Article Text

other Versions

PDF
Current needs for human and medical genomics research infrastructure in low and middle income countries
  1. Diego A Forero1,
  2. Ambroise Wonkam2,
  3. Wei Wang3,4,
  4. Paul Laissue5,
  5. Catalina López-Correa6,
  6. Juan C Fernández-López7,
  7. Raja Mugasimangalam8,
  8. George Perry9
  1. 1Laboratory of Neuropsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
  2. 2Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
  3. 3School of Medical Sciences, Edith Cowan University, Joondalup, Australia
  4. 4Beijing Municipal Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
  5. 5Unidad de Genética, Grupo GENIUROS, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
  6. 6Department of Scientific Affairs, Génome Québec, Montréal, Canada
  7. 7Instituto Nacional de Medicina Genómica, Mexico City, Mexico
  8. 8Genotypic Technology Ltd, Bangalore, India
  9. 9College of Sciences, University of Texas at San Antonio, San Antonio, Texas, USA
  1. Correspondence to Professor Diego A Forero, Laboratory of Neuropsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, 110231, Colombia; diego.forero{at}uan.edu.co

Statistics from Altmetric.com

Genomics has facilitated the identification of a large number of genetic variants that are causal and/or risk factors for both rare and common human diseases. Low and middle income countries (LMIC) represent a large proportion of the human population, with distinct health priorities from the developed world. There have been some initiatives in LMIC focused on medical genomics research. We review successful examples of existing genomics centres in LMIC and suggest some recommendations to develop the research infrastructure that is needed in LMIC. There is an urgent need to improve local infrastructures of many LMIC to carry out medical genomics research.

The World Bank’s list of countries having reduced income includes 139 countries, which have been classified in six groups (East Asia and Pacific, Europe and Central Asia, Latin America and Caribbean, Middle East and North Africa, South Asia, and Sub-Saharan Africa). In addition, as the total population living in LMIC will increase even more in the following decades, basic health research in these populations is of high global importance.1 ,2

Due to the high costs of the needed research infrastructure (eg, high technology equipment that cost millions of dollars and scientific personnel with advanced training and experience in those areas), a large number of the human genomic centres around the globe are located in developed countries.1 Indeed, most of the 400 000 human whole-exome sequencing assays expected to be accomplished in 2015 will be performed in developed countries.

To date, there have been some initiatives in LMIC focused on human and medical genomics research (table 1). In Mexico, the National Institute of Genomic Medicine was created in 2004,3 dedicated to research on diseases with emphasis on the characterisation of population structure of complex traits in admixed populations (type 2 diabetes, hypertension, obesity, cancer).3 India, one of the largest countries in the world (about 1.2 billion people, with a well-known cast system in terms of population structure), has two existing human genomic centres: CSIR-Institute of Genomics & Integrative Biology and the National Institute of Biomedical Genomics.4 In addition, there are three private genomics centres, and next-generation sequencing (NGS) facilities are also present in a few hospitals. Around ten molecular diagnostic laboratories are applying NGS and providing clinical diagnostics services. Thailand has the Genome Institute, National Center for Genetic Engineering and Biotechnology5 and Brazil has the Human Genome and Stem Cell Research Center, affiliated to the University of Sao Paulo.6

Table 1

Selected existing human genomics centres in low and middle income countries*

China is a multicultural country that has arisen from its 56 ethnicities, with a diverse population of over 1.3 billion and an imbalanced economic development. The Chinese sequencing giant, formerly known as the Beijing Genomics Institute (BGI), is the largest technical platform and provides access to technology for massively parallel/next generation DNA sequencing, genotyping and associated bioinformatics support. It possesses over 178 sequencing machines, process at least 25% of the world's genomic data and has sequenced the genomes of many thousands of human samples.7 Another genomics centre, the Zhejiang University Center for Genetic and Genomic Medicine, was established in 2005, by the Zhejiang University School of Medicine and the James Watson Institute of Genomics Sciences. These centres have now become multidisciplinary institutions, serving as hubs for different genomics applications.

China has launched several projects related to the human genome in the past decades. The Chinese Human Genome Diversity Project (CHGDP) has collected and analysed cell lines from 56 Chinese ethnic groups. In 1999, China began to participate in the international Human Genome Project (HGP) and undertook the sequencing of 1% of the human genome working draft (ie, the region 3pter-D3S3610 containing 30 million bp). China is also a contributor to about 10% of the International HapMap Project which was jointly launched in 2002 by the USA, the UK, Japan, China and Canada. In January 2008, the ‘Yanhuang’ (Emperor Yan) Project was started by the BGI, in order to sequence the entire genome of 100 Chinese individuals.7

We were not able to find existing genomic centres in Israel8 or in Africa, a continent with an approximate population of 1.1 billion.9 Clearly, the time has come for African governments to embrace genomics for the benefit of their populations. The prospects for genomic medicine in Africa have been enhanced by major initiatives that are led by international funding agencies and academics, such as the Malaria Genomic Epidemiology Network (MalariaGEN; http://www.malariagen.net), the Human Heredity and Health in Africa Program (H3Africa; http://h3africa.org) and the African Genome Variation Project.9 These consortia, which involve collaborations with scientists in Europe and USA, have started to build the capacity in research skills and to overcome the barriers for the use of genomics to address the disease burden of Africans.9 Despite the obvious lack of many centralised national centres for human genetics and genomics in many African countries, there are encouraging attempts, like the recent launch of the Southern Africa Human Genome Project by the South African government.9

It is important to notice that numerous private companies (eg, Genotypic, Macrogen, Eurofins, ElimBiopharm), located in diverse world regions (including some LMIC), offer complete human genomic services which are frequently used by institutions lacking their own platforms.

There exists a range of potential barriers to the development of genomic medicine in LMIC: the availability of adequate research funding and of trained personnel, in addition to national/international regulatory systems and organisation and structure of healthcare provision.

Human genomics centres in LMIC might include facilities for DNA sequencing (both Sanger and NGS techniques) and for DNA genotyping, complementing the departments focused on specific research topics, such as population genetics and genomics of human diseases.10 In addition to the initial investment for the creation of a human genomics centre (construction or adaptation of buildings, acquisition of high tech equipment and hiring of scientific personnel), it is crucial that novel centres have financial support for their long-term operation. It could be facilitated by an important participation of public funding (trying to achieve an isolation from local political agendas), as commercial companies focused on biotechnology research are scarce in LMIC.

These centres might represent the collaboration of groups from LMIC with previous local experience in human genetics and genomics research.10 These existing local networks could facilitate interactions with clinical centres that have access to the patients and their families. As novel genetic variants found in patients need to have a functional validation, participation of researchers and groups with experience in cell and animal models is of relevance. In addition to ‘wet lab’ infrastructure, local bioinformatics capacity is an important asset to develop. It implies a consolidation of computing infrastructure and, of special relevance, scientific personnel with the adequate training in the computational and statistical analysis of human genomics data.11 There are few postgraduate programmes focused on genomics sciences in LMIC.11

An adequate consolidation of collaborations with research groups and centres located in LMIC is crucial. These collaborations need a bidirectional relationship, facilitating advanced training of scientists and students from LMIC, in addition to processing of samples in laboratories located in developed countries in the context of projects led by researchers from those regions. An interesting example is the Genomic Medicine Alliance.10

As biomedical science is moving to the consolidation of large consortia, medical genomics in the global context implies the establishment of DNA sample banks and data sharing of genetic and phenotypic information in international collaborations.12 For an adequate development of medical genomics in LMIC, it is necessary that regulatory bodies understand the importance of informed consents and ethical approvals that facilitate the adequate sharing and reuse of genetic and phenotypic data.12

In summary, there is an urgent need to improve local infrastructures of LMIC to carry out medical genomics research, which could be realised if their governments implement some of the key recommendations of the W H O Report on Genomics and World Health.13 First of all, capacity building might be achieved through the development of academic and research partnerships between developed countries and LMIC (involving both public and private institutions) and, more importantly, between LMIC themselves, with the implementation of the appropriate incentives. Second, LMIC must consolidate urgently a critical mass of expertise in bioinformatics, to be able to use the huge quantities of genomic data that are being generated.14 Finally, all LMIC need to evolve appropriate national frameworks to consider the ethical implications of genomics research and its applications for their unique social, cultural, economic and religious contexts. It would help to develop effective policies and programmes involving genomics of diseases that affect their populations, with the aim of changing healthcare practices, developing targeted therapies that will give higher efficacy and lesser side effects, making more accurate diagnosis and helping individuals to prevent diseases. Studying human diversity enriches the opportunities to find cures for people throughout the world.15

References

View Abstract

Footnotes

  • Twitter Follow Diego Forero at @daforerog

  • Contributors All authors participated in the writing of the manuscript, in the revision and discussion of its content and in the final approval to be submitted.

  • Funding DAF is supported by research grants from Colciencias and VCTI-UAN; PL is supported by research grants from Universidad del Rosario; WW is supported by the China National ‘12th Five-Year’ Plan for Science and Technology Support, China 2012BAI37B03; Edith Cowan University-SRF 2015–2016; Australian NH&MRC Grant #APP1112767 and the Importation and Development of High-Calibre Talents Project of Beijing Municipal Institutions, China.

  • Competing interests None declared.

  • Provenance and peer review Not commissioned; internally peer reviewed.

Request permissions

If you wish to reuse any or all of this article please use the link below which will take you to the Copyright Clearance Center’s RightsLink service. You will be able to get a quick price and instant permission to reuse the content in many different ways.