Genomics has been revolutionized over the last few years after the successful development of second-generation sequencing (SGS) technology. Recently developed third-generation sequencing (TGS) technology is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes.

Technology Trends

Ten years ago, sequencing was based on a single type of sequencing that is Sanger sequencing. In 2005, NGS emerged and changed the view of the analysis and understanding of living beings. Increased throughput of sequencing and dramatic reduction in costs have led to NGS becoming a widely used genomic technology. Since the release of the first commercially available system with a throughput of 20 Mbp per run, the NGS has improved immensely. The current system is capable of producing 1.8 Tbp of sequencing data per run, nearly a 100,000-fold
increase within a 10-year period.

However, despite its achievements, NGS analysis is still too expensive and time-consuming a process to be carried out routinely on all patients. Over the last decade, considerable progress has been made on new sequencing machines. The demand for technologies that can operate at higher speed and produce longer reads has resulted in the advent of new sequencing approachesthe so-called TGS.

The potential of latest generation of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited. Nanopore sequencing is a promising technique for genome sequencing due to its portability, ability to sequence long reads from single molecules, and to simultaneously assay DNA methylation.

Today's short-read sequencing instruments can generate read lengths between 50-700 bp depending on the specific instrument. These high-throughput sequencing approaches have revolutionized genomic science, allowing hundreds and thousands of full genomes to be sequenced, and have become indispensable.

Unfortunately, these technologies are not well suited for identifying many of the rearrangements and copy-number variations. Long-read sequencing technologies can read contiguous fragments of DNA in excess of 10 kb
and are much better suited for detecting large structural events. The rapid sequencing speed and low upfront instrument cost are features drawing interest in these devices from the genomics community. For example, the MinION device, which is the smallest sequencing device currently available. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MinION has thus generated much excitement and interest in the genomics community.

Road Ahead

DNA sequencing has grown over time at significant pace with millions of sequencing analysis being done per day. This is all due to the technological expansion in this field that improves the speed, accuracy, fidelity, and magnitude of sequencing methods.

Latest, TGS machines are now available in the market, which measure the real-time addition of nucleotides to a single DNA molecule. Developing inexpensive and simple DNA sequencing methods capable of detecting entire genomes in short periods of time could revolutionize the world of medicine and technology.

Neeraj Gupta
Industry Speak
Role of DNA Sequencer in Solving Diagnostic Mystery

DNA sequencing has started making huge strides in our current understanding of mechanisms of various chronic illnesses like cancers, metabolic disorders, inherited disorders, neurodegenerative anomalies, transplant immunology etc. Latest trends in biomedical research are giving birth to a new branch in medicine commonly referred to as precision medicine or personalized therapy. Technology has continuously evolved from Sanger to high throughput next generation and further to third generation long read sequencers. This will reorient medical practice more toward disease prediction and prevention approaches rather than curing them at later stages of their development and progression. With latest ability of long read DNA sequencers to capture all types of structural variations in genomes, allowing detection of causal structural variations in a rare disease that include deletions, duplications, and other structural rearrangements, as well as a highly homologous pseudo gene. A recent study that appeared in Genetics in Medicine utilized long read DNS sequencer to evaluate structural variants, large genetic differences that involve at least 50 base pairs and quickly identified causative mutation, a 2.2 kb deletion that affects PRKAR1A, the gene involved in Carney complex which is a disorder characterized by increased risk for several types of tumors, including benign tumors in the heart.

Increased throughput read length and decreased running cost of current next-gen DNA sequencers-creating opportunity to obtain high quality, ethnicity specific medical grade genomes that better represents haplotypes common in their regional populations, thereby accelerating the use of precision medicine. For example, Craig Ventor genome, the first Human Genome reference completed in 2003, has been resequenced using latest long read DNA sequencer. This allowed identifying unique variations on chromosome 20 alone which include 196 novel insertions and 260 novel deletions with an average size of 634bp.

India is aggressively gearing up to adopt this current trend and many startups are joining hands to provide clinical diagnosis/prognosis utilizing DNA sequencers. Also there is huge push for HLA donor registries to provide that most compatible match and this only possible due to ability of long read DNA sequencers in providing full length high resolution allele level typing results and process large sample volumes.

Fuelled by these technological advancements, precision medicine will use this knowledge to redefine diseases with new therapies and provide hope for generations of patients to come.

Neeraj Gupta
Director – Sales & Marketing,
Founder & CEO – Genes2Me

Dr Jitendra K. Thakur
Second Opinion
Importance of DNA Sequencers and Advancements

In the last 10 years, cost of DNA sequencing has reduced quite significantly. With every passing month, more and more people from different parts of the world are getting their DNA sequenced. Thus, not only medical practitioners but even common people, including patients now know the importance of knowing the sequence of their DNA. We all understand the potential of genome sequencing in improving diagnostic sensitivity and in selection of a precise therapeutic target. All these will contribute a lot toward betterment of patient care. The US National Human Genome Research Institute (NHGRI) has laid out a 20-year plan for translating information from genomics to medicine.Surprisingly, to the best of my knowledge, there is no Indian genome available in the public domain. So, Indian scientists are rightly starting a program to sequence genomes of more than 1000 humans belonging to diverse ethnic groups. Please note that just the North East region of India has more than 220 ethnic groups indicating the rich diversity present in India which must be explored. Such initiatives will help identify the genetic polymorphisms that underlie many diseases.

Latest technologies available in the market are capable of producing several gigabases of data in a single sequencing run facilitating the analysis of large chromosomes and genomes. These diverse next-generation sequencing technologies have significantly enhanced the speed and ease of DNA sequencing and drastically reduced the cost bringing in the so called genomic revolution. Inspired by the success of next-generation or second-generation sequencers, third-generation DNA sequencers based on single molecule sequencing (SMS), real-time sequencing, and nanopore sequencing have also been launched. It is hoped that these third-generation DNA sequencers, especially the nanopore-based ones will produce incredibly long read DNA sequence data far cheaper and much faster than currently possible by the second-generation sequencers.

Dr Jitendra K. Thakur
National Institute of Plant Genome Research, New Delhi

10 Diagnostic Imaging Trends for 2018



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