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World of Genomics: India

Miyako Rogers 20 September 2022

The Republic of India is the most populous democracy in the world, and is a highly diverse country with thousands of different ethnic groups and hundreds of different languages spoken. With a booming genomics and pharmaceutical sector, which has already seen huge growth in the past few years, the future genomics landscape of India looks promising.

The population of India

India is bordered by the Indian Ocean, Arabian Sea, Pakistan, China, Nepal, Bhutan, Bangladesh and Myanmar. This large peninsula is home to the Himalayan mountains in the north, large deserts and plains, and long coastal beaches.

Figure 1 ¦ Map of India

India has been inhabited by humans for over 55,000 years, and the region is second only to Africa in genetic diversity. One of the first examples of settled civilisations, the Indus valley civilisation, was established 9,000 years ago around the Indus river basin. In 1200 BCE Hinduism was established, followed by Buddhism and Jainism 800 years later. In the 10th century, Islam came to India forming strong trade and cultural links between Arabia, North Africa and India. In the 15th century, Sikhism was founded, and during this time the Mughal Empire rose to prominence, ushering in a 200-year-long era of peace.

In the 1600s, the British East India Company was founded. Over the coming century, the power of the British East India Company grew, and in the 1700s it began taking control over huge swaths of land. British crown rule began in 1858 and remained in power until 1947. During this long period of colonisation and oppression by the British, those living in the region experienced a succession of severe famines. Physicians such as Dr. Mubin Syed have suggested that the high prevalence of type-2 diabetes and cardiovascular problems in Indian populations may be attributed to inherited epigenetic and genetic changes as a result of these brutal conditions. After independence, the region was split into India and Pakistan, causing the mass migration of almost 10 million people between the two countries. In 1949 The Constitution of India was drafted, and in 1950 India became a sovereign democratic republic.

Geographic and demographic information

Summary statistics

  • Land area: 2021 estimate: 2,973,190 sq km
  • Gross domestic product (GDP):
    • Total: 2021 estimate: 3.17 trillion USD
    • Per capita: 2,277.4 USD

Population statistics

  • Population size: 2021 estimate: 1.39 billion
  • Birth rate: 2020 estimate: 17 per 1000 people
  • Death rate: 2020 estimate: 8 per 1000 people
  • Infant mortality rate: 2020 estimate: 27 per 1000 people
  • Life expectancy: 2020 estimate: 73 years
    • Male 2020 estimate: 71 years
    • Female 2020 estimate: 75 years
  • Ethnicities: India has more than 2,000 ethnic groups, 2022 estimate: 72% Indo-Aryan, 25% Dravidian, 3% Mongoloid

Healthcare system

Healthcare in India is delivered by public, private for-profit, and private non-profit companies, but the majority of health services are meted out by private providers. Almost 70% of all outpatient visits, 58% of all inpatient care, and around 90% of all medicines dispensed are provided by the private sector. Government underfunding and dependence on private providers have resulted in household out-of-pocket expenses accounting for over 60% of all health spending. The resulting financial burden is pushing 55 million people into poverty every year, and over 17% of Indian households are incurring health expenditures above what they can afford. Moreover, public and private healthcare is regulated at the state level, with relatively little input from the Central (National) Government. As a result, quality, accessibility and standards vary considerably from state to state and provider to provider.

Public sector health services are under the regulation of the state’s own Department of Health with some oversight by the National Medical Commission. Publicly provided primary care services include sub-centres which serve 3,000 – 5,000 individuals, primary health centres for 20,000 – 30,000 individuals, community health centres for 80,000 – 120,000 individuals, and district hospitals. Community health centres and district hospitals are equipped to handle 24-hour emergency services including emergency obstetric and newborn care. Specialist tertiary care is provided by medical colleges or state-level super-speciality hospitals. Again, standards, regulation, upkeep, and maintenance of facilities are largely controlled by the state government and receive limited funding from the Central Government.

The Twelfth Five Year Plan of India is a national effort to improve the accessibility, quality and affordability of health care, with an aim to move the country towards Universal Health Coverage. Expansion of institutional deliveries under National Health Mission (NHM) has led to significant increases in the share of deliveries in health facilities: an increase of 40% from 2004 to 2018. In 2018, a new national scheme called the Pradhan Mantri Jan Aarogya Yojana (PM-JAY) integrated health insurance schemes of several state governments under one umbrella. PM-JAY aims to cover 500 million people with a benefits package of 500,000 Indian rupees annually for each household, including over 1,500 packages provided free to patients from economically and socially disadvantaged groups.

Health priorities

India has made huge progress in communicable diseases over the past few decades, with polio, guinea worm disease, yaws and tetanus having been successfully eradicated. However, communicable diseases still remain a major public health concern with HIV/AIDS, tuberculosis, malaria and neglected tropical diseases endemic in India, and a major cause of mortality and morbidity in the country.

In 1992, India launched the National AIDS Control Organization which in conjunction with state AIDS prevention and control societies runs prevention, care, support and treatment services for those affected by HIV/AIDS. In 2019, 0.22% of adults lived with HIV/AIDS, an estimated 2.34 million people. As of March 2020, 1.48 million HIV patients have received antiretroviral therapy, and 1.38 million receive free lifelong support.

In 2020, India accounted for 27% of global tuberculosis cases, 147,000 of which were drug-resistant forms of TB. The National Tuberculosis Elimination Programme (NTEP), responsible for TB diagnosis, treatment, prevention and control, received 30.4 billion Indian Rupees in funding from the Ministry of Health and Family Welfare from 2020-2021. In the past 3 years, an additional 1.2 million TB cases have been detected through government facilities, and the NTEP has incentivised 1.6 million private providers to report cases, improving case notification by 26% in just 6 years.

Non-communicable diseases (NCDs) cause 60% of deaths in the country, with heart disease, cancer, diabetes and stroke the major causes of concern. Launched in 2008, the National Programme for Prevention and Control of Cancer, Diabetes, Cardiovascular Disease and Stroke (NPCDCS) aims to bring prevent, diagnose, and treat chronic NCDs, as well as promotion of behavioural and lifestyle changes. However, a 2016 study assessing NPCDCS found identified several problems in the context of stroke, including ill-defined screening criteria, referral pathways, a shortage of specialists and a poor quality of rehabilitation services due to the unavailability of suitable equipment and lack of follow-up post-discharge.

Genomic medicine capabilities

As already discussed, India is a highly diverse heterogenous country, and as a result genomic medicine could have transformative potential. With decreasing infant mortality rates, genetic disorders are emerging as an important group of diseases. India is home to about one-third of all rare diseases, and according to a 2021 report by the Ministry of Health and Family Welfare, the number of diseases in India that are globally recognised as rare diseases may encompass from around 7,000 to 8,000 disorders. The Organization of Rare Diseases in India reports that around 1 in 20 individuals in India is affected by a rare disorder.

However, recording of rare disease in India is mostly collected from tertiary care hospitals, and information is limited. Moreover, the lack of diversity and focus on Western populations in global genome databases is another obstacle to securing reliable and robust data. In India, projects like the Thalassemia Screening and Counselling Centre at the Red Cross Society National Headquarters are targeting inherited rare disease and providing genetic testing and counselling services for specific cases.

Direct to consumer testing is a rapidly growing industry in India. Genetics tests such as single-gene, multi-gene, exome and genome sequencing, carrier and new-born screening, prenatal testing and preimplantation genetic diagnosis are all available – for a price. Genetic tests can cost anywhere between 3,000-100,000 INR. According to Dr V L Ramprasand, CEO of MedGenome, “In the initial years, we had to go from one specialist doctor to another to convince them of the possibilities of genomic testing. In the initial years till 2016-17 period, we could do hardly 500-600 tests. Now we do over 10,000 genetic tests a month”.

However, one area of concern is the lack of regulatory oversight to monitor the use of genetic tests, and companies that offer direct-to-consumer testing can market their services without regulation. This lack of oversight is concerning as genetic counselling and proper interpretation of results are essential to ensure individuals are properly educated and informed about what results mean. Moreover, risk factors may be overstated, and inappropriate treatment, be that prescriptions or recommended lifestyle changes, may result in other problems and unnecessary stress.

Notable projects

  • Indigen Project – Genomics for Public Health in India: An initiative run by the Council of Scientific and Industrial Research (CSIR) which aims to perform whole genome sequencing of 1,000 Indian genomes across diverse ethnic groups for clinical applications in rare genetic diseases.
  • Indian Genetic Disease Database (IGDD): A patient-based database of disease-associated variants in the Indian population categorized into different therapeutic areas. The current version covers over 100 diseases.
  • Indian Genome Variation Database (IGVdB): A SNP and repeat polymorphism database of the Indian population with haplotype maps based on large multigeneration families. IGVdB is run by the Council of Scientific and Industrial Research (CSIR), with funding from the Central Government.
  • GWAS Central – India: A genotype-phenotype association database with summary level findings from genetic association studies.
  • Index-dB: Open-access database of exomic variants of Indian individuals, identified using whole exome sequencing. Has a variant browser feature allowing users to search and visualize genomic information, with detailed associated features and information about underlying disease biology.
  • TMC-SNPdB: A germline variant database generated from the exome data of normal samples from tongue, gall bladder, and cervical cancer patients in India.
  • SAGE: A comprehensive resource of genetic variants of 1,213 South Asian genomes and exomes. This data contains more than 154 million variants, 69 million of which were novel variants at the time (2018).

Notable organisations and companies

  • Mapmygenome: Indian genomics company providing a number of genetic tests including NGS, qPCR, microarray, splice variant analysis, SNP genotyping, as well as bespoke tailored services for individuals.  
  • Medgenome: A genetic testing lab in India aiming to bring precision testing solution for quicker diagnosis of complex diseases, including Whole Genome and Whole Exome Testing, offering over 1,300 different genetic tests.
  • Lilac insights: Genetic diagnostics lab in India specifically focussed on reproductive genetics, and cancer genetics. Services include prenatal genetic screening and diagnosis, as well as cancer genetic testing panels for solid tumours, haematological malignancies and sarcomas for diagnosis and prognosis.
  • CORE diagnostics: India-based diagnostics lab that provides diagnostic tests for a variety of diseases, including hereditary cancers, haematological disorders, reproductive genetics, cardiovascular diseases, endocrine disorders, kidney diseases, ophthalmologic conditions, and neurodegenerative diseases. CORE uses cytogenetics, NGS, Sanger sequencing, qPCR and more.

Notable individuals

  • Dr S.S Agarwal: Prominent Indian geneticist and former director of the Advanced Center for Treatment, Research and Education in Cancer, he pioneered medical genetics and clinical immunology education in India. He was an Emeritus Professor of the National Academy of Medical Sciences and was awarded the Shanti Swarup Bhatnagar Prize for Science and Technology, one of the highest Indian science awards.
  • Dr I.C. Verma: Senior Consultant at the Institute for Medical Genetics and Genomics, renowned specialist in Genetic Medicine and former Professor of Paediatrics and Head of Genetics Department at the All India Institute of Medical Science, which was recognised by the WHO Collaborating Centre in Genetics for outstanding performance.
  • Dr S. Phadke: Professor and Head of the Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences. She has greatly contributed to the establishment of medical genetics in India since 1996, having personally trained over 40 medical geneticists. She has also reported 10 new syndromes, and identified the causative gene in 4 of them, as well as authored the popular book “Genetics for Clinicians”.

The future genomics landscape

The future genomics landscape in India is promising. The genomics and pharmaceutical sector has already seen enormous growth in the past few years, with a 200% increase in foreign investment in 2020-21, according to The Economic Survey. While presenting the new Union Budget for 2022, Finance Minister Nirmala Sitharaman identified genomics as a key “sunrise” opportunity, and announced that the government will bring about policies that support and bolster domestic capacities for genomic medicine.

To encourage genomics investment, the government will promote thematic funds which blend private and public finances, with Nirmala Sitharaman saying, “Supportive policies, light-touch regulations, facilitative actions to build domestic capacities, and promotion of research & development (R&D) will guide the government’s approach. For R&D in these sunrise opportunities, in addition to efforts of collaboration among academia, industry and public institutions, government contribution will be provided.”

References

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