Parents always imagine their children to be healthy, and mostly babies born to women of all ages are normal and healthy. Unfortunately, some women are at risk for giving birth to baby with birth defects or genetic conditions. There is a small chance for these problems in any pregnancy, but the risks may be greater than others in certain situations.
It is always considered better that even prior to a pregnancy i.e. during the planning stage the couple consults their OB/GYN care provider to assess the risks by asking the couple about their previous health and pregnancy history, and the health and reproductive history of others in the family. There are a number of tests that are available; the doctor shall recommend them prior to and during the pregnancy. There will be a number of screening tests to determine if the couple may be at an increased risk for delivering a baby with birth defects or inherited conditions. The tests themselves can give the complete analysis of chromosomes, DNA, RNA, genes, and/or gene products to determine whether an alteration is existent that is causing or is likely to cause a specific disease or condition.
What is genetics?
Genetics is the study of heredity. Heredity is the biological process in which a parent passes on certain genes into their children or offspring. Every child inherits some genes from both of his / her biological parents and these genes in turn show specific traits. Some of these traits may be physically seen such as hair & eye colour and skin colour etc. On the other hand some genes may also carry the risk of certain diseases and disorders that may pass on from parents to their offspring.
Reproductive genetics is a field of medical genetics which is integrated with reproductive medicine, assisted reproduction, and developmental genetics.
Scientific research has often shown that the genetic factors are implicated in many diseases. Multiple mutations have been associated with the disease risks, hereditary disorders, and cancer onset and progression. Several well-characterized genes, like HER2, ALK, EGFR, BRAF, and KRAS, are analysed in molecular genetic screening in today’s world, while others are being constantly discovered and investigated. As research continues to uncover the genetic variants associated with clinical outcomes, this information can lead to earlier diagnosis and more targeted treatment therapies.
NGS technology
Next-Generation Sequencing (NGS) is a state-of-the-art technology which analyses all the 24 chromosomes. NGS is a method in which the DNA sequence is tested to detect chromosomal imbalances related to previously identified chromosomal structural rearrangements and can also provide information of the other spontaneous chromosomal abnormalities that are associated with implantation failures, miscarriages, or live births with multiple abnormalities. The optimal accuracy for the testing is 99 per cent when performed on a blastocyst embryo biopsy (day 5/6).
NGS is the latest development in the genomic technologies, enabling investigation of causative mutations and evaluation of the risk level and prognosis. The advent of NGS has changed the molecular pathology paradigm, promising to transform the diagnosis, treatment, and drug development in the future.
“With a panel of genes or whole-genome sequencing, we are able to look at more alterations that might be driving the patient’s cancer than with non-NGS methods, so the inquiry is significantly broader for a lower price and faster turnaround time” Says Elaine Mardis, PhD, co-director of The McDonnell Genome Institute, Washington University School of Medicine.
Advantages of NGS technology
NGS has offered several advantages over traditional approaches such as Sanger sequencing, PCR, amplicon testing, and single-gene assays. The single-gene tests can be labour intensive, costly, and time-consuming processes, and sometimes does not provide answers, requiring further follow-on tests. Such sequential testing might be limited to tissue availability and might require additional biopsies.
In a data published by ThermoFisher Scientific, it is said that NGS offers quick turnaround time and takes only about four hours to complete a run. This time can be different for different platforms and is also based on the number of sample tested in that run. NGS is perfect for:
n Interrogating more than100 genes at a same time, cost effectively.
n Finding novel variants by expanding the amount of targets sequenced in a single run.
n Sequencing samples that have low input amounts of starting material, using, for example, Ion AmpliSeq library preparation, which requires as low as 10 ng of input DNA.
n Sequencing microbial genomes for pathogen subtyping to assist research of critical outbreaking situations.
The growing adoption of NGS technology and the integration of sequencing standards into lab practices reflect the scientific community’s commitment to make molecular testing an integral part of routine clinical practice. Technological advancements have caused sequencing to become more accessible to even small academic and reference labs; with user-friendly desktop instrumentation that circumvents the need for highly trained sequencing experts. With recognition from the leading researchers, medical professionals, and regulatory organizations, NGS is becoming a widely advertised technology for the future of human health.
How NGS improves reproductive outcomes?
NGS enables more in-depth analysis of the genome than ever before, revealing new biological insights, with its unprecedented throughput, scalability, and speed. “NGS offers a faster, more exhaustive, up- to-date method with more decisive performance and higher throughput capabilities for obtaining DNA data than embryo morphology-based analysis” as quoted by illumina.
Extensive application of NGS in clinical Preimplantation genetic screening (PGS) cycles demonstrates that this methodology is reliable, allowing identification and transfer of euploid embryos resulting in ongoing pregnancies. The four main advantages of NGS over classical sequencing technology are:
n speed
n cost
n sample size
n accuracy
NGS is significantly cheaper, quicker, requires significantly less DNA and is more accurate and reliable than Sanger sequencing. NGS is quicker than other sequencing in two ways.
Firstly, the chemical reaction may be combined with the signal detection in some versions of NGS, whereas in other sequencing these are two separate processes. Secondly and more significantly, only one read (maximum ~1kb) can be taken at a time in other sequences such as Sanger, whereas NGS is massively parallel, allowing 300 GB of DNA to be read on a single run on a single chip.
The reduced time, manpower and reagents in NGS mean that the costs are much lower than the other sequencing techniques.
Importance of NGS in reproductive genetics
“This whole new level of access to DNA information has assembled several important breakthroughs, making significant impacts in reproductive and genetic health studies, particularly in the field of IVF, only with the help of NGS technology” as quoted by illumina.
With the advanced age , we see women have become more career oriented and often wait to settle down first and then plan their baby, at a later age infertility increases so does the demand for IVF and assisted reproductive techniques increases. Chromosome aneuploidy (abnormal number of chromosomes) is a major cause of IVF failures. Most embryos with aneuploidy are not implanted, and those embryos that are implanted are often miscarried during the first trimester of the pregnancy.
PGS is used to identify euploid embryos i.e. the embryos with a normal number of chromosomes, increasing the chances that a viable embryo is chosen for transfer during the IVF, which results in better implantation rates, reduced spontaneous abortions and increased ongoing pregnancy rates.
PGS using NGS delivers highly detailed, accurate, and measurable results for improved selection of euploid embryos over visual assessment alone.
NGS platform enables a wide range of applications, allowing researchers to investigate the genome, transcriptome, or epigenome of any organism.
Innovative NGS sample preparation and data analysis options enables a wide range of applications. For example, next-generation sequencing allows you to:
n Sequence whole genomes with high speed
n Zoom in to intensely sequence target regions
n Sequence cancer samples to find rare somatic variants, tumour subclones, and more
n Study microbial diversity in human beings.
NGS is a new technology for comprehensive chromosome testing of IVF embryos. NGS for PGS has replaced all other ongoing technologies due to lower cost and reduced errors by examining the embryo cells, physicians are able to determine whether it has any chromosomal abnormalities. For some patients it is the only possibility for having healthy offspring.
Endometrial Receptivity Analysis
Endometrial Receptivity Analysis (ERA) is another personalized genetic test to diagnose the state of endometrial receptivity in the window of implantation. The ERA test is also performed with NGS technology. The change in technology used in ERA, from Arrays to NGS, has not only increased the sampling capacity to be processed, but it also shows the development of a new and improved predictor, which also allows to enhance the effectiveness of the diagnosis and to add other additional tests.
The data obtained from analysing more than 12,000 samples with ERA was used to develop this new predictor. This enables us to define more clearly each one of the endometrial profiles and their subcategories in relation to the clinical objective of pregnancy and the birth of a child.
Meanwhile, the degree of flexibility in the analysis with NGS technology is a lot higher. This enables the addition of extra tests, such as the endometrial microbiome, which will soon be performed on the same sample, in turn supplementing and improving the data obtained from the ERA test.
Conclusion
Over the last decade, advances in genomics have found a way to an improved understanding of disease biology, which, in turn, has led to new approaches of diagnosing and treating the disorders.
The adoption of sequencing-based methods continues to grow, reducing the time and costs for molecular testing procedures and offering the potential for more specific, individualized patient assessment. This revolution in health care will lead to a shorter time for diagnosis and more effective therapies, ultimately saving many lives.
NGS has enabled significant drills in reproductive and genetic health, notably in IVF, setting a new standard in PGS, improving IVF success rates, and changing the patients’ lives.
(The author is laboratory manager at Igenomix India)