How Genetic Testing can Innovate Healthcare Delivery
Dr. V.L Ramprasad holds a Master’s Degree and Ph.D. from BITS, Pilani. He has worked as Scientist (Molecular Genetics) at Vision Research Foundation, Sankara Nethralaya and was handling Affymetrix and Illumina technologies at Spinco Biotech. He also worked as Principal Scientist at SciGenom Labs. He has 17 peer-reviewed publications to his credit.
Though in a nascent stage, precision medicine is evolving at a fast pace. There are many labs set across the country and world which offer genetic testing at an affordable fee. Moving from a traditional medical model of treating pathologies to an individualized predictive and preventive model of personalized medicine promises to reduce the healthcare cost on an overburdened and overwhelmed system. The increasing number of catalogs of causative and risk genes will provide a foundation for Personalized Medicine and pharmacogenomics. The advent of NGS has helped in bringing down the cost of genome sequencing to less than $1000. However, there are many other new technologies on development that will make the sequencing even faster and more economical.
The current medical model focuses on the detection and treatment of pathologies. Treating disorders, especially on advanced states, is very expensive for patients and society in general. The Human Genome Project not only provided the essential reference map for the human genome but also stimulated the development of technology and analytic tools to process massive quantities of genomic data. Thus, accelerated the early detection of disorders and the identification of pharmacogenetic markers to customize treatments. Furthermore, the Human Genome Project has significantly contributed to the discovery of numerous genetic markers, several human disease-specific genomes, including cancers. Because of increased discovery rate of clinically relevant biomarkers, the relevant application of conventional molecular diagnostic methods like low- and/or medium-throughput sanger sequencing is restricted as they cannot screen such a huge number of genetic markers with a limited tumor/disease specific material. The advent of next-generation sequencing (NGS) technologies has not only reduced sequencing cost by orders of magnitude, but also significantly increased the throughput with just a few or single cell. One such new development in pre-natal genetic testing is “pre-implantation genetic screening”.
Pre-Implantation Genetic Screening
Chromosome segregation during female meiosis is particularly error prone in humans. These chromosomal abnormalities also called as Aneuploidy, worsen with advancing age. Many of recent studies have demonstrated that aneuploidy rates in the oocytes of women over 40 are over 75%, whereas approximately a quarter of oocytes from women in their early 30s are chromosomally abnormal.[1] A majority of human embryos produced from such oocytes using in vitro fertilization (IVF) techniques are aneuploid and has been shown that they fail to implant in the uterus, although a minority do succeed in forming a pregnancy only to later miscarry.[2] Hence, reliable identification of euploid (healthy) embryos is inevitable, but the main obstacle to testing human embryos for aneuploidy is the extremely limited amount of tissue available for analysis. Thus, most methods currently available for the genetic analysis of pre-implantation embryos may not be suitable and suffer from shortcomings which limit their clinical applicability. A few chromosome screening methods applicable to single cells biopsied from pre-implantation embryos are available, but the high cost of testing has restricted their usage.[3] New advancements in NGS technology provided an excellent alternative tool for the identification of chromosomal abnormalities using a few or single cell.
Next Generation Sequencing (NGS)
Next-generation sequencing popularly referred to as ‘high-throughput sequencing’. The advent of next-generation sequencing (NGS) technologies in the context of pre-natal genetic testing provides highly accurate, low-cost diagnosis of aneuploidy in cells from human pre-implantation embryos and is rapid enough to allow testing without embryo cryopreservation. Many reports indicated NGS improves IVF success rates. Thus, NGS becomes a reliable aneuploidy screening method and has the potential to revolutionize pre-implantation genetic screening (PGS).[4]
Furthermore, NGS becomes an integral part of precision medicine as it provides a viable alternative for characterizing genomic aberrations in tumors/other human disease for predictive and prognostic purposes with its massively parallel sequencing capability. This specific advantage of NGS technology enables testing of multiple genes/clinically relevant biomarkers per tumor as the standard-of-care, which may not be feasible with low- and medium-throughput traditional techniques such as Sanger sequencing, pyrosequencing, allele-specific polymerase chain reaction (PCR).[5,6,7]
The predominantly used NGS technologies are from:
• Illumina (HiSeq 2500/4000/X Ten etc.)
• Roche Applied Science/454 Life Sciences
• Life Technologies (Ion Torrent/Proton)
• Pacific Biosciences (Sequel)
The application of NGS technology in genetic testing is enormously increasing because it requires a single input of relatively low-quantity DNA or RNA for the screening of multiple markers, in contrast to traditional sequencing technologies, which need cumulatively larger quantities of input nucleic acid. NGS can provide simultaneous screening of a variety of genomic aberrations such as single-nucleotide variants (SNVs), multiple-nucleotide variants (MNVs), small and large insertions and deletions, and copy number variation (CNVs) of the genes. However, the benefits offered by these NGS technologies come with several challenges that must be adequately addressed before they can be transformed from research tools to routine clinical practices. Integrating NGS into a clinical diagnostic setting requires thorough validation with respect to consistent performance and accuracy, as per the stringent regulations and guidelines established by the regulatory agencies governing the clinical laboratories.[8]
Genetic Testing is Now More Accessible
More than a thousand genetic tests are available today and the number is still increasing. Genetic test panels give patients an insight into diseases which they may have inherited and give them an understanding of what preventive measures need to be taken. The results help understand the chances of a person liable to get inflicted by a genetic disorder and passing it on to someone else and vice versa. An expert in genetics is the best person to seek advice from, for those wanting to take a genetic test as such tests include risks and have their limitations as well. There are many labs set across the country and world which offer genetic testing at an affordable fee. Though many test labs have been established and it has been made more accessible, it continues to remain an expensive affair for the middle and lower middle sections of society in India.
Precision Medicine
Precision medicine or ‘specific treatment’ helps researchers and doctors to understand the exact treatment they need to offer to the patients. The advent of precision medicine is moving us closer to more precise, predictable and powerful health care that is customized for the individual patient. The approach of personalized therapy involves having a deep understanding of the unpredictability in a person’s genes, his/her environment and lifestyle. A complete bespoke treatment with appropriate decisions customized to a person’s medical condition. The therapies adopted range from imaging to molecular diagnostics and analytics/software and will be in accordance with the person’s genetic analysis. As mentioned previously, NGS becomes an integral part of precision medicine because of its high throughput and multiplexing capabilities which enables to analyze many clinically relevant markers across many samples.
The Future
Though it’s a nascent stage, precision medicine is evolving at a fast pace. Moving from a traditional medical model of treating pathologies to an individualized predictive and preventive model of personalized medicine promises to reduce the healthcare cost on an overburdened and overwhelmed system. The increasing number of catalogs of causative and risk genes will provide a foundation for Personalized Medicine and pharmacogenomics. The advent of NGS has helped in bringing down the cost of genome sequencing to less than $1000. However, there are many other new technologies on development that will make the sequencing even faster and more economical, such as Oxford Nanopore technologies (GridION™ System based on nanopore-based sensing). The future perspective of this advanced technology may reduce the cost of screening diseases specific gene panel to $100 within a time-frame of an hour. Research is proving that the therapies which are intended for one type of cancer could, in the future, be used to treat other types of cancers, on the premise of changes occurring in a person’s DNA. Discovery of mutations via sequencing and optional treatments are some of the findings through the process of sequencing and these may offer much hope towards better customized treatments for individuals.
Refernces:
[1] Fragouli E, Alfarawati S, Goodall NN, Sánchez-García JF, Colls P, Wells D. The cytogenetics of polar bodies: insights into female meiosis and the diagnosis of aneuploidy. Mol Hum Reprod, 2011;17:286–95.
[2] Scott RT, Ferry K, Su J, Tao X, Scott K, Treff NR. Comprehensive chromosome screening is highly predictive of the reproductive potential of human embryos: a prospective, blinded, nonselection study.Fertil Steril,2012;97:870-5.
[3] Fragouli E, Alfarawati S, Daphnis DD, Goodall NN, Mania A, Griffiths T, Gordon A, Wells D. Cytogenetic analysis of human blastocysts with the use of FISH, CGH and aCGH: scientific data and technical evaluation. Hum Reprod 2011;26:480–90.
[4] Hong KH, Taylor DM, Forman E, Tao X, Treff NR. Development of a novel next-gen sequencing (NGS) methodology for accurate characterization of genome-wide mitochondrial heteroplasmy in human embryos. Fertil Steril 2012;98:S58–9.
[5] Roychowdhury S, Chinnaiyan AM. Translating genomics for precision cancer medicine. Annu Rev Genomics Hum Genet. 2014; 15():395-415.
[6] Previati M, Manfrini M, Galasso M, Zerbinati C, Palatini J, Gasparini P, Volinia S. Next generation analysis of breast cancer genomes for precision medicine. Cancer Lett. 2013 Oct 1; 339(1):1-7.
[7] Roper N, Stensland KD, Hendricks R, Galsky MD. The landscape of precision cancer medicine clinical trials in the United States. Cancer Treat Rev. 2015 May; 41(5):385-90.
[8] Jennings L, Van Deerlin VM, Gulley ML, College of American Pathologists Molecular Pathology Resource Committee. Recommended principles and practices for validating clinical molecular pathology tests. Arch Pathol Lab Med. 2009 May; 133(5):743-55.
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