Maryam Nazir Personal Genomics: Branch of genomics concerned with the sequencing and analysis of the genome of an individual Once sequenced, it can be compared with published literature to determine likelihood of disease risk or trait expression Main aim: to inform preventative action Techniques SNP arrays Partial sequencing Whole genome sequencing Can be used to evaluate: ○ SNPs ○ Indels ○ Large SVs ○ New sequences ○ Haplotypes Cost of Sequencing Continual development of new sequencing technologies, next-generation sequencing Increased speed and reduced cost of sequencing Now possible to offer genetic testing to consumers Personal Genome Project Large, long-term study Aim: To sequence and publicize the complete genomes and medical records of 100,000 volunteers All data will be available in the public domain Purpose: To enable research in personal genomics and personalized medicine Each participant: Full DNA sequence Extensive phenotype information ○ Medical records ○ MRI images ○ Other measurements Volunteer criteria: Permanent residents of the US, Canada, UK Able to submit tissue and/or genetic samples Informed consent “no promise of anonymity and data return” Personalized Medicine A model of medicine which proposes the customization of healthcare with medical decisions being tailored to the individual patient Goal: To individualize prevention, diagnosis, and treatment--by use of genetic differences as markers Disease risk >2500 diseases have predictive medical value ○ Can be recommended for genetic tests for single genes or whole genome sequencing Gene signatures Gene expression pattern in a cell can be uniquely characteristic of a condition Risk assessment, diagnostic & prognostic applications Match patients and treatments Pharmacogenomics Field that analyzes how genetic makeup affects an individual’s response to drugs Want to tailor treatments for patients based on their genetics Cancer genomics Main goal: to identify genes, or gene signatures, that may provide insights into cancer diagnosis, predicting clinical outcomes or targets for cancer therapies Tumour sequence is compared to a matched normal tissue Personalized cancer treatments Genetic profiles of tumours part of recommended evaluation for certain cancers (colon, breast, lung...) Nutrigenomics Study of how individual genetic variation affects a person’s response to nutrients and impacts their risk of nutrition-related chronic diseases People respond differently to certain foods Human Ancestry Looks at a person’s DNA at specific locations compares results to defined groups Mitochondrial DNA Traces direct maternal line Y-Chromosome DNA Traces a male’s direct paternal line Autosomal DNA Tests all ancestry, shows how closely a person is related to others Commercial Services Gentle most comprehensive genetic test currently on the market screens for >1700 genetic conditions predicts response to certain medications HelloGenome (Korea) genotyping (SNP chips) and full genome sequencing (Solexa machines) Illumina, Sequenom, Oxford Nanopore Technologies, Pacific Biosciences, Complete Genomics, 454 Life Sciences commercializing full genome sequencing do not provide any genetic analysis or counselling component Positive Bioscience (Mumbai) Next-generation sequencing To determine most beneficial cancer treatment for patients Nutrigenomix SNP genotyping Each gene tested is involved in the way the body processes a certain dietary component With information obtained, can tailor the diet to prevent chronic diseases (cancer, heart disease, type 2 diabetes) -ex. Caffeine Only available through registered dieticians $385 23andMe Mail order “spit kits” SNP genotyping (DNA array) Assessment of: inherited traits ancestry genetic risk for >240 diseases and common conditions Information presented in user profile $99 Ethical Issues Personal privacy & misuse of information Whose responsibility? Who owns the genomic info? Genetic discrimination Discrimination based on information obtained from an individual’s genome Genetic Information Nondiscrimination Act (U.S.) ○ Prevents discrimination by health insurers and employers, but does not apply to life insurance or long-term care insurance Psychosocial stress Consequence of knowing one’s predisposition to disease Know risk, have no cure Other Issues How relevant are the results of commercial services? Clinical utility? Education needed in interpreting results and communicating genetic information For the average person/patient For doctors For the public & media genetic counselling Conclusions A fairly large number of loci that are known to be predictive of disease have been identified Many of these can be clinically targeted Immediate applications are limited at present The promise of personal genomics lies in the future Must first build a database of personal genomes Many people envision a future where personal genomic information is one of the essential tools used to tailor one’s medical care References Offit, Kenneth. "Personalized medicine: new genomics, old lessons." Hum Genet. 130. (2011): 3-14. Snyder, Michael, Jiang Du, and Mark Gerstein. "Personal genome sequencing: current approaches and challenges." Genes Dev. 24. (2010): 423-431. Werner, Thomas. "Next generation sequencing in functional genomics." Briefings in Bioinformatics. 2.5 (2010): 499-511. Cooper, David N., et al. "Genes, Mutations, and Human Inherited Disease at the Dawn of the Age of Personalized Genomics." Human Mutation. 31.6 (2010): 631–655. Chin, Lynda, Jannick N Andersen1, and P Andrew Futreal. "Cancer genomics: from discovery science to personalized medicine." Nature Medicine. 17.3 (2011): 297-303.