A Population-Based Study of Autosomal-Recessive
Disease-Causing Mutations in a Founder Population
Jessica X. Chong,1,* Rebecca Ouwenga,1Rebecca L. Anderson,1Darrel J. Waggoner,1,2
and Carole Ober1,3,*
The decreasing cost of whole-genome and whole-exome sequencing has resulted in a renaissance for identifying Mendelian disease
mutations, and for the first time it is possible to survey the distribution and characteristics of these mutations in large population
samples. We conducted carrier screening for all autosomal-recessive (AR) mutations known to be present in members of a founder
population and revealed surprisingly high carrier frequencies for many of these mutations. By utilizing the rich demographic, genetic,
and phenotypic data available on these subjects and simulations in the exact pedigree that these individuals belong to, we show that the
majority of mutations were most likely introduced into the population by a single founder and then drifted to the high carrier frequen-
cies observed. We furthershow that althoughthere is an increasedincidenceof AR diseases overall, themeancarrierburdenis likely to be
lower in the Hutterites than in the general population. Finally, on the basis of simulations, we predict the presence of 30 or more undis-
covered recessive mutations among these subjects, and this would at least double the number of AR diseases that have been reported in
this isolated population.
Founder populations have contributed disproportionally
to the discovery of autosomal-recessive (AR) disease-
causing mutations because affected individuals from these
populations are typically homozygous for founder muta-
tions that reside on relatively long haplotypes, facilitating
mutation discovery by identity by descent (IBD) and
haplotype-sharing methods.1–4Moreover, despite their
negative impact on fitness, many disease-causing founder
mutations occur at relatively high frequencies in these
populations presumably as a result of the effects of random
genetic drift following the founding bottleneck. Classic
examples of high-frequency founder mutations are those
causing Ellis-van Creveld syndrome (MIM 225500) in the
Amish,5congenital chloride diarrhea (MIM 214700) in
the Finnish,6,7Tay-Sachs disease (MIM 272800) in Ashke-
nazi Jews,8Charlevoix-Saguenay spastic ataxia (MIM
270550) in the Charlevoix-Saguenay-Lac-Saint-Jean region
ofQuebec,9andcystic fibrosis (MIM 219700) inthe Hutter-
ites.10However, in nearly all cases, our understanding of
the impact and fate of founder mutations is based on
identifying homozygous individuals with the disease and
studying these individuals and their close relatives. As a
result, our understanding of the frequency spectrum,
carrier burden, and penetrance of AR disease-causing
founder mutations is limited to those that are observed
in homozygous affected individuals. The recent explosion
of next-generation-sequencing approaches to mutation
discovery facilitates more comprehensive surveys of AR
disease-causing mutations and, for the first time, unbiased
estimates of genetic parameters of deleterious mutations
segregating in founder populations.
The North American Hutterites are one of the best-char-
acterized young founder populations.11–14To date, >28 AR
diseases have been observed in members of this popula-
tion,13and causal mutations have been identified in
more than half. We initiated this study to determine the
frequency spectrum of known AR disease-causing muta-
tions in United States Schmeideleut (S-leut) Hutterites
and to identify the AR disease-causing mutations that are
present among the participants in our genetic studies of
complex phenotypes and common diseases.14Using a
combination of exome sequencing, targeted Sanger
sequencing, and direct genotyping, we identified the
mutations causing three AR conditions in the Hutterites
and determined carrier frequencies and carrier burdens
for 14 mutations associated with 13 AR diseases in
1,644 United States S-leut Hutterites. We report here
remarkably high carrier frequencies of all mutations and
temporal trends that predict increasing incidences of
some of these conditions.
Subjects and Methods
The Hutterites are an Anabaptist religious group that originated
during the 1500s in the Tyrolean Alps. To escape religious persecu-
tion, the Hutterites lived throughout central and eastern Europe
for the next >300 years. In the 1870s they migrated from Russia
to the United States and settled on three communal farms (called
colonies) in what is now South Dakota. These three colonies
gave rise to the three major Hutterite subdivisions, referred to as
the Schmiedeleut (S-leut), Lehrerleut (L-leut), and Dariusleut
(D-leut). The population has since undergone rapid expansion,
and today >400 Hutterite colonies of all three ‘‘leut’’ are located
1Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA;2Department of Pediatrics, University of Chicago, Chicago, IL 60637,
USA;3Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
*Correspondence: firstname.lastname@example.org (J.X.C.), email@example.com (C.O.)
http://dx.doi.org/10.1016/j.ajhg.2012.08.007. ?2012 by The American Society of Human Genetics. All rights reserved.
The American Journal of Human Genetics 91, 608–620, October 5, 2012
in the north central plain states of the United States and western
uncommon for at least the past 90 years. Detailed genealogical
records that extend back to the early 1700s during their tenure
in Russia trace the >40,000 extant members of this founder pop-
ulation to fewer than 90 ancestors.15
Our studies have focused on the United States S-leut Hutterites
residing primarily in South Dakota; some participants are from
colonies in North Dakota and Minnesota. Over the past nearly
30 years, we have conducted genetic studies of fertility,16,17
asthma and other common diseases,14,18and quantitative pheno-
types.19–21All of our genetic studies of complex phenotypes have
been population based and have included from ten colonies all
members (six years of age and older) who were home during our
field trips, as well as Hutterite visitors to those colonies on the
days of our field work. Our fertility studies include from an addi-
tional 39 colonies couples in their childbearing years at the time
of enrollment; some of these individuals were enrolled through
the mail. DNA for all subjects was obtained from blood collected
during field trips or from saliva samples collected through the
mail. The final sample for this study includes 1,644 Hutterites,
6–92 years old at the time of our studies, from 56 colonies. These
individuals are related to each other in a 13-generation pedigree
that includes 3,671 individuals, all of whom can be traced to 64
Written informed consent was obtained from all participants
18 years of age or older and from parentsof subjects under18 years
of age; written assent was obtained from subjects between 6 and
18 years of age. These studies were approved by the institutional
review board at the University of Chicago.
Selection of Disease Mutations
Of the 30 AR diseases described in the Hutterites (Table S1, avail-
able online, adapted from Boycott et al., 2008), mutations were
known for 20 prior to this study. We focused these studies on 14
AR disease-causing mutations that fell into one of the following
three groups: (1) known mutations for diseases that were either
observed or reported to have occurred in study subjects or their
children (n ¼ 5), (2) known disease mutations that were present
in the exome sequences of 25 Hutterites in our sample (n ¼ 6),
or (3) disease mutations that were discovered in our laboratory
during the course of this study (n ¼ 3). These 14 disease mutations
are described in Table 1. The eight remaining AR disease-causing
mutations that have been reported in the Hutterites were either
not present or could not be reliably assessed (i.e., insertions and
deletions) in the 25 exomes, and, to our knowledge, the diseases
attributed to those mutations are not present in the families in
We selected 25 Hutterites for exome sequencing with the goal of
capturing as much of the genetic variation present in the Hutter-
ites in our sample as possible.33To achieve that goal, we selected
individuals who were relatively unrelated to each other (mean
pairwise kinship ¼ 0.038 versus 0.041 in the entire sample) and
who had the largest number of genotyped descendants in the
pedigree (median number of genotyped descendants ¼ 31). After
sequencing, we searched among the called variants for previously
reported AR mutations;13,22,25,34all mutations identified in the
exome sequences were confirmed by Sanger sequencing. Three
(out of five) mutations from group 1 and one (out of three) muta-
tion from group 3 were also present in the 25 exomes. Group 2 was
composed of six additional mutations that were present in the
exomes but for which no individuals affected by these diseases
had been observed or reported in our study participants or their
The third group included three mutations that were identified in
our laboratory in DNA from affected individuals or from obligate
carrierparents. Here, we studied individuals and families with ocu-
locutaneous albinism (OCA1A [MIM 203100]), parents of children
with nonsyndromic deafness (DFNB1A [MIM 220290]), and
parents of a child who died of restrictive dermopathy (RD [MIM
275210]). Sanger sequencing of all five exons of TYR (MIM
606933) was performed in an adult with albinism; variants were
identified by comparison to hg18, and a mutation (RefSeq acces-
sion number NM_000372.4: c.272G>A) resulting in a protein
alteration, p.Cys91Tyr, was identified at a conserved site. This
mutation was then confirmed in DNA from parents whose chil-
dren had albinism and did not participate in our studies
(Figure S1A). The GJB2 (MIM 121011) c.35delG mutation (RefSeq
NM_004004.5) commonly causes nonsyndromic AR deafness in
European populations35but had not been identified as a cause
of AR deafness in the Hutterites. This mutation was identified
and confirmed by sequencing in both parents of multiple deaf
children (Figure S1B). The ZMPSTE24 (MIM 606480) c.1085dupT
(RefSeq NM_005857.3) mutation causing RD was discovered
simultaneously in our and another laboratory.26Sequences were
analyzed with 4Peaks (Mekentosj, Amsterdam).
We determined the frequency of each of these 14 mutations in
1,644 subjects by direct genotyping (Table S2). In addition, we
used a haplotype-based method to study the SMN1 (MIM
600354) deletion causing spinal muscular atrophy type III (SMA
[MIM 253300]) in 1,415 subjects, as previously described.23All
genotypes were in Hardy-Weinberg equilibrium according to a
test that adjusts for the Hutterite population structure and
relatedness.36Mendelian errors were identified by Pedcheck;37
these errors were corrected, but if they could not be unambigu-
ously resolved, the implicated nuclear families were removed
from further analyses. Four couples in our sample were ascertained
because they had children with cystic fibrosis (CF [MIM
219700]);24these couples and their children were excluded
from population-based estimates of carrier and homozygote
frequencies for CF.
To determine whether each mutation occurred on a single founder
haplotype, we used genotypes for 1,415 subjects who were geno-
typed on the Affymetrix 500k, 5.0, or 6.0 SNP arrays. SNPs under-
went quality control (QC) checks as previously described.20We
included in these studies the 271,486 SNPs that were present on
all three arrays and passed all QC checks.
For the seven mutations that occurred in at least one homozy-
gous individual in our sample, we identified the haplotype
carrying the mutation directly in those individuals. However, to
identify the haplotype(s) shared by carriers of the seven mutations
that did not occur as homozygous in our sample, we used a
phasing algorithm33that uses both the known IBD structure of
the population and the Affymetrix genotypes to generate a ‘‘refer-
ence haplotype’’ from a heterozygote that was selected at random.
Then, we used a Perl script to identify the extent to which the
The American Journal of Human Genetics 91, 608–620, October 5, 2012
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