What You’re Missing Matters: Summit India 2026

Recent viral outbreaks in many areas of the World is an important reminder of the difficulties of predicting when and where the next outbreak will occur. These also highlight the need to greatly expand our ability to rapidly identify and stop these threats. The 2013-16 Ebola outbreak took many months to detect, and it expanded in part due to the lack of local diagnosis. Similarly, despite regular disease outbreaks by known agents in many places in the world, many more viruses (known and unknown) are cryptically circulating and undetected.

Infectious diseases are often characterized by fever, and are among the most common causes of morbidity and mortality in tropical developing countries. They have devastating burden on the African continent, because differentiating the causative agents of fevers are challenging. Advances in genomic technologies have revolutionized biomedical research, and created the potential to transform the clinical care, surveillance, and understanding of infectious diseases.

Researchers at the African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s university, Ede, Nigeria, are translating microbial genomics knowledge and technologies into new field deployable diagnostics tools that can rapidly test for a wide array of known and novel microbes simultaneously. These tools are helping local health workers to perform diagnosis and treatment of patients by the patients’ bedsides and prevent outbreaks from escalating. These new developments lay the groundwork to pursue key scientific questions about the pathophysiology, epidemiology, transmission, evolution, and biology of the microbes causing disease.

In this presentation, we provide insights into how we are using new genomic knowledge and technologies to: 1) build Africa capacity and leadership toward preparedness and containment of future infectious diseases outbreaks;2) promote state-of-the-art genome sequencing and field-deployable genetic tools for microbial infections detection in West Africa, and 3) enable a surveillance network for some of the world’s greatest global health threats.

Rare genetic disorders continue to be a cause of illness and death in children in India but getting fast cheap genetic tests is hard. This talk describes the goals and results of the national Mission program for genetic disorders in children. It also explains how these goals match with the DBT-UMMID initiative to improve medicine all over the country. The Mission program has made it possible for about 3,000 families to get exome sequencing. This has led to finding 10 genes linked to diseases. It has also given families answers that help with their medical care planning and talking with counselors. A major part of the work has been checking out changes in genes that clinicians are not sure about. We use computer predictions looking at how the genes pass through families and do laboratory tests to understand these changes better and make sure the answers are right. We also are making efforts to teach doctors, patients and people in charge how to recognize rare diseases better. These efforts help with referring patients to the higher centres and helping families who are affected. We are using Oxford Nanopore Technologies (ONT) as a way to check genetic changes. This is a choice instead of Sanger sequencing because it is easier to use, gives results quickly and costs less. The small size of the machines, ability to get results quickly and the lower cost make ONT good for institutes that don’t have a lot of resources. We are making a plan to create tests for parents before they have children. These tests will use ONT to find genetic problems in different parts of India. These tests can help find out if a person carries a gene for a disease. This helps parents make choices when they are planning to have children. It also helps reduce the number of genetic diseases. All these steps show a way to take discoveries and put them into action. They show that genetic tests can help make sure that children, with diseases get proper care in India.

Our research primarily leverages long-read, high-throughput metagenomic shotgun sequencing to establish early warning systems for public health threats like virus and bacteria. Our earlier studies in India to directly sequence SARS-CoV-2 viral fragments from open urban drains using the Nanopore MinION platform helped during covid-19 pandemic and later. We successfully caught mutations associated with the Delta variant lineage in wastewater samples as early as December 2020—months before they were widely flagged in clinical data. In long-term surveillance tracking post-Omicron phases up to 2024, we proved that wastewater analysis could spot critical viral spikes or "silent waves" and track highly diverse recombinant clades (like XBB) well in advance before they were clinically identified in patients. We also utilize high-throughput Nanopore sequencing to map urban "resistomes"—the collection of antibiotic-resistant genes spreading through wastewater systems in Pune metro city. I shall talk about some case studies on environmental surveillance using Oxford Nanopore Technologies.

South Africa is home to rich and extraordinary indigenous biodiversity, spanning three of the world's 36 recognised biodiversity hotspots. Yet its human population carries one of the world's highest disease burdens, including an estimated 3.6 million people living with a rare disease, many of whom face years-long diagnostic odysseys with no clear answer. The Centre for Proteomic and Genomic Research (CPGR), a national multi-omic technology platform, and its hosted programme, DIPLOMICS (DIstributed PLatform in OMICS), have built the continent’s largest long-read sequencing capacity and infrastructure, enabling researchers to pursue opportunities and tackle challenges facing South Africa. Two flagship programmes run on those Nanopore platforms. 1KSA, our national biodiversity genome sequencing project, generates de novo reference assemblies for indigenous South African species, supporting conservation, agriculture and national claims to digital sequence information (DSI). Nngwe applies long-read whole-genome sequencing and multi-omics to patients with rare and undiagnosed diseases, targeting the structural and repeat variation that short reads miss. Our infrastructure model, supported by Oxford Nanopore Technologies, centralises sequencing and bioinformatics, distributes sampling and expertise, and builds a talent pipeline that keeps African data in African hands. Real challenges remain: securing sustainable funding, accessing computing resources, and assembling complex genomes de novo. The common thread is simple: what you miss matters, whether it is a species never sequenced or a variant never seen.

India, with its population of 1.4 billion and over 5000 endogamous groups, represents a rich tapestry of ethnolinguistic, geographic and genetic diversity. However, global sequencing consortia often rely on diaspora samples, leading to a severe underrepresentation of the subcontinent’s genetic architecture in genomic datasets. This bias hinders the equitable delivery of precision medicine across the Indian population. Furthermore, existing short-read Indian genomic datasets do not fully capture structural variants (SVs), which encompass diverse classes of genomic rearrangements of ≥50 bp and contribute substantially to human genetic diversity. To address these gaps, we used Oxford Nanopore Technologies (ONT) to generate long read sequences of over 450 genomes from self-declared healthy individuals across India. Our sampling strategy ensured comprehensive geographical coverage and represented all four major linguistic groups: Indo-European, Dravidian, Tibeto-Burman, and Austroasiatic. This is the first large-scale long-read genomic study of its kind in India. Leveraging the gapless CHM13-T2T reference genome, we identified more than 250,000 SVs, a significant proportion of which are novel to existing global databases. Notably, we discovered many high-confidence SVs located within complex, repeat-rich regions previously inaccessible to short-read based studies. Our work provides a foundational India-specific SV resource that serves as a baseline for clinical variant comparison, improving variant interpretation and advancing public health genomics and precision medicine in India.

Tandem nucleotide repeats represent a highly dynamic and polymorphic class of genomic variations. While traditionally challenging to analyze, expansions in these repetitive elements are now recognized as the primary molecular drivers for a growing number of severe neurodegenerative and neuromuscular disorders, including various spinocerebellar ataxias, Huntington’s disease, and forms of Parkinsonism. Despite their clinical significance, the full pathogenic landscape of tandem repeats has remained partially obscured by the technical limitations of conventional short-read sequencing, which often fails to accurately resolve these complex regions. I will speak about the critical role of tandem nucleotide repeats in the pathogenesis of neurodegeneration. I will highlight the transition from legacy diagnostic techniques to advanced, high-throughput methodologies, specifically focusing on the utility of long-read sequencing technologies, such as Nanopore sequencing. By utilizing targeted, multi-gene panels, we can now simultaneously characterize tandem repeat expansions and single nucleotide variations across hundreds of candidate genes associated with neurological phenotypes. The talk will examine the mechanisms by which tandem repeat expansions induce neurotoxicity, including RNA toxicity, repeat-associated non-ATG (RAN) translation, and protein loss-of-function. We will also address the clinical implications of these findings, demonstrating how the precise sizing of repeat tracts and the identification of sequence interruptions can influence disease penetrance, age of onset, and phenotypic severity.

Long-read sequencing (LRS) has rapidly evolved in accuracy and throughput, enabling the detection and resolution of genomic and epigenomic variation that remains challenging for conventional short-read approaches. LRS has the potential to serve as a unified platform for clinical genomic testing, particularly in rare disease diagnosis, where a substantial proportion of patients remain undiagnosed. I will present our work on a cohort of previously undiagnosed pediatric patients with rare diseases where whole genome LRS improved pathogenic and novel variant discovery by resolving complex genomic variation and expanding the range of detectable variant types. Building on this, I will show how whole genome LRS followed by targeted genomic and epigenomic profiling in hypotonia and muscle weakness enhanced timely comprehensive variant discovery, demonstrating the application of targeted LRS analysis (LRS genome slice) for highly heterogeneous diseases with known genomic and epigenomic disease loci. Ongoing projects also include targeted long-range PCR to enrich for complex loci, such as thalassemia, as well as targeted adaptive-sampling LRS for cost-effective premarital screening. By combining the breadth of genome-wide long-read sequencing with the focused resolution and efficiency of targeted approaches, LRS has the potential to bridge current diagnostic and screening gaps and enable more comprehensive, timely, and scalable genomic testing.

Comprehensive diagnosis of acute leukemia currently depends on several parallel techniques — morphology, immunophenotyping, cytogenetics, FISH and molecular assays — a workflow that is expensive, operationally fragmented and slow to deliver a final subtype assignment. This is a particular problem in high-volume centres in low- and middle-income countries, where the full panel of tests is often unavailable and therapy is initiated before classification is complete. DNA methylation offers an alternative route, since lineage and subtype-defining epigenetic signatures are retained across the major categories of acute leukemia. This talk will discuss how low-pass whole genome sequencing on nanopore platforms can be used to obtain methylation profiles suitable for classification, the computational approach required to work with data of this kind, and the practical considerations of running such an assay in a diagnostic laboratory: turnaround time, cost per sample, and the feasibility of deployment across multiple centres.

Modern treatment protocols in acute leukemias risk stratify patients based on genomic characteristics of tumor cells. Comprehensive genomic characterization requires techniques like flow cytometry, karyotyping, fluorescence in situ hybridization (FISH), targeted PCR panels, and microarrays. Comprehensive classification of pediatric cancer using single platform short-read RNA sequencing is established in research settings, allowing determination of leukemia lineage, genomic subtypes, small mutations, and aneuploidy. However implementation in clinics is challenging due to higher infrastructure costs and scales of economy. Oxford Nanopore Technology based sequencing promises to be a cost-effective sequencing approach to improve comprehensive pediatric cancer diagnosis in LMICs. We used transcriptome sequencing, adaptive sequencing and methylation classifiers to subtype and classify acute leukemias.