UK NATIONAL
COLLABORATIVE USHER STUDY
Institute of Child Health, UCL
Institute of Ophthalmology, UCL
Moorfields Eye Hospital
Wellcome Trust Sanger Institute
UCL Ear Institute
Glossary
A few of the terms used in this report are quite technical.
Here is a list terms to help guide you through the report.
Q. What is DNA?
DNA is a molecule that is responsible for the overall
structure and function of an organism by the production of
specific proteins. It is an ‘instruction booklet’ involving many
codes (genetic information) that is read and followed. Each
parent passes on their genetic information via DNA to their
children.
Q. What is a gene?
A gene is a section of DNA that codes for a specific protein
or part of a protein that is responsible for/involved in a
specific function. You inherit genes from each parent. Each
individual has approximately 25,000 genes. A faulty version
of a gene may cause a medical condition because the
protein that is produced may be faulty or may not be
produced at all. It is like a dominoes effect.
Q. What is a candidate gene?
A candidate gene is a gene which has not yet been
confirmed to have a role in the specific topic of interest but
may have the potential to do so. In the case of this study, the
candidate gene SLC4A7 has not been classed as an Usher
gene, however, the researchers of this NCUS study believe it
may have a potential role in Usher syndrome; hence why it is
called a candidate gene
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Q. What is a protein?
Proteins are machines that make all living cells function.
Cells produce protein from the information they receive from
genes in the DNA sequence; which we inherit from our
parents. There are different types of proteins that all have
different functions, which are coded by different genes.
Q. What is a polymorphism?
A polymorphism is a change in a DNA sequence that is
common in a specific population of people. It is not disease
causing (not pathogenic).
Q. What is a mutation?
A mutation is when there is a change (variant) in the DNA
sequence, causing a change in the ‘instructions’ being given
out for producing proteins.
Mutations can have 3 consequences. One result could be a
neutral effect, whereby the mutation still produces a
functional protein. Another result could be a beneficial
effect, whereby the mutation actually improves the proteins
function (these two effect can be classes as a polymorphism
(see below)). The final result could be a detrimental one,
whereby the mutation could produce a protein that does not
function properly or stops the production of the specific
protein, which may result in a genetic disorder (the variant is
pathogenic (see below)).
Q. What is pathogenicity?
Pathogenicity is the ability to cause disease.
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Q. What is a variant?
Changes in the DNA sequence are called variants. Variants
can be pathogenic or they could be neutral (this is when they
would be called polymorphisms).
Q. What is haplotype analysis?
Haplotype analysis is a test to identify sections of DNA that
are similar to each other.
Q. What is a genotype?
A genotype is the description of an individual’s set of genes.
In the case of Usher syndrome, it is the molecular diagnosis,
such as a mutation in one of the Usher genes.
Q. What is a phenotype?
A phenotype is the description of an individual’s observable
physical and behavioural characteristics. In the case of
Usher syndrome, it is the clinical features of an individual
such as the severity of deafness or RP.
Q. What is a genotype-phenotype correlation?
A genotype-phenotype correlation is the relationship
between the two previous descriptions. The link between the
presence of a mutation(s) and the resulting pattern of
changes it has on normal function of an individual.
An example of a genotype-phenotype correlation is sex
determination. Whether an individual is female or male is
determined by the set of genes that individual has inherited
from his/her parents. If an individual has 2 X genes (XX) then
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that individual will be a female. If the individual has 1 X and 1
Y gene (XY) then that individual will be a male.
Q. What does remote location in the DNA sequence mean?
Remote location means that the specific DNA sequence is
found in a region of the DNA that is not involved in the
production of a protein. Variations in such regions may not
be detrimental to actual protein production and function,
which is why the variants found in ‘remote locations’ were
not further analysed in this study.
Q. What is next generation sequencing?
Next generation sequencing is the name given to methods
that are able to read a big chunk of an individual’s genetic
information in one go but at a low cost compared to older
methods. This is important as researchers would be able to
look for mutations in new genes that may not have been
identified by older methods.
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Background
The National Collaborative Study (NCUS) was initiated in 2003 at
Moorfields Eye Hospital in collaboration with Sense. It was funded by
a Big Lottery Fund grant allocated to Sense. The Institute of Child
Health (the clinical and molecular genetics department as well as the
audiovestibular medicine department), Institute of Ophthalmology, the
UCL Ear Institute as well as the Wellcome Trust Sanger Institute
were also part of this study.
The aim of the study was to evaluate the genetic cause of Usher
Syndrome in the UK; specifically looking at the contribution of Usher
genes as well as a new candidate gene to the development of Usher
syndrome. Usher syndrome is a condition characterised by changes
in hearing, vision and sometimes balance. The NCUS also looked at
non-Usher cases such as Alstrom syndrome to see if Usher genes
also had a role in individuals not clinically diagnosed with Usher
Syndrome. The findings of this study were presented in a paper
called ‘Comprehensive sequence analysis of nine Usher syndrome
genes in the UK National Collaborative Usher Study’ by Stabej et al
(2012). This report will summarise the main findings of this study.
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Clinical assessments
Participants:
A total of 188 individuals, all from various ethnic
backgrounds, and their families (456 family members
including parents and siblings) were recruited for the NCUS
study. 172 of these were individuals with Usher syndrome.
It is important to have suitable people to compare results
with (these individuals are called controls). In this case, DNA
sequences from people of various ethnic backgrounds, as
well as known polymorphisms, were collected to compare
with the DNA sequence from the 188 individuals and their
families. This ensures that any change in the DNA sequence
detected could actually be disease causing rather than a
change commonly found in individuals without Usher
syndrome.
Controls:
There were 3 groups of controls used for this study. The 1st
was the use of DNA samples from 381 unrelated blood
donors from different ethnic backgrounds. The 2nd was the
use of 48 control DNA samples containing known
polymorphisms from the Fondation Jean Dausset-CEPH (the
Center for the Study of Human Polymorphisms). Lastly, DNA
from 57 individuals of a Pakistani origin was also used.
Q. What is a polymorphism?
A polymorphism is a change in a DNA sequence that is
common in a specific population of people. It is not disease
causing (not pathogenic).
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Clinical classification of Usher syndrome
Vision, hearing and balance of each individual were
assessed; the results of each were then used to determine
which subtype of Usher syndrome the individual had. A brief
summary of each test clinically used for assessment is
available in the appendix of this document.
There are 3 main clinical subtypes for Usher syndrome.
Type 1 is characterised by:
 Profound congenital hearing loss on audiometry
 Absent vestibular (balance) function on formal testing
 Retinitis pigmentosa present during vision assessment
Type 2 Usher syndrome is characterised by:
 Sloping moderate to severe congenital sensorineural hearing loss
on audiometry
 Normal vestibular (balance) function on formal testing
 Retinitis pigmentosa present during vision assessment
Type 3 Usher syndrome is characterised by:
 Progressive sensorineural hearing loss
 Variable vestibular (balance) function
 Retinitis pigmentosa present during vision assessment
Cases that do not fit into any of the above subtypes are
classed as Atypical Usher syndrome.
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Genetic assessment
What genes were sequenced?
The NCUS study sequenced all 9 known Usher genes as
well as the candidate gene.
The nine Usher genes were:
1.
2.
3.
4.
5.
6.
7.
8.
9.
MYO7A
USH1C
CDH23
PCDH15
USH1G
USH2A
GPR98
WHRN
CLRN1
The candidate gene sequenced was:
 SLC4A7
DNA samples were taken from each individual’s blood
samples by standard methods. Once collected, the DNA
samples from the 188 individuals, as well as the 48 CEPH
controls, were sequenced for the 9 Usher genes as well as
the candidate gene SLC4A7.
Assessment of pathogenicity
Q. What is pathogenicity?
Pathogenicity is the ability to cause disease.
Q. What is a variant?
Changes in the DNA sequence are called variants. Variants
can be pathogenic or they could be neutral (this is when they
would be called polymorphisms).
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Q. What is a polymorphism?
Polymorphism is a change in a DNA sequence that is
common in a specific population of people. It is not disease
causing (not pathogenic).
A change in DNA sequence is graded according to the
guidelines provided by the Clinical and Molecular Genetics
Society. The grades used to classify variants are:





UV4: probably pathogenic
UV3: Likely pathogenic
UV2: Uncertain pathogenicity
UV1: probably neutral variants
Neutral variants
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Genetic evaluation
Analysis of variants
A total of 774 variants were recorded from the 188 NCUS
individuals.
319 variants were not further analysed due to their remote
location in the DNA sequence.
Q. What is a variant?
Changes in the DNA sequence are called variants. Variants
can be pathogenic or they could be neutral (this is when they
would be called polymorphisms).
Q. What does remote location in the DNA sequence mean?
Remote location means localization in a region of the DNA
that is not involved in the production of a protein. Variations
in such regions may not be detrimental to actual protein
production and function, which is why the variants found in
‘remote locations’ were not further analysed in this study.
The remaining 455 of the variants were then classified using
the grading system mentioned above. The results were as
follows:






115 variants were pathogenic
15 variants were UV4
11 variants were UV3
18 variants were UV2
201 variants were UV1
95 variants were neutral
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Diagnosis
Based on clinical assessment, a total of 47 individuals were
diagnosed with Usher syndrome type 1, 121 were diagnosed
with Usher syndrome type 2 and 4 were diagnosed with
Usher syndrome type 3. A further 11 were diagnosed with
atypical Usher syndrome; 4 individuals had typical RP but
atypical hearing loss, whilst the other 7 had both atypical RP
and atypical hearing loss.
There were also 5 individuals who did not have Usher
syndrome; 1 had autosomal-recessive RP, 1 had Alstrom
syndrome, 1 had sector RP and hearing loss and a further 2
had an unknown syndrome.
Total participants in NCUS study and their
diagnosis (N=188)
6% 3%
2%
25%
USH1
USH2
USH3
Atypical USH
Non-USH
64%
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Genetic features in Usher syndrome type 1 families
There are 5 genes associated with Usher type 1; shown
below. These genes are referred to as USH1 genes.





MYO7A (USH1B)
USH1C (USH1C)
CDH23 (USH1D)
PCDH15 (USH1F)
USH1G (USH1G)
The overall diagnosis in the Usher type 1 families is
illustrated below. 88% had pathogenic variants in 1 of the 5
USH1 genes. No mutation in any of the Usher genes was
found in 4% of the participants. 2% of the participants carried
a variant with uncertain pathogenicity, whilst a further 6%
had mutations suspected to be associated with USH1 genes
due to haplotype analysis.
Q. What is haplotype analysis?
Haplotype analysis is a test to identify sections of DNA that
are similar to each other.
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Molecular diagnosis in Usher type 1 families
(N=47)
2% 4%
6%
Pathogenic variant
Suspected
involvement of
USH1 genes
Unclear UV2 variant
88%
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No mutation
detected in the 10
sequenced genes
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The pie chart below shows which Usher genes were
responsible for the mutations found in 88% of the Usher type
1 participants in this group.
Percentage of pathogenic variants linked to the 9
Usher genes (N=41)
10%
MYO7A
12%
USH1C
CDH23
PCDH15
17%
61%
A mutation in MYO7A was the most common cause of Usher
type 1 in this group as it accounted for 61% of the cases.
The second most common cause of Usher type 1 was a
mutation in the USH1C gene. Mutations in CDH23 and
PCDH15 were responsible for 12% and 10%, respectively, of
Usher type 1 cases. No mutations were associated with the
USH1G gene, the remaining Usher genes or the candidate
gene.
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Genetic features in Usher syndrome type 2 families
There are 3 genes associated with Usher type 2; these are
referred to as USH2 genes. These are:
 USH2A
 GPR98
 WHRN
The overall diagnosis in the Usher type 2 families is
illustrated below. A total of 86% of the Usher type 2 families
had mutations associated with 1 of the 9 Usher genes; 79%
had mutations in the USH2A gene, whilst 7% had mutations
in the GPR98 gene. However, mutations associated with the
3rd Usher type 2 gene, WHRN, were not found in this cohort.
A further 9 (7%) had no mutations linked with any of the
Usher genes or the candidate gene. The mutations identified
in the remaining individuals could not be confirmed as being
associated with an Usher gene; they have been classed as
‘uncertain’ instead.
Mutant genes identified in USH2 families
(N=121)
7%
USH2A
7%
7%
GPR98
No mutation
detected in the 10
sequenced genes
Uncertain
79%
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Genetic features in Usher syndrome type 3 families
There is only 1 gene currently associated with Usher type 3;
this is referred to as a USH3 gene. It is:
 CLRN1
The pie chart below illustrates the diagnosis in the families
clinically diagnosed with Usher type 3. There were only 4
families clinically diagnosed with this subtype of Usher
syndrome, demonstrating its rareness in the UK population.
Within this cohort of families, only 2 individuals had
mutations in the CLRN1 gene. Mutations identified in a 3rd
person were not found to be associated with any of the
Usher genes nor the candidate gene. A 4th person was
clinically diagnosed with Usher type 3 due to the phenotype
exhibited, however, the mutations identified may be linked to
CDH23 or WHRN, which are USH1 and USH2 genes,
respectively.
Mutant genes identified in USH3 families (N=4)
25%
CLRN1
50%
25%
October 2012
Uncertain
No mutation
detected in the 10
sequenced genes
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Genetic features in atypical Usher syndrome families
A total of 11 individuals were clinically diagnosed with
atypical Usher syndrome.
From this subgroup, 4 people exhibited typical RP but
atypical hearing loss. They were not found to have a
mutation in any of the 9 Usher genes or the candidate gene.
A further 7 people from this subgroup exhibited atypical RP
as well as atypical hearing loss. Only 2 individuals had a
mutation in one of the Usher genes whilst the remaining 5
had no mutations in any of the Usher genes nor the
candidate gene.
This demonstrates the lack of genotype-phenotype
correlation.
Q. What is a genotype?
A genotype is the description of an individual’s set of genes;
this is actual physical material (DNA) that is passed on by
the individual’s parents. In the case of Usher syndrome, it is
the molecular diagnosis, such as a mutation in one of the
Usher genes.
Q. What is a phenotype?
A phenotype is the description of an individual’s observable
physical and behavioural characteristics. In the case of
Usher syndrome, it is the clinical features of an individual
such as the severity of deafness or RP.
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Q. What is a genotype-phenotype correlation?
A genotype-phenotype correlation is the relationship
between the two previous descriptions. The link between the
presence of a mutation(s) and the resulting pattern of
changes it has on normal function of an individual.
An example of a genotype-phenotype correlation is sex
determination. Whether an individual is female or male is
determined by the set of genes that individual has inherited
from his/her parents. If an individual has 2 X genes (XX) then
that individual will be a female. If the individual has 1 X and 1
Y gene (XY) then that individual will be a male.
Overall, 82% of the 11 atypical individuals did not have a
mutation in any of the Usher genes nor the candidate gene.
The remaining 18% did.
Atypical Usher syndrome cases: detection
of mutation in one of ten sequenced genes
18%
Mutation detected
No mutation
detected
82%
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Genetic features in non-Usher syndrome families
There were 5 individuals who did not have Usher syndrome.
From this subgroup, 1 had autosomal-recessive RP. When
screened, the person was found to have two known USH2A
mutations.
In the case of 1 person who was clinically diagnosed with
Alstrom syndrome, genetic screening did not show mutations
in any of the 9 Usher genes nor the candidate gene.
Another person was clinically diagnosed with sector RP and
hearing loss. Genetic screening revealed two USH1C
mutations.
The final 2 people from this group were diagnosed with an
unknown syndromic disorder. However, they tested negative
for the Usher genes and the candidate gene.
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Non-Usher syndrome cases: detection
of a mutation in one of the ten
sequenced genes
40%
60%
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Mutation
detected
No mutation
detected
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Overall
Out of the 188 individuals studied, 86% of the mutations
identified were linked to the 9 Usher genes. There were no
mutations associated with the candidate gene, SLC4A7.
This study has highlighted that type 2 Usher is the most
common form of Usher syndrome in the UK, and that a
mutation in 1 of the 3 genes, USH2A, is the most common
cause of this subtype of Usher. Also, type 3 appears to be
very rare in the UK.
The remaining 14% of Usher syndrome cases may be due to
mutations in undiscovered genes or may be due to mutations
in one of the already identified Usher genes that were not
detected by the method of genetic screening used in this
study.
Percentage of cases whereby a mutation in
one of the ten sequenced genes was detected
14%
Mutation detected
No mutation
detected
86%
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Mutations in USH2A and GPR98 are the most common
cause of Usher syndrome regardless of ethnic background
and across the whole spectrum in general in the UK.
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Future directions
Researchers at the Institute of Ophthalmology now plan to
send all the mutation negative samples off to undergo next
generation sequencing.
Q. What is next generation sequencing?
Next generation sequencing is the name given to methods
that are able to read a big chunk of an individual’s genetic
information in one go but at a low cost compared to older
methods. This is important as researchers would be able to
look for mutations in new genes that may not have been
identified by older methods.
This will determine whether mutations in new genes may be
responsible for Usher syndrome in the mutation negative
patients.
This team of researchers are now also investigating the
genotype-phenotype correlation in mutation positive patients;
this will allow them to observe the natural progression of
retinitis pigmentosa in individuals that have Usher syndrome,
including its effect on the individual’s central vision.
Understanding the genotype-phenotype will enable doctors
to know what age is best to treat retinitis pigmentosa with
gene therapy (if and when it is approved as a treatment for
retinitis pigmentosa), ensuring successful treatment.
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Reference
Polona Le Quesne Stabej, Zubin Saihan, Nell Rangesh,
Heather B Steele-Stallard, John Ambrose, Alison Coffey,
Jenny Emmerson, Elene Haralambous, Yasmin Hughes,
Karen P Steel, Linda M Luxon, Andrew Webster, Maria
Bitner-Glindzicz. Comprehensive sequence analysis of nine
Usher syndrome genes in the UK National Collaborative
Usher Study. J Med Genet 2012; 49:27-36.
This document was produced by:
Yemi Tadesse
Research Officer, Sense
Telephone: 02070149369
Email: yemi.tadesse@sense.org.uk
Sense, 101 Pentonville Road, London, N1 9LG.
Please do contact me if you have any queries.
October 2012
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