Long Read Sequencing for Basic Research

CD Genomics is a leading provider of custom solutions for long-read sequencing. We help customers accelerate their basic research by leveraging the ability of third-generation sequencing platforms to evaluate large and complex regions of the genome. We provide you with reliable genome assembly, full-length transcript detection, and base modification detection, etc.

Long-read sequencing is a DNA sequencing technology that can sequence longer DNA fragments compared to traditional short-read sequencing methods. Although short-read sequencing can capture most genetic variations, long-read sequencing can detect complex structural variations that are difficult to detect with short reads, including inversions, deletions, or translocations of large fragments, some of which are related to genetic diseases. Related. Currently, long-read sequencing is widely used in basic research such as epigenomics, epitranscriptomics, transcriptomics, and genomics. Long-read technology can help resolve complex genomic regions by sequencing thousands of bases:

• Resolve previously difficult-to-map genes or genomic regions, such as those containing highly variable or highly repetitive elements.
• Perform phased sequencing to identify co-inherited alleles, haplotype information, and phased de novo mutations.
• Generate long reads for applications that de novo assemble and construct genome completion maps.

Fig. 1. Long-read data provide insights into the biological relevance of structural variation. (Logsdon et al., 2020)

Our Long Read Sequencing Solutions for Basic Research

CD Genomics proudly offers long read sequencing solutions for basic research based on the PacBio SMRT sequencing and ONT Nanopore sequencing platforms. Our extensive experience in the sequencing industry puts us at the forefront of this development. Notably, our solutions are highly customizable and flexible, and we will design the best long read sequencing solution for your basic research in epigenomics, epitranscriptomics, transcriptomics, and genomics.

Solutions include but are not limited to:

• Genome Assembly

We have become very proficient in the use of long-read sequencing for genome assembly. For species with available reference genomes, long read sequencing can be used to narrow genomic gaps, especially in the human genome. In addition, long-read sequencing allows the resolution of genes or genomic regions that are difficult to map, for example, genes or genomic regions that contain highly variable or highly repetitive elements.

• Constructing New Reference Genomes

Our strength lies in our ability to make genome assembly of genomes of all sizes more time and cost-effective.

We can use long-read sequencing to assemble initial reference genomes for many non-model organisms. For example, Rickettsia, Maccullochella sellii, Amphiprion ocellaris, Maniola jurtina, Varanus komodoensis, Pavo cristatus, Panthera leo, and Eumeta heterochromatica, to name a few.

We can use long-read sequencing to construct RNA viral genomes while eliminating the need for traditional reverse transcription steps, including Mayaro virus, Venezuelan equine encephalitis virus, chikungunya virus, Zika virus, vesicular stomatitis Indiana virus, oropouche virus, influenza A, and human coronaviruses.

• Chromatin Conformation

Linear chromatin undergoes multiple folding and condensation into the nucleus of eukaryotic cells, and chromatin structural domains and loops are important elements of chromatin structure and dynamics. The three-dimensional conformation of chromatin affects gene expression during development, evolution, and disease. CD Genomics offers complete long-read sequencing solutions for studying chromatin conformation, including genome-wide assessment of combinatorial chromatin interactions, disease rearrangement reconstruction, and de novo genomics, etc. We ensure that you get a panoramic view of chromatin interactions, which can provide critical information on the impact of chromatin structure on transcriptional regulation.

• Splice Variation

Splice variants play an important role in increasing proteomic diversity and cellular function within cells. Splice variants are also associated with disease states and may play a role in their etiology. The development of long-read sequencing technologies has provided powerful tools for studying selective splicing, heterodimer expression, genome assembly, and the detection of complex structural variants. CD Genomics provides professional long read sequencing solutions for splice variants, allowing full-length transcript recovery and quantification, enabling transcript-level analysis of alternative splicing processes and how these processes change with cellular states.

• Recognizing Large Structural Variants

Structural variants (SV) represent genomic rearrangements, including large insertions, deletions, inversions, duplications, translocations, and complex combinations of these mutations, and are the largest form of genetic variation in the human genome. SV is closely linked to gene regulation, evolution, phenotype, and human disease. CD Genomics offers long-read sequencing to comprehensively detect SV at higher resolution.

• Characterizing the Full-Length Transcriptome

Full-length sequences improve genome annotation to identify gene structures, regulatory elements, and coding regions, and serve as an ideal method to characterize transcriptional isoforms within a target gene or across the entire transcriptome. CD Genomics provides professional Full-Length Transcript Sequencing (Iso-Seq) service that can help you obtain more accurate transcript information and identify more variable splice sites, novel loci, new isoforms, fusion genes, etc.

• Characterizing Epigenetic Markers

CD Genomics provides Epigenetics and Methylation Analysis Using Long-Read Sequencing service to characterize the methylation groups of different biological samples, such as 6mA in microbial reference communities, and 5mC and 6mA in the genomes of E. coli, Chlamydomonas reinhardtii, and humans. This epigenomic analysis can be performed in a haplotype-resolved manner and will therefore be informative for the discovery of allele-specific methylation associated with imprinted genes, as well as stereotyped genomic variants and chromatin states, even in heterogeneous cancer samples.
CD Genomics is committed to exploiting the potential of long-read sequencing to ensure that our customers remain at the forefront of basic research. If you have any questions, please feel free to contact us. We look forward to working with you on projects of interest.

Related Services

PacBio SMRT Sequencing
Oxford Nanopore Sequencing
Human Genomics with Long-Read Sequencing
Human Genome Structural Variation Detection
Full-Length Transcript Sequencing (Iso-Seq)
Epigenetics and Methylation Analysis Using Long-Read Sequencing