Long Read Sequencing for Genetic Disease Research

Genetic diseases are health problems caused by one or more abnormalities in the genome. Many human diseases have a genetic component. Deciphering the causal relationship between single gene mutations and inherited diseases can provide important information for biochemistry, molecular biology, and medical genetics (such as genetic counseling) and the development of treatment strategies. CD Genomics is a leading global life sciences company providing professional long read sequencing solutions for genetic disease research. Our goal is to help our clients characterize different types of disease-causing mutations in individuals with genetic diseases.

Introduction to Genetic Diseases

A genetic disease is a disease caused in whole or in part by changes in the DNA sequence that deviate from the normal sequence. Genetic diseases can be caused by mutations in one gene, mutations in multiple genes, a combination of genetic mutations and environmental factors, or chromosomal damage. In genetic diseases, pathogenic variants range from small mutations (including single nucleotide substitutions or small nucleotide insertions/deletions) to large changes (including tandem repeat duplications, large deletions, translocations, inversions, transposable elements insertion or complex rearrangement). Therefore, different detection strategies are needed to identify different types of mutations. The widespread application of next-generation sequencing (NGS) technology has revolutionized the field of medical genetics. However, the short read lengths of currently used sequencing methods impose limitations on the identification of structural variants, sequencing of repetitive regions, phasing of alleles, and distinguishing highly homologous genomic regions. These limitations may significantly impact diagnostic gaps for patients with genetic diseases undergoing standard NGS such as whole-exome or even genome sequencing. Long read sequencing technology promises to overcome certain limitations of NGS-based research on human genetic diseases.

Fig. 1. Overview of the main advantages of current long-read sequencing approaches in medical genetics. (Mantere et al., 2019)

Solutions Offering at CD Genomics

Our advanced sequencing platforms, such as PacBio SMRT sequencing and ONT Nanopore sequencing platforms, are capable of generating long reads, often spanning thousands of base pairs. Our solution allows the characterization of complex genomic rearrangements in individuals with multiple genetic diseases. These disorders include autism spectrum disorders, Temple syndrome, congenital anomalies, glycogen storage disease type Ia, mental retardation and epilepsy, epilepsy, Parkinson's disease, Gaucher's disease, ataxia-telangiectasia, and severe immune disorders, etc.

Our long read sequencing solutions for genetic disease research are as follows.

• Tandem Repeat Amplification Sequencing

There are approximately 1 million tandem repeat sequences in the human genome. Alterations in tandem repeats are known to cause more than 30 human genetic diseases. Analysis of genome-wide tandem repeats using short-read sequences is difficult. We provide long read sequencing to analyze human genetic disease repeat sequences, identify repeat length and repeat structure, and characterize the association between repeat structure and clinical phenotypes. Our long read sequencing technology is a straightforward way to detect repeat changes in genetic diseases, with reads long enough to contain the entire extended repeat as well as flanking unique sequences.

• Detection and Characterization of Structural Variants

Smaller structural variants (e.g., TE insertions) or structural variants without copy number changes (e.g., inversions) in genetic diseases are difficult to identify by routine analysis. We provide long read sequencing to efficiently identify nascent chromosomal cleavage rearrangements and explore novel genetic variants missing from short-read data. We aim to discover many novel mutations causing human disease through the comprehensive detection of structural variants and indels.

• Haplotype Analysis

We offer long read sequencing technology to directly resolve haplotypes of two heterozygous single nucleotide variants in genetic diseases, allowing phasing of variants separated by many kb, even in full-length assemblies in diploids and phasing complex genomic regions. We can also use long read sequencing for preimplantation genetic diagnosis to directly phase parental genotypes by discrete single nucleotide polymorphism (SNP) genotypes for single-cell whole-genome haplotyping. reconstruction.

• Pseudogene Identification

Pseudogenes are sequences that resemble known functional genes but do not produce functional proteins. The human genome contains over 14,000 pseudogenes. We provide long read sequencing to study genetic disease-associated genes with highly homologous pseudogenes. These studies rely heavily on target enrichment by long-range PCR using primers that localize to rare mismatch sites and thereby distinguish genes of interest from their pseudogenes.

Advantages of Our Long Read Sequencing Solutions for Genetic Disease Research

• Allows detection and characterization of disease-causing structural variants (SVs), e.g., due to large inversions or translocations.
• Enables direct and more accurate sequencing of long tandem repeat amplification and extreme GC-rich regions.
• Enhanced phasing, i.e., assignment of genetic variants to homozygous paternal or maternal chromosomes, to identify inheritance patterns, parental origins of ab initio events, chimeras, allele-specific expression, and disease risk haplotypes.
• Distinguish clinically relevant genes from their pseudogenes.

CD Genomics is committed to providing accurate, comprehensive, and high-resolution long read sequencing solutions to accelerate genetic disease research. We aim to comprehensively characterize human genetic variation using real-time long read sequencing to aid in genetic diagnosis. 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 Mitochondrial DNA Sequencing
Human Genome Structural Variation Detection