PERSONAL GENOME SEQUENCING BI 420 Introduction to Bioinformatics

PERSONAL GENOME SEQUENCING BI 420: Introduction to Bioinformatics Department of Biology, Boston College

CHARTING A COURSE FOR GENOMIC MEDICINE FROM BASE PAIRS TO BEDSIDE Nature Volume: 470, Pages: 204– 213 Date published: (10 February 2011)

Genomic achievements since the Human Genome Project. ED Green et al. Nature 470, 204 -213 (2011) doi: 10. 1038/nature 09764

The essence of genomics • Comprehensiveness • Scale • Technology development • Rapid data release • Social and ethical implications

Imperatives for genomic medicine • Making genomics-based diagnostics routine • Defining the genetic components of disease • Comprehensive characterization of cancer genomes • Practical systems for clinical genomic informatics • The role of the human microbiome in health and disease

Bioinformatics and Computational Biology • Data analysis • Data integration • Visualization • Computational tools and infrastructure • Training

Education and Training • Primary and secondary education • Public outreach • Healthcare providers’ genetic competencies • Next generation of genomic researchers

Genomics and society • Psychosocial and ethical issues in genomics research • Psychosocial and ethical issues in genomic medicine • Legal and public policy issues • Broader societal issues

Schematic representation of accomplishments across five domains of genomics research E D. Green et al. Nature 470, 204 -213 (2011) doi: 10. 1038/nature 09764

Ethics Issues Discussion • Pros and Cons of Personal Genome Sequencing Comparative example: nuclear power Pros: plentiful energy source. Military existence has reduced ground-based war Cons: destructive pollutant. Long cleanup time.

Some Companies and Specialized Organizations

23 andme

23 andme approach SNP chip. Problem: no legal standards for information

Navigenics SNP chip approach; Works through physicians http: //www. navigenics. com

Navigenics approach SNP chip. Problem: no legal standards for information

KNOME Knome interprets human genomes for pharmaceutical and clinical researchers.

Knome approach Bioinformatics analysis service. Multigenome analysis. Also provide sequencing. Issue: how much value do they provide?

PERSONAL GENOMES Academic group at Harvard Med Goal: allow individuals to volunteer their DNA for the purpose of datamining.

Personal Genomes Research organization. Personal issues: is it a good idea to give up your DNA even anonymized? Analogy: Facebook information. How private can it possibly be? Or should we relax our standard for privacy?

An Agenda for personalized Medicine Nature 461, 724 -726 (8 October 2009)

Comparison of disease predictions of 23 andme and navigenics

Results 5 individuals surveyed Significant disagreement in risk for many diseases

Conclusions Recommendations: • Monitor behavioral outcomes. • Carry out prospective studies with hundreds to thousands of individuals. • Replicate associations in other ethnicities. • Sequence instead of genotype.

Ethics guidelines

Genetic Nondiscrimination Act of 2008 The Act prohibits group health plans and health insurers from denying coverage to a healthy individual or charging that person higher premiums based solely on a genetic predisposition to developing a disease in the future. The legislation also bars employers from using individuals' genetic information when making hiring, firing, job placement, or promotion decisions. Issues: reasonable enforcability, data availability, indirect use, accuracy of disease prediction