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Saudi Human Genome Program Building a Foundation for Personalized Medicine

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Saudi Human Genome Program Building a Foundation for Personalized Medicine Saudi Human Genome Program Building a Foundation for Personalized Medicine Brian Meyer, PhD What is Personalized Medicine? • The ability to determine an individual's unique molecular characteristics – to use those genetic distinctions to diagnose more finely an individual's disease – select treatments that increase the chances of a successful outcome – reduce possible adverse reactions. • Personalized medicine also is the ability to predict an individual's susceptibility to diseases and thus to try to shape steps that may help avoid or reduce the extent to which an individual will experience a disease. What does it require? • Essential features for personalized medicine to be a fully functioning reality at the clinical level include: – an electronic medical record – personalized genomic data – physician access to electronic decision support tools – personalized treatments – personal clinical information available for research use Why Personalized Medicine? • The past decade has seen a revolution in human genetics – it is having a very significant impact on virtually all specialties of medicine • Several scientific advances are responsible for this revolution – First is the recognition and validation that the genetic composition of individuals play a significant role in that individual's health and predisposition to common diseases such as heart disease and cancer. – Second is the availability of the human genome sequence and the many high throughput technologies developed and advanced during and since the Human Genome Project. – Third is the imminent ability to completely sequence and analyze the human genome in real time at relatively low cost. OMIM 2012/2013 9 Characteristics of the Saudi Population ─Homogeneity Iraq Iran ─Tribal organization (multiple independent Jordan RUWALLA Kuwait homogeneous units with limited founders) ENAZA SHAMMAR Awazim Arabian ─8 tribes MUTAIR Gulf Ajman ─Tribal affiliation maintained Juhainah Qatar Gulf of HARB SUHUL OTAIBAH Oman Jahadila SUBAI Manasir U.A.E. Egypt Oman ─Consanguinity Quraish Buqum Ghamid MURRA ─57% Consanguinity rate Red Sea Zahran QAHTAN Dawasir ASIR ─Up to 98% in specialty clinics Sudan Yam Arabian ─Mostly first cousin marriages Yemen Sea ─Large family size ─Nuclear family size of 8-10 is common ─High incidence of rare recessive Mendelian traits and common diseases such as type 2 diabetes The Saudi Human Genome (SGP) is a national program which aims to sequence 100,000 samples (normal and disease) from the Saudi population in the next 5 years. Create multiple satellite centers across the Kingdom WORKFLOWS There are three (3) main work flows: Gene panels: 13 panels specifically designed for inherited diseases. These panels cover all genes in OMIM; unique to SHGP Exome Sequencing: Predominantly Index cases from families with Autosomal recessive diseases for gene discovery Genome Sequencing: For cataloging population variants in health and disease GENOME vs. EXOME vs. MENDELIOME / GENE PANELS “Actionable” Monogenic disorders are encountered by every discipline of medicine • Investigation of underlying causes • Whole Genome Sequencing • Most comprehensive but expensive, inefficient and has ethical questions that need to be answered • Growing number of large Whole Exome Studies • Expensive, ethical questions (Clinical Exome $2,500; long turnaround) • Significant technical commitment & interpretation required • ~25% yield • Mendeliome/Gene Panels • ~3,200+ known Mendelian genes • Requires less technical expertise and interpretation, cheaper, faster • Specifically applied • Jaundice GI panel • Recurrent infection Primary Immune Deficiency (PID) panel • Unusual facial appearance Dysmorphology Mendeliome - Gene Panel Design Two Medical Geneticists developed the gene content of the “SHGP/Mendeliome” panels Defining the Mendeliome: - monogenic disorders [autosomal, X-linked, mtDNA] - symptom/sign based design: (i.e. neuro, ophth, derm, renal, heme, etc.) ~ 4,300 monogenic disorders - OMIM; PubMed; Genetic Testing Registry (GTR); & Gene Tests (https://www.genetests.org/) Number of Entries in OMIM (Updated 9/15/2015, http://omim.org/statistics/entry Prefix Autosomal X Linked Y -Linked Mito- * Gene description 14,234 700 48 35 + Gene & phenotype, combined 82 2 0 2 # Phenotype description, molecular basis known 4,214 297 4 29 % Phenotype description/locus, ? molecular basis 1,511 129 5 0 Phenotypes with suspected mendelian basis 1,706 112 2 0 Totals 21,747 1,240 59 66 Gene Panel Design • Develop multiplexed gene panels using Ion AmpliSeq Designer software • Primer design was based upon generating amplicons with an average length of 200 bp providing 90% minimum coverage of the CDS, and on average 10 bp flanking regions of associated exons. • Following in silico design coverage was assessed for compliance with design criteria and manual processes applied on a gene by gene basis to ensure adequate coverage and resolve factors such as 3’- SNPs that could impact primer efficiency. MENDELIOME GENE PANELS Gene Panel Signs & Symptoms # Genes IEM AA, OA, FAO, Mito-ETC, Peroxisomal, LSDs, GSD, SLCs, Steroids, Neurotransmitters 570 CARDIO-VASCULAR Cardiomyopathies (HCM/DCM/Restrictive), Arrhythmias, CHD, CAD/MI 426 DEAFNESS Sensorineural hearing loss 124 Alopecia/Hypotrichosis/Hypertrichosis/abnormal sweating; Bullous lesions, Cafe au lait spots/lentigines, DERM Diffuse pigmentation disorders, Hyperkeratosis, Icthyosis, Lax/tight skin, Peeling Skin deficiency/pits, 214 Unexplained facial papules/rash, Unexplained itch, Urticaria/angioedema, White mouth, Xanthomas DYSM/DYSPLASIA Dysmorphism, Skeletal dysplasia 422 DM, Growth Failure-Short Stature, Hyperlipidemias, HTN, Hypoglycemia-Hyperinsulinemia, ENDOCRINE Hypogonadism, Infertility/Ovarian failure/Ambig.Genitalia, Obesity, Disorders of Pit., Para/Thyroid 311 Aganglionosis, Bowel rupture/ diverticulosis, Cholelithiasis, Chronic diarrhea/malabsorption, Chronic vomiting, Esophageal leio myomatosis/ strictures/perforation, GI bleeding, Hepatomegaly/cirrhosis/liver GASTRO-INTESTINAL failure, Heterotaxy, Imperforate anus, Jaundice, Omphalocele, Pancreatic insufficiency/agenesis/ 189 inflammation, Pyloric stenosis/atresia, Unexplained abdominal pain HEME Anemias hemolytic, Aplastic Anemias, Excessive Bleeding-Clotting 405 Ataxia/Dystonia/Spasticity/Myotonia; Brain malformation, Brain malformation/ Microcephaly/ 758 NEUROGENETICS Macrocephaly, Epilepsy, Hypotonia/Weakness/hypoventilation, ID/speech delay/autism, Lactic acidosis, Narcolepsy, Neurodegeneration, Neuropathy Abn. Lymphocytes, Agamma, Allergic Rhinitis, Candidiasis, Complement def., Eczema-Urticaria, PID Hemophagocytosis/FHL, Auto-Inflammatory syndromes, chronic Meningitis, ID + Herpes simplex, 265 Osteomyelitis, Phagocyte abn., Pneumonia/Sinusitis, SCIDS, Autoimmunity synd, recurrent Viral infxns PULMONARY Surfactant, Apnea/Narcolepsy, Cilia/Bronchiectasis/Emphysema 120 CKD, Cystic KD, Hematuria, Nephrolithiasis/ Nephrocalcinosis, Nephrotic syndrome, Renal agenesis/ RENAL hypoplasia/dysplasia, Renal tubular diseases, VUR 96 Abnormal cornea, Apraxia, Cataract, Ectopia lentis, Glaucoma, Microphthalmia/Coloboma, Ocular VISION albinism, Ophthalmoplegia/apraxia, Optic atrophy, Retinal dystrophy/ achromatopsia 334 - 15% redundancy among different panels SHGP Neuro - Panel = 24 samples 24 x 758 genes (18093 amplicons) ~162 x coverage Absent in Total Variants: QS>100: Coding or Missense/ dbSNP,1000G, Homozygous: 1106 717 splicing: 643 Nonsense: 263 1000 Arabs, 1000 1 Saudi: 21 Variant Analysis Pipeline - All Panels Panel Input Functional Public Pop. SGP Quality Zygosity sites DBs Pop. DB Cardiovascular 746 338 76 26 9 2 Deafness 828 257 63 50 17 6 Dermatology 1113 271 71 41 17 5 Dysmorphology/Dysplasia 1529 369 80 43 15 2 Endocrinology 1129 326 61 42 19 5 Gastroenterology 362 190 60 20 6 1 Hematology 1474 324 79 39 18 3 IEM 1955 571 94 54 24 4 Neurology 2885 718 158 87 29 4 PID 633 309 111 22 6 1 Pulmonology 723 230 74 39 21 3 Renal 507 132 35 21 7 1 Vision 906 341 75 51 17 3 Total (averages) 1138 337 80 41 16 3 The table entries are the average number of variants per panel after applying the respective filter in the column title. The column titled ‘Input’ is the input without applying any filter. The column titled ‘Functional sites’ is for the step of filtering intronic, UTR, synonymous variants. The column titled ‘Public Pop. DBs’ is for the step of filtering variants based on the 1000 Genomes Project database. The column titled ‘SGP Pop. DBs’ is for the step of filtering variants based on the in-house database. The column titled ‘Quality’ is for the step of filtering based on the quality criteria. The column titled ‘Zygosity’ is for the step of excluding non-homozygous variants Genome Biol. 2015 Jun 26;16:134. “MENDELIOME ASSAY” CLINICAL SENSITIVTY Total patients Overall clinical Selected subgroup clinical Gene Panel type run sensitivity sensitivity Cardiovascular 243 28% Cardiomyopathy 32% Congenital heart disease 10% Arrhythmias 31% Aneurysms 29% Deafness 147 54% Hearing loss - Dermatology 68 62% Various derm. features - Dysmorphology/Dysplasia 354 38% Skeletal dysplasia 45% Dysmorphism 32% Endocrinology 36 61% Pituitary and thyroid disorders - Gastroenterology 73 29% Persistent jaundice - Hematology 33 24% Aplastic anemia - IEM 122 59% Metabolic disorders - Neurology 524 40% Syndromic DD/ID (recognizable 47% syndromes) Syndromic DD/ID NYD (not yet 25% determined, unrecognizable syndrome) Structural brain (cerebral/cerebellar/brain 34% stem) and spinal malformations/anomaliesa Non-syndromic
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