Next Generation Sequencing Of Human Diseases

Aziz, N., Qin, Z., Bry, L., Driscoll, D. K., Funke, B., Gibson, J. S., & ... Voelkerding, K. V. (2015). College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests. Archives Of Pathology & Laboratory Medicine, 139(4), 481-493 13p.

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Scientist is studying the human genome to determine its sequence. Understanding the genomic sequence can prevent any form of disease, however, each person does not contain the same genomes which means it is hard to understand each genomes sequences. The advantage of understanding the genomics, is to understand how human genomic mutations can lead to life-threating conditions such as cancer and prevent them from happening again. The disadvantage for researching genomics cost a lot of money, the research nearly cost thirteen-billion

If the lifetime of the polymerase is long enough, both strands can be sequenced multiple times (called ‘‘passes”) in a single polymerase read. Moreover, the polymerase read could be split to multiple reads (called subreads) by recognizing and cutting out the adaptor sequences. The consensus sequence of multiple subreads in a single ZMW yields a circular consensus sequence (CCS) read with higher accuracy. If a target DNA is too long to be sequenced only one time in a polymerase read a CCS read cannot be generated, and only a single subread is output instead. Whereas, the CCS sequences are usually generated by transcript sequencing due to its relatively short length. According, Pacific Biosciences developed an independently protocol, Iso-Seq, for long-read transcriptome sequencing, including library construction, size selection, sequencing data collection, and data processing. Iso-Seq allows direct sequencing of transcripts up to 10 kb without use of a reference

Genome-wide association studies (GWAS) are often correlated with personalized medicine. GWAS studies often involve sequencing the entire genome of patients suffering from a specific disease, to look for shared mutations within their genomes (Bush et al., 2012, p.1). These shared mutations are then investigated to assure their direct correlation with the disease, in which this mutation can be used to diagnose future patients by identifying the same mutation in their genome sequence (Bush et al, 2012, p. 3). Occasionally, it is identified that multiple mutations within the genome lead to the same disease (Bush et al., 2012, p.1). In cases where groups of individuals suffer from specific mutations in disease,

The human genome project is an incredible feat. The significance and contributions of the project to the science world has and will have a significant impact of the way we treat, diagnosis, and prepare for diseases if an individual knows they have a predisposition to it. There are two significant contributions that I believe has been very beneficial to the health field. The first is recording and storing all the new found information on genomics into one database. More importantly though is having this enormous information in a database that is easy to navigate and that is useful to multiple different professional fields of study. With this database health personal can see the genomes of different species and over time can be able to the evolutionary changes of genetics of different species. Health professionals can also take the genome of a patient and compare it to the human genome in the database to see if they have a genetic predisposition to a disease or an abnormal genome to diagnose a disease. “Such detailed, fundamental understanding about our bodies will have profound effects on the ways diseases are diagnosed, on the prevention of disease, and on treatments.” (Collins, McKusick, Jegalian, 2012) With the identification/belief that there are “approximately 20,000-25,000 genes in human DNA,” (U.S. Department of Energy Human Genome Project, 2014) we have now begun to identify which genes contribute to diseases. The identification of these mutate genes can be recorded

Genome sequencing – allows us to understand and be able to read the genes in organisms

to find the cause to the disease but they have for 20 genes that may increase and decrease

The field of genomics is quickly and steadily gaining momentum in the field of systematics. Based on an organism’s genetics, it applies novel methods of DNA sequencing and bioinformatics to sequence, construct, and analyze the structure, and consequently, the function, of entire genomes, using the resulting genetic information from different specimens in fine-scale genetic mapping. Advancements in other fields such as human biomedicine may also be dependent on progress made in genomics, especially unresolved problems focused on changes in genes triggered or disrupted in development, susceptibility to infectious disease, mechanisms of DNA recombination and genome plasticity which cannot be adequately interpreted without a precise evolutionary context or hierarchy.

Exome sequencing is one example of NGS that is useful when the identity of the specific genes involved in the disease has not yet been identified. The technique, which entails sequencing only the 1% of the genome that is exons and thus codes for proteins, is less costly than whole-genome sequencing and is increasingly being used for the diagnosis of rare inherited disorders. A 2013 study on MHS using exome sequencing was able to identify over 100 RYR1 and CACNA1S variants in an asymptomatic population, reclassify several previously classified pathogenic variants as likely non-pathogenic due to high prevalence, as well as alert several individuals with a high likelihood of MHS based on known pathogenic mutations7. The major use of large scale exome sequencing efforts in MHS is that they will allow researchers to identify the pathogenicity of variants identified in RYR1 and CACNA1S genes. In addition, the technique can be used in combination with functional studies to identify new mutations in families for whom traditional methods have not identified a mutation. A limitation of this technology, however, is that many variants of unknown significance (VUS) are frequently identified, making interpretation and large scale clinical application of the results

The genome is the total genetic information carried by an organism. The 10K Genomes Initiative was the plan to sequence all DNA from 10000 species. The Human Genome Project established databases and refined analytical software to make data available on the Internet. Bioinformatics and genomics are two terms that are often hashed up. While bioinformatic is the application of computational methods to the storage and analysis of biological data, genomics is the study of whole sets of genes and their interactions the two are often confused. Next-Generation Sequencing is the different modern sequencing technologies. NCBI genbank is the NCBI database of sequences. Systems biology is used to define gene circuits and protein interaction networks. A

Sanger Sequencing was introduced in 1977 by Frederick Sanger and has been extensively used for at least 35 years (10,11). Even now, it is still frequently used for small scale sequencing work. No breakthrough of whole genome sequencing techniques was made until the launches of Roche 454 GS20 (12) and ABI SOLID (13) in the mid 2000. Soon after that, Ion Torrent (14), PacBio (15) and Illumina (16) platforms have been introduced and quickly occupied the market of genomic sequencing. Not until recently, the third generation sequencing, such as the nanopore (17), has been commercialized and initially tested. A timeline of the development of DNA sequencing platforms was described in Figure 1.

There are more than 10,000 recorded genetic diseases that are passed on through generations affecting millions of people, often with fatal or severely debilitating illness. Scientist worldwide are working to crack the genetic codes to identify genes linked to disease, diagnose abnormalities, and discover new treatment. “The Genetic Disease Foundation is a non-profit 501c (3) organization that established since 1997 by patients and families affected by genetic disorder” (GDF, 2010). The Foundation furnish education programs for everyone and physicians to enhance the knowledge about genetic diseases and the necessity for and availability of testing for many disorders. In addition, the research designed to enhance genetic testing and to find out ways to treat, cure and ultimately avoid genetic disorders. GDF mission is to help prevent and treat genetic disease by supporting research, education and counseling.

The HGP employed a two-phase approach to uncover the human genome sequence. The first phase used DNA shotgun

Science has led to the discovery of DNA and then identification of specific genes in organisms that control heredity and determine a cell 's function. With the advancement of research we are now able to explore the different roles of genes and understand how they might be correlated with diseases.