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Personal genome sequencing: current approaches and challenges.

ABSTRACT: The revolution in DNA sequencing technologies has now made it feasible to determine the genome sequences of many individuals; i.e., "personal genomes." Genome sequences of cells and tissues from both normal and disease states have been determined. Using current approaches, whole human genome sequences are not typically assembled and determined de novo, but, instead, variations relative to a reference sequence are identified. We discuss the current state of personal genome sequencing, the main steps involved in determining a genome sequence (i.e., identifying single-nucleotide polymorphisms [SNPs] and structural variations [SVs], assembling new sequences, and phasing haplotypes), and the challenges and performance metrics for evaluating the accuracy of the reconstruction. Finally, we consider the possible individual and societal benefits of personal genome sequences.

SUBMITTER: Snyder M

PROVIDER: S-EPMC2827837 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature

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Personal genome sequencing: current approaches and challenges.

Snyder Michael M Du Jiang J Gerstein Mark M

Genes & development 20100301 5

The revolution in DNA sequencing technologies has now made it feasible to determine the genome sequences of many individuals; i.e., "personal genomes." Genome sequences of cells and tissues from both normal and disease states have been determined. Using current approaches, whole human genome sequences are not typically assembled and determined de novo, but, instead, variations relative to a reference sequence are identified. We discuss the current state of personal genome sequencing, the main st ...[more]

PMID: 20194435

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Project description:In this era of clinical genomics, the accumulation of knowledge of pharmacogenomics (PGx) is rising dramatically and attempts to utilize it in clinical practice are also increasing. However, this advanced knowledge and information have not yet been sufficiently utilized in the clinical field due to various barriers including physician factors. This study was conducted to evaluate the attitudes of physicians to PGx services by providing them their own genomic data analysis report focusing on PGx. We also tried to evaluate the clinical applicability of whole exome sequencing (WES)-based functional PGx test. In total 88 physicians participated in the study from September 2015 to August 2016. Physicians who agreed to participate in the study were asked to complete a pre-test survey evaluating their knowledge of and attitude toward clinical genomics including PGx. Only those who completed the pre-test survey proceeded to WES and were provided with a personal PGx analysis report in an offline group meeting. Physicians who received these PGx reports were asked to complete a follow-up survey within two weeks. We then analyzed changes in their knowledge and attitude after reviewing their own PGx analysis results through differences in their pre-test and post-test survey responses. In total, 70 physicians (79.5%) completed the pre-test and post-test surveys and attended an off-line seminar to review their personal PGx reports. After physicians reviewed the report, their perception of and attitude towards the PGx domain and genomics significantly changed. Physician' awareness of the likelihood of occurrence of adverse drug reactions and genetic contribution was also changed significantly. Overall, physicians were very positive about the value and potential of the PGx test but maintained a conservative stance on its actual clinical use. Results revealed that physicians' perception and attitude to the utility of PGx testing was significantly changed after reviewing their own WES results.

Dataset Information

Personal genome sequencing: current approaches and challenges.

Publications

Personal genome sequencing: current approaches and challenges.

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