Medical Genomic Sequencing

Genomic sequencing has huge impact on the field of medicine. Till date, cost and throughput limitations have made general clinical applications infeasible. At present, though, the price of about 5000 United States Dollars for a normal human genome sequence, exclusive of analysis, and fast throughput; several days to a few weeks, is fast making medical sequencing practical. The high-throughput sequencing is used to help diagnose highly genetically heterogeneous disorders, such as X-linked intellectual disability, congenital disorders of glycosylation and congenital muscular dystrophies; to detect carrier status for rare genetic disorders; and to provide less-invasive detection of fetal aneuploidy through the sequencing of free fetal DNA.

While this is a hopeful start for high-throughput sequencing in the clinic, scientists believe these technologies should be used with care as they have non-negligible false-positive and false-negative rates due to sequencing errors and amplification biases, which need to be improved upon with best library construction methods, enhanced sequencing technologies or filtering algorithms. On the other hand, medical sequencing could possibly be useful in a wide range of settings in the near future. The main areas are cancer, hard-to-diagnose diseases and personalized medicine.

Cancer is a genetic disease, both in predisposition and somatic growth. High-throughput sequencing of cancer genomes has been a major factor in the understanding of the genetics of this complex disease. Exome sequencing (targeted exome capture; strategy to selectively sequence the coding regions of the genome as a cheaper but still effective alternative to whole genome sequencing), RNA sequencing, paired-end sequencing and whole-genome sequencing of cancer genomes have led to a dramatic increase in the number of known recurrent somatic alterations, such as mutations, amplifications, deletions and translocations.

Studies have revealed many interesting findings. As a recent example, using paired-end sequencing, Koichiro Inaki, Axel M. Hillmer and group and co-researchers in 2011 discovered that approximately half of all structural rearrangements in breast cancer genomes result in fusion transcripts, where single segmental tandem duplication spanning multiple genes is a major source. They estimated that 44% of these fusion transcripts are potentially translated, and found a novel RPS6KB1–VMP1 fusion gene that is recurrent in a third of breast cancer samples analyzed, with potential association with prognosis. Simultaneously, Axel Hillmer, PhD, and group of The Genome Institute of Singapore in 2011 applied paired-end sequencing on cancer and non-cancer human genomes, and found that non-cancer genomes contain more inversion, deletions and insertions, whereas cancer genomes are dominated by duplications, translocations and complex rearrangements. Recent works from group of Jan Korbel found that cancer genomes lacking p53 often contain genomic regions that undergo extensive rearrangements called ‘chromothripsis’ (tens to hundreds of chromosomal rearrangements occur in a one-off cellular crisis. Cancer is driven by somatically acquired point mutations and chromosomal rearrangements, conventionally thought to accumulate gradually over time. In chromothripsis, rearrangements involving one or a few chromosomes crisscross back and forth across involved regions, generating frequent oscillations between two copy number states. These genomic hallmarks are highly improbable if rearrangements accumulate over time and instead imply that nearly all occur during a single cellular catastrophe) suggestive of complex chromosome shattering and rejoining in a single event. Much work has also been done on matched tumor–normal pairs and revealed that extensive somatic single nucleotide variants and structural variants occur in cancer genomes.

One important medical conclusion that has emerged from this work is that every tumor is genetically different but that common pathways are often activated. Thus, the sequencing of cancer genomes can help reveal the activated pathways and the information used to suggest therapeutic treatments. For example, the detection of novel fusion transcripts in a difficult diagnostic case of acute promyelocytic leukemia that were previously missed in a regular diagnosis was used to influence the medical care of the patient by John S. Welch, MD, PhD; and colleagues in 2011. In addition, sequencing of carefully selected samples could lead to interesting discoveries of cancer evolution and mutational processes.

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