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Exploring the Human Body's Genetic Diversity: The SMaHT Project's Revolutionary Approach

TAIPEI, TAIWAN, Jul 31, 2023- In an ambitious effort to uncover the genetic variations among different cells within the human body, the US National Institutes of Health (NIH) recently unveiled the Somatic Mosaicism across Human Tissues (SMaHT) program. This groundbreaking $140 million initiative, funded for at least five years, aims to amalgamate diverse sequencing technologies to tackle the challenge of identifying genuine genetic differences between cells of the ame individual and understanding their implications for health and disease. The SMaHT program brings together 14 technology development grantees and five genome characterization centers, making it a massive and pioneering investment in the realm of genomics research.

The primary objective of the SMaHT program is to create an extensive catalog of human somatic variation. Somatic variations refer to mutations unique to specific tissues, while mosaic variants are extremely rare within a tissue. By sequencing samples from a wide array of tissues, collected from around 150 individuals, including the brain, blood, skin, muscle, colon, spleen, uterus, vas deferens, ovaries, and testes, the project aims to uncover the genetic variations unique to each tissue type. Understanding these variations is critical in deciphering how they differ between individuals and populations, thereby shedding light on the interplay between genetics and human health.


The SMaHT project, while promising, is not without its challenges. One of the primary hurdles is identifying numerous very rare variants, many of which fall below the detection limit of conventional long- and short-read sequencing approaches. Innovative techniques like duplex sequencing, which verifies the authenticity of variants, will play a crucial role in this aspect. Moreover, assigning these variants to specific cell types requires the use of single-cell and high-resolution spatial methods. The project's success will also depend on evaluating different clonal populations for phenotypic traits, considering the context of epigenetic or multiomic data.


Researchers involved in the SMaHT program face the complexity of working with diverse tissue types, each with its unique architectural characteristics. As such, a one-size-fits-all approach is not feasible. Instead, the technology and methodologies used need to be informed by the specific tissue architecture. This necessitates a novel universe of variant identification, allowing researchers to explore uncharted territories of genetic research.


The SMaHT program brings together researchers from various institutions, each contributing unique tools and techniques to propel the project forward. Among these, the single-cell whole-genome amplification from BioSkryb is used to study cells that don't readily grow into large colonies for bulk sequencing. Additionally, duplex-consensus sequencing, a Tn5-based method, and Slide-seq, a spatial omics method, play vital roles in detecting rare variants and enhancing genomic resolution for spatial analysis of DNA, respectively.


A crucial aspect of the SMaHT project involves the integration of single-cell transcriptomics with other omics data layers, such as histone modification, DNA methylation patterns, and protein expression. This integration will aid in the comprehensive phenotyping of specific genotypes in the context of somatic mosaicism, enabling the determination of how somatic variants influence cell growth and function.


The SMaHT project presents the opportunity to study conditions like clonal hematopoiesis of indeterminate potential (CHIP). While often overlooked in standard pathology testing, molecular assays can reveal mutations in a significant proportion of cells, signifying an increased risk of certain disorders. Understanding the phenotypic traits associated with somatic genotypes will provide invaluable insights into how these cells behave differently and how they influence tissue function.


The SMaHT program stands at the forefront of human genomics research, promising to unlock the mysteries of genetic diversity within our bodies. By addressing the challenge of somatic mosaicism, the SMaHT project will revolutionize our understanding of human genetics, paving the way for groundbreaking discoveries in health and disease. As the SMaHT program progresses, its impact on the field of genomics will undoubtedly shape the future of personalized medicine and the quest to unlock the intricacies of the human genome.


References:

[1] Somatic Mosaicism Across Human Tissues (SMaHT)

[2] NIH Somatic Variant Detection Program to Develop Novel Assays, Computational Tools







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