24HG008956
to S.B.). The Genome Sequencing Program is funded by the
National Institute of Health (NIH) National Human Genome
Research Institute (NHGRI), the National Heart, Lung, and
Blood Institute (NHLBI) and the National Eye Institute (NEI).
G.L.W. received support for this work from NHGRI
(R35HG011944).
Author contributions
G.L.W., J.M., J.L.E. and A.E.H. researched the literature.
G.L.W., J.M., A.G.I., S.B. and A.E.H. provided substantial con-
tributions to discussion of the content. G.L.W., J.M., S.B. and
A.E.H. wrote the article. All authors reviewed and/or edited
the manuscript before submission.
Competing interests
C.R.G. owns stock in 23and Me. M.A.R. is a scientific founder
of Broadwing Bio, a consultant for MazeTx, and is currently
on leave at HiBio. The other authors declare no competing
interests.
Peer review information
Nature Reviews Genetics thanks the anonymous reviewer(s)
for their contribution to the peer review of this work.
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional
claims in published maps and institutional affiliations.
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Related links
1000 Genomes Project: https://www.internationalgenome.
org
All of Us: https://www.researchallofus.org/
AnviL: https://anvilproject.org
BioData Catalyst: https://biodatacatalyst.nhlbi.nih.gov
CCDG: https://ccdg.rutgers.edu
Csvs: http://csvs.babelomics.org/
dbGaP: https://www.ncbi.nlm.nih.gov/gap/
dbGaP ALFA: https://www.ncbi.nlm.nih.gov/snp/docs/gsr/
alfa/
eGA: https://ega-archive.org
estonian Biobank: https://genomics.ut.ee/en/content/
estonian-biobank
FinnGen: https://finngen.gitbook.io/documentation/
data-download
GenomeAsia 100K: https://browser.genomeasia100k.org
gnomAD v.2.1: https://gnomad.broadinstitute.org/
downloads
gnomAD v.3.1: https://gnomad.broadinstitute.org/downloads
H3Africa: https://catalog.h3africa.org
HGDP: https://www.internationalgenome.org/data-portal/
data-collection/hgdp
iNTeRvAL: https://www.intervalstudy.org.uk
jMorp: https://jmorp.megabank.tohoku.ac.jp/202109/
downloads/
Researcher workbench: https://www.researchallofus.org/
data-​tools/workbench/
sGDP: https://cloud.google.com/life-sciences/docs/
resources/public-datasets/simons
sisu v4.1: https://sisuproject.fi
Taiwan Biobank: https://taiwanview.twbiobank.org.tw/
browse38
TOPMed: https://topmed.nhlbi.nih.gov
TOPMed Bravo: https://bravo.sph.umich.edu/freeze8/hg38/
UK Biobank: https://biobank.ctsu.ox.ac.uk/crystal/label.
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