With recent advancements and a radical decline in sequencing costs, the popularity of next-generation sequencing (NGS) has skyrocketed. As costs become less prohibitive and methods become simpler and more widespread, researchers are choosing NGS over microarrays for more of their genomic applications.

Rising maturity in NGS systems and ancillary protocols such as library preparation and data analysis tools have certainly contributed to increasing its popularity among the research community. Whether it is a need for more accurate data, better resolution, pressure from granting agencies, or just plain fear of being left behind the technology forefront, it is clear that the demand for revolutionary sequencing technologies that deliver fast, inexpensive, and accurate genomic information has never been greater.

Microarrays' Proven Track Record

With all the advancements that NGS has made, why is anyone still using microarrays? The answer is, "lots of reasons!" Microarray platforms have a proven track record spanning nearly two decades in the lab. And with practice comes mastery – researchers have grown comfortable both with operating the technology and analyzing the results. Microarrays are generally considered easier to use with less complicated and less labor-intensive sample preparation than NGS. The same goes for data analysis. While there are still many tools for data analysts to choose from, a general consensus has emerged on the major methods for processing the data. And, despite the rapid drop in the cost associated with NGS, arrays are still economical and yield higher throughput, providing significant advantages when working with a large number of samples.

NGS and microarray trends based on application needs. The relative fit of microarrays and NGS for key applications is based on a variety of factors such as application maturity, cost per sample, desired output, and research goals (e.g., discovery versus profiling).

Time to Make the Switch?

So when is it time to make the switch from microarrays to NGS? What factors should be considered when deciding between these two technologies? While researchers facing such choices may feel overwhelmed, it boils down to just a few key areas, such as research goals (e.g., discovery versus profiling), access to technology, maturity of applications, cost per sample, and desired throughput. For some applications, such as chromatin immunoprecipitation, the transition to NGS is nearly complete, while for others, like cytogenetics, the transition has barely begun.

Indian Market Dynamics

The Indian clinical microarray instruments and consumables market was valued at 12 crore in 2015-16, with consumables dominating with a 70 percent share. The government, which is a major buyer, did not place any orders in 2015-16. Three vendors are driving the segment in India: Illumina marketed by Premas Biotech; Affymetrix marketed by Imperial Life Sciences; and Agilent Technologies.

The segment may be viewed in three dimensions:

  • lCytogenetics, where the microarrays leverage the investigative power of SNP genotypes to reliably detect chromosomal imbalances of copy number and allelic homozygosity, which are commonly associated with genetic constitutional disorders.
  • lAgrigenomics, which transforms the future of agriculture with genomics. It has and will continue to help drive sustainable productivity and offer solutions to the mounting challenges of feeding the world's growing population. Agrigenomics technologies help plant and animal breeders and researchers identify desirable traits, leading to healthier and more productive crops and livestock.
  • lPersonal genomics is important for identifying the genetic predisposition of an individual for common diseases, carrier status for inherited diseases, familial traits and efficacy, and adverse reactions to common drugs.

Fast gaining popularity in India is chromosomal microarray analysis, a technique that can identify major chromosomal aneuploidy as well as submicroscopic abnormalities that are too small to be detected by conventional karyotyping. In contrast to the conventional karyotype, which detects primarily genetic abnormalities resulting from large changes in the number or structure of chromosomes, microarray analysis also can provide information at the submicroscopic level throughout the human genome. There are two types of microarrays used in clinical prenatal testing: comparative genomic hybridization (CGH) and SNP arrays. Although both of these techniques detect copy number variants, they identify different types of genetic variation. With each of these technologies, DNA from a fetal sample is hybridized to a DNA chip or array containing DNA fragments of a known identity (known sequences). The fetal DNA to be studied is typically derived from aminocytes or chorionic villi samples.

Imperial Lifesciences has had good success with leading diagnostic centers as Lal Pathlabs, Metropolis, Gangaram, AIIMS, SRL, SGPGI (Sanjay Gandhi Postgraduate Institute of Medical Sciences), and Manipal in adopting chromosomal microarray analysis in 2015-16. The ACMG guidelines, which recommend replacing karyotyping with chromosomal microarrays as first-line postnatal test, have contributed to their acceptance.

Advancing breakthroughs have been made with genomic solutions in noninvasive prenatal tests (NIPT). Evolving noninvasive screening options offer early genetic screening for chromosomal conditions using just one tube of blood – as early as 10 weeks into a patient's pregnancy. Other types of prenatal screening and diagnostic tests may require more than one office visit, multiple blood draws, or carry a higher risk of false positive results. Diagnostic tests, such as amniocentesis, provide definite results for most chromosome conditions but have an associated risk of miscarriage.

Dr Shiva Priya Eswaran, Senior Microbiologist, Fortis Flt. Lt. Rajan Dhall Hospital, New Delhi
Second Opinion
A Bright Future Ahead

"With the human genome sequence completion in 2001, many research areas emerged; one such area was identifying the regions of DNA, which control normal and disease states. Functional genomics is the study of gene function through parallel expression measurements of a genome. The most common tools used to carry out these measurements include complementary DNA microarrays, oligonucleotide microarrays, or serial analysis of gene expression (SAGE). Microarray analysis can be divided into two main steps – probe production and target (cDNA) production. Specific sequences are immobilized to a surface and reacted with labeled cDNA targets. A signal resulting from hybridization of the labeled target with the specific immobilized probe identifies which RNAs are present in the unknown target sample.

Microarray provides a basis to genotype thousands of different loci at a time, which is useful for association and linkage studies to isolate chromosomal regions related to a particular disease. This array also can be used to locate chromosomal aberrations related to cancer, such as segments of allelic imbalance, which can be identified by loss of heterozygosity. Gene microarray technology rests on the ability to deposit many different DNA sequences on a small surface, usually a glass slide (often referred to as a chip). The different DNA fragments are arranged in rows and columns such that the identity of each fragment is known through its location on the array. Two types of microarrays are gene expression microarray and tissue microarray (TMA). Techniques like Northern blot and reverse transcriptase-polymerase chain reaction (RT-PCR) allow testing for only a few genes per experiment. But microarray or global expression profiling not only looks at orders of magnitude more genes than was possible previously, but also has the advantage that the genes examined are not influenced by pre-selection of genes.

The technique, though limited at present in its applications due to the cost factor, may be used widely in future. Microarray is one of the most recent advances being used for cancer research to test the incidence of a particular marker in tumors."

Dr Shiva Priya Eswaran
Senior Microbiologist,
Fortis Flt. Lt. Rajan Dhall Hospital, New Delhi

 

Illumina has recently launched the GSA, a highly economical tool for genetic risk screening of large global populations. It offers genomic coverage and imputation performance across 26 continental populations and features approximately 50,000 hand-curated variants relevant to clinical research, including markers for pharmacogenomics, newborn screening research, risk profiling, and confirmation of putative clinical associations. Leveraging the 24-sample Infinium format, the array includes 660,000 markers, and allows for the cost-effective addition of up to 50,000 custom markers. It has found great acceptance in India. In USA, where it was first launched, the company received orders for more than 3 million samples of the new consortia-developed array. Initial customers include human disease researchers at The Broad Institute and deCODE Genetics, health systems Avera Health, Codigo46, Diagnomics, Eone Diagnomics Genome Center (EDGC), Sanford Health, and UCLA Health System, genomic service providers Centre National de Genotypage, Human Genomics Facility HuGeF, Erasmus MC, Life and Brain, and consumer genomics company 23andMe, Inc. The early adoption of the GSA, represented by these deals, illustrates the widespread market demand for genotyping products and the continued relevance of arrays in human disease and translational research. The value of the content on this array will lead to widespread use in clinical research, including precision medicine programs, predictive risk screening, large-scale genome-wide association studies, and in biobank sample characterization and quality control.

Premas Biotech, Illumina's Indian counterpart, too has had good success with GSA. The company is focused on microarrays for pre-natal genetic screening, and NIPT. Some of the clinics and translational research centers, which were its leading customers in 2015-16, were The National Institute of Biomedical Genomics (NIBMG), National Design and Research Foundation (NDRF); Sandor Life Sciences; Positive Bioscience, Lal Path Labs; and service providers as Genotypic Technology.

Agilent delivers industry-leading CGH and NGS solutions for pre-implantation and human genetics.

Way Forward

Microarrays have expanded far beyond their early uses as simple gene-expression profiling tools and now have applications that span the genomic gamut. While broad-based arrays are still attractive, such as those designed to look at genome-wide single-nucleotide polymorphisms (SNPs), biotech companies are creating focused arrays that contain subsets of genes known to be involved in various human diseases. These targeted approaches allow clinical researchers to use multiple microarrays as molecular diagnostic tests for a number of different disorders.

A quick perusal of the scientific and pop-sci literature will ultimately yield a number of articles with a relatively regular periodicity predicting the ultimate demise of microarrays, often to be replaced by some newer, advanced technology. Yet, here we are in 2016, assembling a 40-year or so retrospective. Seemingly the sky is still the limit for the technology that had some very simple beginnings and blossomed into a fundamental laboratory tool.


 

randox

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