The RNA-Seq (RNA sequencing) program at The Hospital for Sick Children (SickKids) is focused on developing new tools for Pediatric Rare Disease research. Their clinically approved RNA sequencing platform combines RNA and Genome sequencing methods to create personalized medicine. The study also reviewed the applicability of Trio RNA sequencing methods in identifying mutations causing inherited diseases in a family.
The last decade’s advancement in Next-Generation Sequencing (NGS) has allowed researchers to perform genome and exome sequencing for several diseases. Genome Sequencing is the most preferred approach for sequence analysis due to its low cost and ability to produce fast and accurate data. Genome Sequencing can review around 90% of the human genome, and recent advancements in the field have highlighted the use of genomic sequencing for several other areas.
Genome Sequencing can identify conventional and complex mutations, coding variants, intronic variants, and tandem repeats. Though Genome Sequencing methods can identify almost all types of mutations in coding regions, their interpretation in the non-coding regions of the genome remains an issue. DNA and RNA sequencing can bridge the gap by identifying variants of unknown significance (VUS). This can help researchers decipher the inheritance pattern behind rare pediatric diseases.
Genome Sequencing for Rare Pediatric Diseases
The incidence of rare diseases is very low, and about 7000 rare disorders have been identified. Several other diseases remain undiagnosed. It has been seen that most of them are of genetic origin. Lack of research and insufficient data regarding the rare disease makes its diagnosis extremely difficult. It takes around 4 to 5 years to diagnose a rare disease correctly.
With pediatric rare disease research gaining momentum over the last few years, new and advanced technologies are being incorporated for accurate and timely diagnosis of disease. Research and development for rare pediatric disorders can help parents make informed decisions regarding the risk of transmission of the disease to offspring. In-depth information on the inheritance of the disease in offspring can aid in devising a proper management plan, from diagnosis to adequate treatment. Researchers at The Hospital for Sick Children (SickKids) have designed a revolutionary technique to use RNA sequencing methods in the research process.
Pediatric rare diseases lack a streamlined treatment plan due to their low occurrence. Drugs and treatments are available for some diseases. Early detection and appropriate treatment for diseases, like in the case of Phenylketonuria (PKU), have been helpful in disease management in newborns. PKU is an inherited congenital disability where amino acid phenylalanine levels are increased in the blood, leading to intellectual disabilities. Newborn screening for PKU, along with dietary treatment, has been very helpful in controlling the disorder.
Enhancing Prognosis Through DNA and RNA Sequencing
Though DNA-based genome sequencing helps us understand the genetic makeup of a person, RNA-Seq analysis gives us an understanding of the transcriptome of an organism. In a particular biological state, a set of RNA is transcribed. The collection of all RNA in that state is termed a transcriptome. Transcriptome analysis allows us to detect coding and non-coding RNA to give us an idea of the molecular mechanism behind a particular biological process, such as the incidence of a particular disease.
RNA-Seq is done by first isolating the RNA and converting it into cDNA fragments by adding connectors to one or both ends. This is followed by sequencing the cDNA fragments and ligating the sequencing adaptors to the fragments. Fragments undergo PCR amplification, forming an RNA-Seq library, and can be sequenced on the NGS platform.
Advantages of RNA sequencing and its applications
1. It is highly sensitive and can easily identify all transcripts within the cell.
2. It can accurately identify the individual nucleotide of a transcript.
3. It doesn’t require a probe to carry out mapping or identifying transcriptomes
RNA-Seq application includes the determination of spliced transcripts, observing post-transcriptional modifications, and identifying changes in gene expression, mutations, and gene fusion. In combination with various improved DNA sequencing methods, RNA sequencing presents a greater opportunity to identify rare genetic diseases. With the reduced cost of sequencing, RNA-Seq may replace microarrays for certain applications.
Researchers at The Hospital for Sick Children (SickKids), along with Brock University, performed genome sequencing using their state-of-the-art RNA sequencing method. They were able to detect patterns of genetically inherited RNA. The researchers have been trying to harness the information stored in the RNA and device-appropriate RNA-testing diagnosis in the field of rare Pediatric diseases. They also revealed RNA sequencing method, along with genome sequencing, could identify the transmission pattern of variants from parents to offspring.
A recent study published in the American Journal of Human Genetics states Trio based RNA-seq method can be used to identify mutations by performing RNA sequencing on the offspring along with both parents. The study performed genome analysis as well as RNA-seq on 97 individuals with rare medical conditions, and RNA-seq identified two mutations. The researchers also found that Trio RNA-seq analysis failed to identify any new mutation apart from the existing ones. The study further supported the need for singleton RNA-seq methods.
TRIO RNA sequencing
Trio-based RNA sequencing method can be advantageous in detecting Rare Pediatric Disorders. It may detect genetic mutations like insertions, deletions, and single nucleotide variants by analyzing several genes simultaneously and classifying them as dominant or recessive diseases. Recessive diseases are often caused when the offspring inherits two mutated copies of genes from both parents. Whereas dominant disease is a result of direct transmission of the dominant gene from affected parents. RNA-Seq can also detect unique mutations in offspring that are absent in parents.
Research in the field of rare Pediatric diseases has gained much attention over the past few years. Pediatric genomics is largely unknown. Advanced Computational techniques are being incorporated into research workflows through genome sequencing methods to reduce the time for diagnosis and help in better management of a disease. This has helped several affected families to understand the complicated nature of inherited diseases. A detailed understanding of the molecular mechanism of the disease can produce better treatments.
Sipra Das is a consulting scientific content writing intern at CBIRT who specializes in the field of Proteomics-related content writing. With a passion for scientific writing, she has accumulated 8 years of experience in this domain. She holds a Master's degree in Bioinformatics and has completed an internship at the esteemed NIMHANS in Bangalore. She brings a unique combination of scientific expertise and writing prowess to her work, delivering high-quality content that is both informative and engaging.