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Long-read sequencing for Cancer Provides New Insights into Difficult Region Detection

TAIPEI, TAIWAN, Feb.28, 2023- Cancer is a complex disease that results from the accumulation of genetic alterations in cells, leading to uncontrolled growth and proliferation. These genetic alterations can be difficult to detect and characterize, particularly in regions of the genome that are challenging to sequence using traditional methods. However, advances in long-read sequencing technologies are now enabling researchers to more accurately and comprehensively analyze these difficult regions, providing new insights into the biology of cancer.

Long-read sequencing technologies, such as Pacific Biosciences' (PacBio) single-molecule real-time (SMRT) sequencing and Oxford Nanopore Technologies' nanopore sequencing, offer several advantages over traditional short-read sequencing. One of the key advantages is the ability to sequence much longer DNA fragments (over 5,000 and up to millions of base pairs), which enables researchers to capture more complex and difficult-to-sequence regions of the genome. Long-read sequencing also produces higher-quality data with fewer errors and can help resolve complex genomic rearrangements that are difficult to detect with short-read sequencing.


In cancer genomics, long-read sequencing is particularly useful for analyzing regions of the genome that are highly repetitive or structurally complex, such as centromeres, telomeres, and other heterochromatic regions. These regions are often associated with important cancer-related genes, but their complex structure and repetitive nature have made them difficult to study using traditional sequencing methods.


For example, a team from the University of British Columbia, Canada's Michael Smith Genome Sciences Centre, and BC Cancer shared their findings associated with long-read sequencing and breast cancer structure variants in the European Journal of Human Genetics. The team used long-read sequencing to identify genetic alterations in individuals with breast cancer-related genes. The study identified 14 copy number variants in moderate- or high-penetrance genes that were difficult to detect using traditional short-read sequencing. The researchers suggest that long-read sequencing can reveal complex rearrangements that may contribute to cancer susceptibility and are often underappreciated using traditional sequencing methods.


Long-read sequencing has also been used to study telomere length and structure in cancer cells. Telomeres are the repetitive DNA sequences at the ends of chromosomes that protect them from degradation and rearrangement. In cancer cells, telomeres are often shortened or rearranged, leading to genomic instability and increased tumor progression. Long-read sequencing can provide a more accurate and comprehensive analysis of telomere length and structure, enabling researchers to better understand the role of telomere dysfunction in cancer.


In addition to analyzing difficult regions of the genome, long-read sequencing can also be used to detect complex genomic rearrangements that are difficult to identify with traditional sequencing methods. These rearrangements, such as translocations, inversions, and deletions, are common in cancer cells and can drive tumor progression by altering the expression or function of key oncogenes or tumor suppressor genes. Long-read sequencing can provide a more accurate and comprehensive analysis of these complex rearrangements, enabling researchers to identify novel driver mutations and potential therapeutic targets.


Overall, long-read sequencing technologies are revolutionizing cancer genomics research by enabling researchers to more accurately and comprehensively analyze difficult regions of the genome. By providing a more complete picture of the genomic alterations driving cancer, long-read sequencing is helping to identify new therapeutic targets and improve patient outcomes. As the technology continues to evolve and become more accessible, it has the potential to transform cancer diagnosis and treatment in the years to come.




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