Suntou
Thanks for sharing with us such an important scientific information.
SUNTOU TOURAY <[log in to unmask]> wrote:
A national DNA bank in The Gambia, West Africa,
and genomic research in developing countries
To the editor:
The Gambian National DNA Bank, the first
National Bio-Bank developed in Africa,
was funded in November 2000 by the
Medical Research Council (MRC) as one of
14 DNA collection sites established to
study the genetics of complex diseases. One
of these sites is housed at the MRC
Laboratories in The Gambia and has a
special, though not exclusive, focus on
malaria, HIV and tuberculosis. Additional
projects include analyses of genome
diversity in West African populations and a
collection of twin-sister pairs to study the
genetic basis of dizygotic twins (∼2% of
live births in the country). So far, more
than 30,000 DNA samples have been
collected, with many ongoing studies and
more planned.
For the first time in a sub-Saharan country,
a centralized structure and database for
archiving DNA samples has been created, in
collaboration with the Jean Dausset
Foundation-CEPH. The bank is regulated by
guidelines (Supplementary Note online) for
sample collection, archiving, data storage and
privacy protection, which were developed and
approved by the MRC, the MRC Laboratories
Scientific Coordinating Committee and by the
Gambia Government/MRC Joint Ethics
Committee. The Guidelines, which are
enforced by these Committees, stemmed from
the need to adapt to the local reality the many
existing recommendations on bio-banking,
privacy protection, genetics research and,
generally, on medical research in developing
countries (http://www3.who.int/whosis/
genomics/pdf/genomics08.pdf,
http://www.mrc.ac.uk/pdf-devsoc.pdf,
http://www.mrc.ac.uk/pdf-tissue_guide_fin.
pdf, http://www.nuffieldbioethics.org/
publications/pp_0000000013.asp).
The Gambian DNA Bank promotes
sharing of information and resources with
centers around the world, and one of its
ultimate goals is health improvement. In the
short term, benefits should accrue to the
participants in the studies. A recent example
is a large project on genetic and
environmental factors for susceptibility to
tuberculosis, designed as a household
association and family-based study and
carried out in The Gambia, Guinea-Bissau
and Guinea-Conakry1. The project focused
on the systematic detection of tuberculosis
cases in the families of individuals with
tuberculosis and controls. Clinical services
© 2004 Nature Publishing Group http://www.nature.com/naturegenetics
CORRESPONDENCE
were considerably augmented within the
framework of the genetic study, to the benefit
of the populations involved.
During research projects at the MRC Unit
in The Gambia, biological samples (mostly
blood, buffy coats and peripheral blood
mononuclear cells) were taken and stored at a
time when molecular genetics was still in its
infancy. The process of obtaining consent has
evolved enormously over time, and in the
past, samples may have been taken from
subjects who were not made specifically aware
that the samples were going to be used for
genetic studies. The Guidelines now regulate
the use of these archived DNA specimens: in
almost all circumstances they can be used
only after anonymization and unlinking
(Supplementary Note online), and all use
requires approval by the Ethics Committee.
Regrettably, most African countries do not
have the infrastructure necessary to carry out
genomic studies, and so most scientific
exchange has taken place with developed
countries. The Ethics Committee has a key
role in sanctioning shipment of any samples
to external collaborators. The Committee
evaluates the specificity of the project and reevaluates
projects in case their focus changes
over time. All transfer of DNA samples to
collaborators is accompanied by signed
agreements and detailed documentation
describing the projects involved. The review
of sample transfer to third parties is
compulsory and is not permitted from one
collaborator to another without consent of
the Ethics Committee.
In the long term, understanding genetic
determinants of infection can lead to
prevention and improved treatment, but this
does not mean that genetic research will cure
infectious diseases. Even more complicated is
the situation of population-genetics studies
promoted by interest in the greater genomic
diversity found in Africans compared with
Europeans and Asians, and consistent with the
hypothesis of an African origin of modern
humans. Where sampling is not part of
research aimed directly at disease, the
connection to health interventions seems
weak. But this does not imply that studies on
genome diversity should not be done, for the
contribution of both inter- and intraethnic
genetic variability comparisons is crucial in
our understanding of immunity to infections.
For example, the findings that West African
Fulani have fewer malaria attacks and lower
parasitemia by Plasmodium falciparum than
two sympatric ethnic groups2, and that they
have intragroup variation in immune
responses to malaria3, open the possibility of
identifying genetic factors determining
malarial immunity. Immunogenetic
associations with infectious disease, such as
the association between HLA-B53 and
resistance to severe malaria found in Gambian
children4, can affect vaccine development.
The ethics guidelines adopted for the
Gambian National DNA Bank do not
presume to be the last word on the matter.
Rather, we hope their publication will
stimulate discussion of the appropriate way
to regulate genomic research in developing
countries. We hope that our initiative will be
seen as an important experience in a complex
and fast-evolving venture from which Africa
should not be excluded, and as a possible
template to be adapted by similar initiatives
in other parts of the world.
Note: Supplementary information is available on the
Nature Genetics website.
ACKNOWLEDGMENTS
This work was supported by the MRC (UK) to G.S.
Giorgio Sirugo1, Maarten Schim Van Der Loeff1,
Omar Sam2, Ousman Nyan3, Margaret Pinder1,
Adrian V Hill4, Dominic Kwiatkowski4,
Andrew Prentice1,5, Claudia de Toma6,
Howard M. Cann6, Mathurin Diatta1,
Muminatou Jallow1,7, Gareth Morgan1,
Malcolm Clarke8, Tumani Corrah1,
Hilton Whittle1 & Keith McAdam1,5
1MRC Laboratories, PO Box 273, Banjul, The
Gambia. 2Department of State for Health, Banjul,
The Gambia. 3University of The Gambia, School
of Medicine, The Gambia. 4Wellcome Trust Centre
for Human Genetics, University of Oxford, UK.
5London School of Hygiene and Tropical
Medicine, UK. 6Fondation Jean-Dausset-CEPH,
Paris, France. 7Royal Victoria Teaching Hospital,
Banjul, The Gambia. 8Gambian Government /
MRC Laboratories Joint Ethics Committee,
Fajara, The Gambia. Correspondence should be
addressed to G.S. ([log in to unmask]).
1. Lienhardt, C. et al. Am. J. Epidemiol. 155,
1066–1073 (2002).
2. Modiano, D. et al. Proc. Natl. Acad. Sci. USA 93,
13206–13211 (1996).
3. Luoni, G. et al. Genes Immun. 2, 411–414 (2001).
4. Hill, A.V. et al. Nature 352, 595–600 (1991).
786 VOLUME 36 | NUMBER 8 | AUGUST 2004 NATURE GENETICS
Evidence for lateral gene transfer from salmonids to
two Schistosome species
To the editor:
Two detailed studies of the genomes of Asian
and African and American schistosomes were
recently published1,2. In the former, some
13,131 gene clusters from Schistosoma
japonicum EST clones were analyzed and
their hypothetical protein products were
compared with those of model organisms,
uncovering about 30% homologous proteins
(at E ≤ 10–10). In their report on the
evolutionary implications of their
sequencing project1, however, the authors
did not mention that one of their libraries
(SjC7/94) contained many inserts with high
homology to genomic DNA of salmonid fish.
This was recorded in GenBank, in which it
was stated that these homologous inserts
amounted to 2–3% of the library clones. Our
analysis showed that more than 10% of the
SjC7/94 clones matched (E ≤ 10–10) DNA of
salmonid fish; more than 95% of these were
the best matches found in the entire nr
database.
Our analysis of the SjC7/94 library also
showed that nearly all of the salmonidhomologous
inserts are found in noncoding
regions of the salmonid genes and seem to
comprise salmon-specific mobile genetic
elements. For example, the clone BU712912
contains a 480-bp sequence that is almost
identical (94% identity; E = 0) to the
Oncorhynchus mykiss LINE Rsg-1 (ref. 3);
searches of the mammalian database for
similar sequences produced no matches
(E > 0.05), and none were found in other
invertebrates (E > 0.06). The SjC7/94 library
also contains sequences homologous to the
salmonid SINEs SmaI (found only in
Oncorhynchus keta and Oncorhynchus
gorbuscha, possibly after lateral transfer4;
E = 90–50) and HpaI (found in all salmonids;
E = 10–78). There are even S. japonicum
sequences homologous (E = 10–27) to FokI,
which is supposed to be specific to the genus
Salvelinus4,5; these show a higher level of
identity than is seen in other salmonids.
To verify the presence of these sequences in
the schistosome genome and to elucidate
more about their expression, we carried out
PCR using primers designed to amplify six of
these salmonid-specific sequences, initially
© 2004
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