Update on Medical Genetics for Family Practitioners Genetic Testing, Newborn Screening, and Direct to Consumer Testing Sandhya Parkash, MD, FRCPC, FCCMG Maritime Medical Genetics Service, IWK Health Centre May 9, 2018 Disclosures No disclosure to declare Objectives To provide a review of different types of genetic tests and their limitations To provide some background on direct to consumer genetic testing and its limitations To provide an overview of newborn screening and the role of family physicians in this process Genetic Testing https://pixabay.com/en/dna-white-male-3d-model-isolated-1889085/ RNA Protein Types of Genetic Tests Cytogenetic DNA DNA Molecular/DNA Protein Protein Dogma of Genetics (Metabolic) Substrate Enzyme Substrate Enzyme Product Product 1
Points to Consider in Genetic Testing Process should include: Informed consent Test interpretation Follow-up medical and psychosocial services as indicated Testing often done by specialized laboratories (due to rarity of conditions) Points to Consider in Genetic Testing Genetic testing rarely rules out a condition Most informative when there is a high pre-test probability Genetic etiology for some conditions are unknown Hypermobility Ehlers Danlos Syndrome Results: Can affect medical management and personal decisionmaking Can have implications to the patient and their family members Interpretation of results is a big challenge Modified from www.genereviews.org Bill S-201 The Genetic Non Discrimination Act This enactment prohibits any person from requiring an individual to undergo a genetic test or disclose the results of a genetic test as a condition of providing goods or services to, entering into or continuing a contract or agreement with, or offering specific conditions in a contract or agreement with, the individual. The enactment provides individuals with other protections related to genetic testing and test results. Fact Sheet: http://www.geneticseducation.ca/uploads/cagc_s201_facti sheet_genetic_nondiscrimination_17may2017.pdf Use of Genetic Testing Diagnosis Reproductive Decision Making Carrier Testing Known genetic condition in family Risk based on ethnic background Prenatal diagnosis Fetus with multiple congenital anomalies Predictive testing for known condition in family http://www.parl.ca/documentviewer/en/42-1/bill/s-201/royal-assent Karyotype Karyotype Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition. 2003 by Saunders, an imprint of Elsevier, Inc. 2
Some indications for karyotype analysis Couple/family history of multiple miscarriages (> 3) or infertility To confirm mechanistic nature of chromosome abnormality Can be used in lieu of microarray for more recognizable aneuploidies (ie Down syndrome) Short stature in a female (Turner syndrome) Down Syndrome DNA/Molecular Tests DNA/Molecular Tests Microarray Rapid aneuploidy detection DNA sequencing Next generation sequencing Exome sequencing Patient s DNA Control DNA Interpretation of Results Hybridization x1 x3 Normal Pathogenic Variant of unknown significance Incidental finding Pathogenic with respect to autosomal recessive disease Microarray 3
RAD = Rapid Aneuploidy Detection RAD DNA based test that is a fast way to determine the chromosome count for chromosomes 13, 18, 21, and the sex chromosomes 1-2 day turnaround Advantages Quick Specific Indicated when there is increased suspicion of common aneuploidy or sex chromosome abnormality Down syndrome Trisomy 18 Trisomy 13 Turner syndrome (45,X) Klinefelter syndrome Can be used pre or postnatally DNA sequencing Determines the order of nucleotides (A,G,C,T) within a strand of DNA Variations may (but not always) have clinically significant effects Does not detect all types of causative genetic variations Types of DNA variations Normal gene: The person fed the dog. Point mutation: The persop fed the dog. Deletion: The person the dog. Insertion: The person fed the dog yesterday Frameshift: The person edt hed og Variant of unknown significance: The individual fed the dog DNA Mutations Can be Inherited from a parent De novo Germline Acquired Limitations to DNA sequencing tests Variants of unknown significance Normal test results do not rule out disease Labs vary in quality of testing and reporting 4
Examples of when DNA Sequencing would be considered BRCA gene testing in the context of a personal and family history of early onset breast and/or ovarian cancer Patient who meets (or comes close to meeting) diagnostic criteria for Marfan syndrome (FBN1 gene analysis) Next Generation Sequencing Describes a number of different modern sequencing technologies Allows quicker and cheaper DNA sequencing than the previously used Sanger sequencing Next Generation Sequencing Exome sequencing Sequencing all the protein-coding genes in the genome simultaneously Requires special approval and typically coordinated by Medical Genetics Variant interpretation remains a challenge Diagnostic rate ~40% so normal results still do not rule out genetic disorder Application of Molecular and Serological Diagnostics in Veterinary Parasitology - Scientific Figure on ResearchGate. Available from: https://www.researchgate.net/basic-principle-of-next-generation-sequencing-technologies_fig4_ 291171327 [accessed 28 Apr, 2018] Direct to Consumer Genetic Testing Direct to Consumer Genetic Testing Sold directly to individuals Information offered can include: Ancestry Risks for developing certain conditions Carrier status for recessive disorders Predicted drug response https://geneticliteracyproject.org/2017/12/01/healthancestry-how-choose-right-genetic-test-you/ 5
Numerous Companies Points to Keep in Mind Can be performed in individuals with low pretest probability of having disease Not diagnostic Full coding sequence is not analyzed May offer risk information for limited set of conditions Concerns about DTC Testing Inaccurate results Overestimation of the role genetics play in disease Confusion over methodology Difficulty in interpreting disease risk Increased anxiety or false sense of security Complexity of understanding and interpreting genetic testing results among health care providers Concerns about patient privacy Can end up being more costly due to cascade testing done after results obtained unknown impact of privately obtained testing on a publicly funded health care system Raw Data Some companies provide customers with raw genotyping data, which could be diagnostic Usually accompanied by a disclaimer that information is not validated for accuracy not intended for medical use Interpretation services can be accessed, but these can be erroneous Confirmatory clinical genetic testing should be offered (if indicated) from clinical diagnostic laboratory to guide patient care DTC Testing in US ACMG Position statement, 2016 A knowledgeable professional should be involved in the process of ordering a genetic test with medical implications and laboratory results should be interpreted and delivered by a board-certified genetics professional Tandy-Connor et al, 2018 Analysis of 49 patient samples from DTC testing with genetic variants 40% of variants were determined to be false positives Not regulated in Canada DTC Testing in Canada CCMG Stance, July 2015 Our concerns with DTC genetic testing services are focused on the potential for misleading and/or deceptive marketing practices, a lack of validation of test accuracy or reliability, the risk of misinterpretation of results, and their downstream implications, including issues of potential discrimination and negative effects on the Canadian healthcare system. CMA Policy Statement, May 2017 Physicians should generally avoid using DTC genetic tests unless they have been clinically and empirically validated Physicians should generally avoid recommending and/or ordering DTC genetic tests if they do not have a clear understanding of the validity and limitations of the tests they select 6
Prenatal/Preconception Reproductive Genetic Carrier Screening NIPT Reproductive Genetic Carrier Screening Joint SOGC-CCMG Committee Opinion, 2016 Thalassemia/hemoglobinopathies: should be offered to women/families from ethnic backgrounds with reported increased carrier frequency, when MCV<80 fl, or electrophroresis reveals an abnormal hemoglobin type CBC, Hb electrophoresis, +/- ferritin CF Carrier screening should be offered if at increased risk due to ethnic background, personal or family hx "https://clipartxtras.com/ Reproductive Genetic Carrier Screening Ashkenazi Jewish population Couples of AJ heritage should be offered carrier screening for: Tay Sachs (1/30) Canavan disease (1/37-1/53) Familial dysautonomia (1/32) If only one member of couple is of Ashkenazi Jewish ancestry, screening should be offered or Tay Sachs disease only using biochemical testing Additional carrier screening should be offered when a positive fam hx elicited for one of the conditions known to be present at increased frequency in this population Founder effects in local population NIPT Maternal DNA Fetal DNA Modified from https://pngtree.com/ NIPT Non invasive prenatal testing Non diagnostic testing Performance depends on pretest probability Not covered by many provincial health programs >$450 Offered in certain high risk situations Invasive testing still recommended for diagnostic purposes Newborn Screening 7
Newborn Screening Not diagnostic All positive newborn screens require further diagnostic workup Diagnostic workup arranged through various pediatric specialists/subspecialists Conditions Screened through Maritime Newborn Screening Program Amino Acid Disorders Maple Syrup Urine Disease Phenylketonuria (PKU) Organic Acid Disorders Glutaric Acidemia type 1 Isovaleric Acidemia Methylmalonic Acidemia Proprionic Acidemia Fatty Acid Oxidation Disorders Carnitine Palmitoyl Transferase I and II deficiency Carnitine Uptake Disorder Long Chain 3-Hydroxyacyl-CoA Dehydrogenase deficiency MCAD VLCAD Urea Cycle Defects Arginosuccinic Acidemia Citrullienemia Type 1 Other Congenital Hypothyroidism Cystic Fibrosis Sickle Cell Disease/Hemoglobi nopathy Severe Combined Immunodeficiency Trifunctional Protein Deficiency Processes employed after positive newborn screen Family physician/ordering physician notified Family contacted for an appointment with appropriate subspecialist Diagnostic workup initiated, which can take some time Outcome of newborn screening Diagnostic testing can take weeks to months to become available Until diagnosis is either confirmed or ruled out, babies are often assumed to be affected with specific management recommendations These recommendations may change once confirmatory results available Summary Genetic testing is complex and results require careful interpretation Direct to consumer genetic testing has many limitations Reproductive genetic carrier screening can provide patients with important information that should ideally be assessed preconceptually Confirmation of a positive newborn screen can take some time, but preventative/precautionary measures are often put in place until a diagnosis can be confirmed or excluded References Tandy-Connor et al. 2018. False-positive results released by direct-to-consumer genetic tests highlight the importance of clinical confirmation testing for appropriate patient care. Genetic in Med advance online publication 22 march 2018 ACMG Board of Directors, 2016. Direct to consumer genetic testing: a revised position statement of the American College of Medical Genetics and Genomics. Genet in Med 18(2): 207-208 Wilson et al. 2016. Joint SOGC-CCMG Opinion for reproductive genetic carrier screening: an update for all Canadian providers of maternity and reproductive healthcare in the era of direct to consumer testing. J. Obstet Gynaecol Can 38(3); 742-762 8