Genetic diversity and admixture patterns in Indian populations

Profile of Newly Diagnosed Childhood Glaucoma in India: Indian Childhood Glaucoma Study (ICGS) Group 1

OBJECTIVE

To report the profile of newly diagnosed childhood glaucoma using the Childhood Glaucoma Research Network (CGRN) classification, presenting over 1 year from across centers in India.

DESIGN

Prospective observational multicentric study.

SUBJECTS

Newly diagnosed children aged < 18 years diagnosed with childhood glaucoma according to CGRN criteria presenting between January and December 2019 to 13 centers across India.

METHODS

All children underwent a comprehensive ocular examination, including examination under anesthesia for younger children, and were diagnosed with childhood glaucoma as per CGRN. Data were entered in a standard Excel chart. Refraction and visual acuity assessments were done when feasible.

MAIN OUTCOME MEASURES

The profile of newly diagnosed childhood glaucoma in different parts of India and the severity of glaucoma at presentation.

RESULTS

A total of 1743 eyes of 1155 children fulfilled the definition of glaucoma and were analyzed. Primary congenital glaucoma (PCG) comprised the single largest group (34.4%), most of which were infantile onset (19%). Neonatal-onset PCG comprised 6.2% of all glaucoma. Secondary glaucoma constituted 53.4% of all glaucoma, one-half of which were acquired conditions (28%), followed by isolated ocular anomalies (14.7%), glaucoma after cataract surgery (6.7%), and glaucoma with nonacquired systemic diseases (4.5%). Of the 1743 eyes with glaucoma, all 3 parameters for severity grading were available in 842 eyes, of which 501 (59.5%) eyes presented with mild, 320 (38%) with moderate, and 21 (2.5%) with severe glaucoma. Nearly one-third of the children (28.5%) were not brought back for follow-up after the initial treatment given.

CONCLUSIONS

Our study has one of the largest numbers of consecutive children with glaucoma classified according to the CGRN classification. Despite a widely diverse population, the profile of childhood glaucoma was relatively uniform across India. Childhood glaucoma is a significant problem in India, primarily treated in tertiary care hospitals. The data presented may be the tip of the iceberg because we have only reported the children who reached the hospitals offering treatment for this challenging disease.

FINANCIAL DISCLOSURE(S)

The author(s) have no proprietary or commercial interest in any materials discussed in this article.

Understanding influences of culture and history on mtDNA variation and population structure in three populations from Assam, Northeast India

OBJECTIVES

Positioned at the nexus of India, China, and Southeast Asia, Northeast India is presumed to have served as a channel for land-based human migration since the Upper Pleistocene. Assam is the largest state in the Northeast. We characterized the genetic background of three populations and examined the ways in which their population histories and cultural practices have influenced levels of intrasample and intersample variation.

METHODS

We examined sequence data from the mtDNA hypervariable control region and selected diagnostic mutations from the coding region in 128 individuals from three ethnic groups currently living in Assam: two Scheduled tribes (Sonowal Kachari and Rabha), and the non-Scheduled Tai Ahom.

RESULTS

The populations of Assam sampled here express mtDNA lineages indicative of South Asian, Southeast Asian, and East Asian ancestry. We discovered two completely novel haplogroups in Assam that accounted for 6.2% of the lineages in our sample. We also identified a new subhaplogroup of M9a that is prevalent in the Sonowal Kachari of Assam (19.1%), but not present in neighboring Arunachal Pradesh, indicating substantial regional population structuring. Employing a large comparative dataset into a series of multidimensional scaling (MDS) analyses, we saw the Rabha cluster with populations sampled from Yunnan Province, indicating that the historical matrilineality of the Rabha has maintained lineages from Southern China.

CONCLUSION

Assam has undergone multiple colonization events in the time since the initial peopling event, with populations from Southern China and Southeast Asia having the greatest influence on maternal lineages in the region.

Perspectives on Translational Genomics and Public Health in India

It is now recognized worldwide that anticipation and prevention of diseases have significant advantages for the health and healthy ageing of the population. Early recognition of the disease in a vulnerable population such as in children aged <5 years and adults aged >60 years enhances our preparedness for any eventualities and future burden of the diseases to society. It is also recognized that current public health practices alone cannot bring about the desired outcome. When tackling public health-related issues, such problems must be recognized and state-of-the-art principles and innovations from genomic sciences, information technologies, and medical specialties must be encompassed and embraced. These will enhance strategies for preparedness and provide us with a better understanding of how to identify, manage, and control disease burdens. The ever expanding landscape of genomics research also includes experimental and computational approaches for effectively utilizing DNA sequence information. From these perspectives, the intricacies of Mendelian single gene disorders are the least challenging compared to intricacies of multi-dimensional host factors for infectious diseases or complex disorders such as cancer. The concepts of public health in India are on firm footing; however, integration of contemporary advances to implement public health principles into practice has neither been attempted nor impacted on disease burden or our preparedness to prevent eventualities. At the same time, translational genomics is gradually paving the way for personalized medicine. Principles of personalized medicine remain to be fully understood and practiced despite the pharmacogenomics-based future of drug development, and treatment has not been as exciting as the advances in genomics we are witnessing today. The relevance, importance, and translational impediments of these advances will be discussed.

Unity in diversity: an overview of the genomic anthropology of India

CONTEXT

India is considered a treasure for geneticists and evolutionary biologists due to its vast human diversity, consisting of more than 4500 anthropologically well-defined populations (castes, tribes and religious groups). Each population differs in terms of endogamy, language, culture, physical features, geographic and climatic position and genetic architecture. These factors contributed to India-specific genetic variations which may be responsible for various common diseases in India and its migratory populations. As a result, interpretations of the origins and affinities of Indian populations as well as health and disease conditions require complex and sophisticated genetic analysis. Evidence of ancient human dispersals and settlements is preserved in the genome of Indian inhabitants and this has been extensively analysed in conventional and genomic analyses.

OBJECTIVE AND METHODS

Using genomic analyses of STRs and Alu on a set of populations, this study estimates the level and extent of genetic variation and its implications.

RESULTS

The results show that Indian populations have a higher level of unique genetic diversity which is structured by many social processes and geographical attributes of the country.

CONCLUSION

This overview highlights the need to study the anthropological structure and evolutionary history of Indian populations while designing genomic and epigenomic investigations.

Population and genomic lessons from genetic analysis of two Indian populations

Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.