Presented by: Tess L. Crisostomo Laboratory Quality Assurance/Compliance Officer Naval Medical Center San Diego

Transcription

1 Presented by: Tess L. Crisostomo Laboratory Quality Assurance/Compliance Officer Naval Medical Center San Diego

2 Discuss the difference between DNA Genotyping and Genome Sequencing What makes you who you are? What is Preventive Medicine? Know the Benefits of Personalized Preventive Medicine Know the CLIA 88 and CAP Standards for Clinical Genome Sequencing What is the future of Genomics in Pathology The Way Forward for the Medical Technology Field Profession

3 The goal is to make 100 years old the new 60 with genome sequencing serving as the catalyst for this ambitious achievement. Peter H. Diamandis Founder of Human Longevity Incorporated

4 1% No two people are genetically identical (identical twins being the exception). It is these "differences" that make you, YOU! One person's genome sequence is very similar to another's. In fact, more than 99% of the human genome sequence is common to all people. Since the genome sequence is more than three billion DNA letters, there is still a lot of room within that 1% difference for variations to exist from person to person.

5 AKA Whole Genome Sequencing (WGS) Full Genome Sequencing Complete Genome Sequencing Entire Genome Sequencing NGS (Next-Generation Sequencing) The human genome sequence has about three billion bases, and each cell contains two copies of your DNA sequence, one inherited from your mother and the other from your father. A genotype describes the DNA bases present at a specific location in the two copies.

6 With genotyping, only a certain number (1 to 100,000s) of specific DNA changes are assessed. If new DNA changes are discovered to be important after your genotyping has been completed, you will likely have to be genotyped again to learn about the new information. With genome sequencing, the entire sequence of your two copies is decoded. This tells you the order of DNA bases, or letters, over a larger area of the genetic code rather than focusing in on specific locations

7 To learn how variations in your genome may impact you. The data can then be analyzed by: Genetic Specialists Doctors Researchers NOTE: Medical and research doctors' ability to analyze and interpret genome information is still quite LIMITED.

8 When someone refers to the genome, they often mean all of the information contained within an individual's DNA. In fact, your genome actually refers to all of your DNA plus the proteins required to read and maintain it, as well as the many particles that help store and give shape to your DNA. Think of the entire genome as a library, and DNA as a genome encyclopedia.

9 A laboratory process that determines the complete DNA sequence of an organism's genome at a single time. Whole genome sequencing should not be confused with DNA profiling, which only determines the likelihood that genetic material came from a particular individual or group, and does not contain additional information on genetic relationships, origin or susceptibility to specific diseases.

10 Each individual has two nearly identical copies of each chromosome volume, one copy from each parent. All of the entries in your genome encyclopedia are written in a special language-the DNA code. The DNA alphabet has only four letters, A, C, T, and G, representing the four different chemical bases. In total, each person has more than three billion DNA letters in each set of their 23 chromosomes.

11 It may reveal DNA variants or differences in your genome associated with physical traits such as height, eye color and skin color Reveal information about genetic disorders (Huntington s disease, sickle cell disease) Some variants in your genome can give clues to where your ancestors lived Risks of developing common diseases Whether a certain medication will work for you or not; experience unpleasant side effects Type II Diabetes Risk of developing personal psychiatric Type II Disorders (Schizophrenia, Alzheimer's) Diabetes Response to medication

12

13 Reactive Medicine versus Personalized Medicine This will help doctors: Make more accurate and timely diagnoses Tailor more effective treatments for conditions that you have Discuss with you some of the diseases your genetics predisposes you to getting in the future and determine things that you can do to prevent these diseases BEFORE you get them.

14 One in 100 babies worldwide is born with a disease caused by a single gene, according to the World Health Organization. Two genetics companies Counsyl and GoodStart.

15 Sequencing technology from Illumina. The company offers tests for 23 different diseases, 15 of which are based on sequencing technology. The company launched in April 2012 and says it has processed over 100,000 tests. Counsyl began rolling out sequencing-based screening in January The company screens for more than 100 different genetic disorders.

16 Family Prep Screen If you re pregnant or thinking about it, find out if you or your partner carry genetic diseases that could affect your family. Informed Pregnancy Screen As early as week 10, find out if your baby has an increased chance for chromosome conditions like Down syndrome. Inherited Cancer Screen If you have a personal or family history of cancer, find out your chances of developing breast, ovarian, colon, and other cancers. Focus on diseases where advanced knowledge makes a difference in health outcomes, whether it s changing a behavior, pursuing preventative measures, or simply preparing for what lies ahead.

17 Provides high-quality DNA analysis services, including next-generation sequencing (NGS), to the research community since In CLIA-certified, CAP-accredited clinical laboratory, Illumina Clinical Services Laboratory, for the purpose of offering human whole-genome sequencing services to physicians and genetic counselors.

18 Bachelor's degree in a field of biological science, with the majority specifically in cell and molecular biology. NCA-certified in molecular genetics with active California licenses as Clinical Molecular Genetic Scientists and Californiaapproved Medical Technologists (ASCP). Laboratory staff are required to take continuing education units to maintain licensure. At least two years of experience working in a clinical laboratory setting, and over five years of experience in the bioscience field.

19 The TruGenome Sequence information is generated by licensed personnel using an analytically validated process. Laboratory Developed Tests, it has not been cleared or approved by the U.S. Food and Drug Administration. This genome sequence information can be analyzed to potentially aid physicians in the evaluation of a broad range of health conditions or physiological traits. Patients will not receive medical results, or a diagnosis, or a recommendation for treatment from Illumina. Any results arising from the analysis of genome sequence information that might be deemed medically actionable should be confirmed using alternative testing.

20 Genomics as being the way toward preventing the manifestations of inherited disease. Hopefully, genomics and genetic testing will do for inherited disease what vaccines have done for infectious disease.

21 The fastest technologies can sequence an entire human genome, 3 billion bases, in hours, and corresponding costs have dropped from $30,000 to $4,000 within about a year. The much-heralded $1,000 genome is within grasp. This will empower doctors to design specific tests for each person to track his progress along their genetic roadmap as well as recommendations for behaviors likely to improve one s health by diminishing the chance of a given disease.

22 If a person has a family history of breast cancer and genetic tests indicate that they have one of the BRCA 1 or BRCA 2 mutations, then they should make sure that they have regular mammography exams. Familial breast cancer is one of the complex diseases that is not 100 percent penetrant. 20% of individuals carrying these mutations will not get breast cancer or ovarian cancer during their entire life. Angelina Jolie, the famous American actress, recently tested positive for a mutation in the brca1 gene a mutation that drastically increases the chances of getting breast or ovarian cancer later in life. As a preventive measure, she chose to have a double mastectomy. If one has two or three of the genes that predispose them to Type 2 diabetes, they should watch their weight, exercise regularly and have their blood glucose measured routinely. Also knowing the type of genetic defects associated with a person s Type 2 diabetes can help in planning their treatment.

23 Pathology is the backbone of modern medicine. It is the job of pathologists to conduct or direct the full spectrum of fundamental laboratory tests and to interpret the results. They are the direct link between the evidence-based analysis and interpretation of medical data and the delivery of proper care by the patient s physician.

24 Ability to conduct diagnostics using the compound microscope came nearly 150 years after its invention. Digital imaging took nearly 10 years to become standard practice in medical pathology, despite being established in virtually all other branches of the hospital. Polymerase chain reaction (PCR) technologies took approximately 5 years to take hold, again despite widespread adoption in medical research.

25 Pathologists cannot afford to ignore the sequencing revolution. The use of whole-genome analysis can, should, and will replace many current standard pathology practices of diagnosis and prognosis on which proper therapy and disease management rely. First, define guidelines that establish when a genetic variation (or set thereof) can be used to support clinical decisions, including assessment of risk, diagnosis, prognosis, and treatment plan.

26 Second, a clinical interpretation system, which involves close coupling between clinicians and biomedical informatics specialists, must be designed to generate medical impact reports from sequencing data and whole-genome analysis. Finally, a training program aimed at producing a new breed of genomic pathologist through novel, national education programs must be put in place

27 The higher throughput and lower per-base cost of next-generation sequencing (NGS). CLIA 1988/College of American Pathologists (CAP) laboratory standards had not yet been developed. To develop the necessary regulatory framework for NGS and to facilitate appropriate adoption of this technology for clinical testing, CAP formed a committee in 2011, the NGS Work Group, to deliberate upon the contents to be included in the checklist.

28 The NGS-specific checklist is part of CAP's revised molecular pathology checklist for accrediting clinical laboratories, released in The checklist to CAP-accredited labs, includes 18 requirements that address each step of using sequencing as a clinical test, including library creation and sample prep, the actual sequencing itself, bioinformatics, variant calling, annotation, and the final patient report.

29 The new guidelines are effective immediately, so any clinical lab that wants to start offering NGS-based diagnostic tests in a CAP-accredited lab will have to adhere to these requirements. Laboratories that are already accredited by CAP will need to make sure their NGS-based tests adhere by their next inspection.

30 Documentation, Validation, Quality assurance, Confirmatory testing, Exception logs, Monitoring of upgrades, Variant interpretation and reporting, Incidental findings, Data storage, Version traceability, and Data transfer confidentiality.

31 Master degree in Microbiology with at least 1 year of Molecular Lab experience or Clinical Laboratory Specialist degree or any Biology degree plus CLS experience. EXAMINATION MODEL The MB(ASCP) and MB(ASCPi ) certification examination is composed of 100 examination questions given in a 2 hour 30 minute time frame.

32 All examination questions are multiple-choice with one best answer. The certification examination is administered using the format of computer adaptive testing (CAT The weight (value) given to each question is determined by the level of difficulty. Therefore, the examinee must answer enough difficult questions to achieve a score above the pass point in order to successfully pass the certification examination.

33

34

35 "The Story of Tomorrow's Health." Tomorrows Health. 14 May Web. 10 Dec < "Whole Genome Sequencing and You." YouTube. YouTube. Web. 12 Mar < "About the Lab." Clinical Services Lab Expertise. Web. 14 Mar < "What Personal DNA Testing Can Reveal about Your Potential Health and Future Well-being." Scope Blog. Web. 15 Mar "Counsyl Is on a Mission." Counsyl. Web. 18 Mar "Better Screening for Deadly Genetic Diseases." MIT Technology Review. Web. 18 Mar < MB (ASCP) Web. 21 Mar < "This New Genetics Startup Wants to Make '100' the New '60'" Entrepreneur Web. 21 Mar <