General Genetics and New Technologies in Testing

Transcription

1 B3 General Genetics and New Technologies in Testing Karlene Coleman, RN, MN, CGC Clinical Instructor Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA Certified Genetics Counselor Children s Healthcare of Atlanta, Atlanta, GA The speaker has signed a disclosure form and indicated she has no significant financial interest or relationship with the companies or the manufacturer(s) of any commercial product and/or service that will be discussed as part of this presentation. Session Summary This session will provide an overview of the main patterns of inheritance, including chromosomal, single gene, and multifactorial. New technologies in testing will be included. Session Objectives Upon completion of this presentation, the participant will be able to: name the three main categories of genetic disorders; list the four main patterns of Mendelian inheritance; name the three etiologies of Down syndrome; correctly state the recurrence risk for a normal parent who carries a balanced 21/21 translocation; list three main features of Trisomy 13 and Trisomy 18; name five main features of Trisomy 21; name the features of the acronym CATCH22; state what percentage of all individuals born with the 22q11.2 deletion are sporadic and what percentage are inherited; state the main heart defects associated with Williams syndrome; define UPD and list the etiologies associated with Prader Willi and Angelman syndromes; describe the difference between routine chromosomes and a chromosomal microarray; list the main limitations of a chromosomal microarray; match classic pedigree diagrams to the correct Mendelian and maternal Mitochondrial patterns of inheritance; know the correct parent of origin where the gene for myotonic dystrophy will likely expand; state three main features of Mowat Wilson syndrome; define trinucleotide expansion and give two examples; define Multifactorial Inheritance and give three examples; list one main feature of the teratogens: diabetic embryopathy and PKU. B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 1 of 25

2 Test Questions 1. Which of the following statements are correct with regard to chromosomal submicroscopic deletions? a. They may be detected by FISH or acgh b. DNA sequencing is a useful means by which they can be detected c. They may result from unequal crossing over between two repeat sequences on the same arm of a chromosome d. Breaks in both arms of a chromosome can result in a ring chromosome containing a centromere 2. Which of the following statements are true of uniparental disomy? a. It results in a total of 47 chromosomes b. Both homologues of an autosome are from one parent with loss of the corresponding homologue from the other parent c. Uniparental disomy can result in an autosomal recessive condition only if both parents are carriers d. Uniparental disomy of both the maternal copies of chromosome 15 results in Angelman syndrome 3. Which of the following findings in a pedigree would most likely indicate autosomal dominant inheritance? a. affected individuals are all in the same generation b. female to female transmission c. male to male transmission d. male to female transmission in multiple generations 4. Which of the following conditions are inherited in an X-linked dominant fashion? a. Hemophillia B b. Marfan c. Galactosemia d. Fragile X 5. In myotonic dystrophy, the trinucleotide repeat expansion always occurs when: References a. the gene is passed through the father b. the mutation occurs after fertilization c. the parents are first cousins d. the gene is passed through the mother Gene Tests: Jones, K.L. (2006). Smith's recognizable patterns of human malformation (6th ed.). Philadelphia: Elsevier Sanders. Nussbaum, Robert L. et al. (2007). Thompson &Thompson genetics in medicine (7th ed.). Philadelphia: Elsevier Sanders. OMIM -Online Mendelian Inheritance in Man: B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 2 of 25

3 Session Outline See presentation handout on the following pages. B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 3 of 25

4 NNP Program curriculum guide: 2013 How Do I Know You? Let me count the genes Karlene Coleman, RN, MN, CGC Certified Genetic Counselor Children s Healthcare of Atlanta karlene.coleman@choa.org Genetics Principles of human genetics Genetic testing and screening Genetic abnormalities Human Genome Project Gene therapy Chromosomal disorders Inborn errors of metabolism Families eventually want to know.. What Happened? Why did it happen? Will it Happen again? Is it Genetic? Is it Inherited? Is there Treatment? Is there Prenatal Testing? Genetic diseases Chromosomal Single gene Mendelian Inheritance Dominant, Recessive, X-linked Multifactorial Cytogenetics G-banding The general population risk for a birth defect or genetic disease is 3% or 1/33 births! B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 4 of 25

5 Chromosome Technology Progress Technology Resolution Sample Diagnosis Karyotype Whole Down syndrome (1970 s) Chromosome Large Deletions or duplications (> 4 Mb) Fluorescence in situ ~ 100 kb 22q11.2 syndrome Hybridization (FISH) VCFS (1990 s) Tests a single locus at a time Need Prior knowledge of region Array CGH Flexible, only Submicroscopic (2000 s) limited by probe deletions/duplications spacing (> 1 kb) anywhere in the genome Can test whole-genome simultaneously Down Syndrome Signs in the Neonate 80% Hypotonia 85% Poor Moro reflex 80% Hyperflexibility of joints 80% Excess skin on back of neck 90% Flat Facial Profile 80% Upslanted palpebral l fissures 60% Anomalous Auricles small, overfolded helix 70% Dysplasia of Pelvis on x-ray 60% Dysplasia of midphalanx of fifth finger 45% Single transverse palmar crease 6 or more of above features are found in 89% of Down syndrome neonates 1:600 live births advanced maternal age effect Slide courtesy of Jennifer Mulle PhD Down syndrome other features Head Brachycephaly with flat occiput Eyes Speckling of iris (Brushfield spots) 70% refractive errors myopia 45% strabismus Cardiac anomalies in 40% AVC, Endocardial cushion defect Feet Wide gap between toes 1 & 2 Plantar crease between toes 1 & 2 Genitalia Small penis Decreased testicular volume Primary gonadal deficiency is common Palmar & Plantar creases in Down syndrome Trisomy 21- Down Syndrome most common chromosomal abnormality in newborns Standard Trisomy 21 (95%) Translocation Down Syndrome (4%) Mosaic Down Syndrome (1%) Single Transverse Palmar Crease Deep plantar furrow & gap between toes 1 and 2 Standard Trisomy 21 Translocation Down Syndrome B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 5 of 25

6 Translocation Down Syndrome Translocation 21/21 Carrier Parent Mosaicism abnormal cell division resulting in two or more types of cells containing different numbers of chromosomes M7 AML (Acute Myeloid Leukemia) Down syndrome or Mosaic Non Down Syndrome Need Low dose chemotherapy Prognosis very good Need High dose chemotherapy Prognosis not very good Down Syndrome Resources Down Syndrome Association of Atlanta National Down Syndrome Congress (NDSC) National Down Syndrome Society (NDSS) Parent to Parent of Georgia click on Genetic Clinics and then Down Syndrome Clinic B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 6 of 25

7 Trisomy 13 Incomplete development of the Forebrain (holoprosencephaly) Olfactory Optic nerves (micro/anophthalmia, colobomas) Seizures - hypsarrhythmia pattern Microcephaly (> 50%) Sloping forehead Cleft lip and/or palate (60 to 80%) Single umbilical artery (>50%) Trisomy 13 Cutis aplasia of scalp (> 50%) Polydactyly (> 50%) Cardiac (80%): VSD, PDA, ASD Deafness (> 50%) Apnea in early infancy Severe mental retardation Incidence - 1:5000 live births Median age of survival 7 days 91% deceased by 1 year Cutis aplasia Polydactyly Trisomy 18 Features > 50% of patients IUGR, polyhydramnios, and single umbilical artery Hypotonia weak cry Prominent occiput Low set malformed ears Short palpebral fissures Short Sternum Clenched Hand with overlapping fingers Rocker Bottom feet Male cryptorchidism Severe mental retardation Monosomy -Turner syndrome (45,X) Short stature, coarctation of the aorta, cystic hygroma/webbed neck, infertility, normal IQ Incidence - 1:1000 live births The only aneuploid that seems unrelated to mother s age Incidence - 1:3000 live births 90 to 95% deceased by 1 year Cutis gyrata SGA CHD: coarc Ao or HLHS Excess skin at neck Shield chest Lymphedema Sm hyperconvex finger nails Hypoplastic finger/toe nails 45,X Newborn New Technologies in Testing - FISH Looks for small specific sections of DNA (30-50 genes) that would be missed by routine chromosome analysis Detects microdeletion syndromes like: 22q11.2 deletion aka velo-cardio-facial synd. aka DiGeorge synd. 7q11 del Williams B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 7 of 25

8 FISH advantage 24 hour turn around time 22q11.2 deletion, Velo-cardio-facial syndrome, DiGeorge syndrome 22q11.2 Region and FISH Incidence ~1:2000 live births Conotruncal cardiac defects: 76% IAA, Truncus arteriosus, TOF, VSD Abnormal facies 100% (more difficult to assess in African American infants) Thymic aplasia/ hypoplasia: 77% Clefting/ palate abnormalities: 83% Hypoparathyroid - hypocalcemia: 49% 22q11.2 deletion 22q11.2 deletion, Velo-cardio-facial syndrome, DiGeorge syndrome 90% of cases are sporadic (not inherited) 10% of cases are inherited from mom/dad Parents who have the deletion have a 50% chance of passing it on to every future pregnancy Most parents with the deletion required Special Education in school Facial Features: short and narrow palpebral fissures, long faces, high palates with hypernasal speech History of heart defects or GI problems Facial Features in 22q11.2 deletion Hooded eyelids Short and narrow palpebral fissures Bulbous nose or bifid nasal tip hypoplastic alae nasi Microstomia Developmental & speech delay 22q11.2 deletion - Features in infants Normal ear Typical ear for 22q11.2 deletion: deficient upper helix overfolded helix small ear C-shaped ear B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 8 of 25

9 22q11.2 deletion - What to offer families Ryan and Jenny Dempster Family Foundation 22q Resources on the Web International 22q Foundation Ryan and Jenny Dempster Family Foundation emory edu/22q Southeastern Center for Excellence in 22q Genetic Conditions and Rare Conditions Support Groups Parent to Parent of Georgia DiGeorge phenotype without 22q11.2 deletion Do not rely on FISH results only. 10% of patients with DiGeorge phenotype do NOT have the 22q11.2 deletion They are still DiGeorge and need to be treated accordingly Fish for Williams syndrome Incidence 1:15,000 to 20,000 Normal Deleted Williams syndrome 7q11 deletion by FISH Contiguous gene deletion syndrome Hemizygosity at the elastin (ELN) locus is thought to explain the supravalvular aortic stenosis (SVAS), hoarse voice and rapidly aged-appearing skin Flanking genes to the 7q11 region are thought to cause the other manifestations Disruptions of (ELN) at 7q11.23 cause the autosomal dominant form of isolated SVAS B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 9 of 25

10 Williams syndrome Williams syndrome 7q11.23 del Intermittent infantile hypercalcemia Growth retardation IUGR, SGA Cardiovascular anomalies: supravalvular aortic stenosis (SVAS) peripheral pulmonic stenosis (PPS) Mild to moderate mental retardation Outgoing friendly personality Incidence 1:15,000 to 20,000 live births Mild prenatal growth deficiency FTT in infancy (70%) Poor linear growth the first four years Mean adult height is below 3rd percentile Williams syndrome 7q11.23 del Periorbital fullness Bitemporal narrowing Short nose Full nasal tip Malar hypoplasia Long philtrum Wide mouth Small jaw IUGR/SGA Prader Willi (PWS) & Angelman (AS) syndromes Chromosome 15q11-q13 del PWS Obesity (onset 6 months to 6 years), hypotonia, MR, small hands and feet, short stature, almond shaped eyes, narrow bifrontal diameter, hypogonadism Chromosome 15q11-q13 del AS -MR, seizures, short stature, blond hair, hypopigmentation, large mouth, wide spaced teeth, prognathia Prader Willi Syndrome (PWS) PWS & AS: Need not only 46 chromosomes Need one from each pair from mom and one from dad Neonates present with: Hypotonia - FTT May require ventilator support Hypogonadism in males Incidence - 1:15,000 live births Embryonic Trisomy Rescue Uniparental Disomy UPD: the presence in the karyotype of two copies of a specific chromosome, both inherited from one parent, with no representative of that chromosome from the other parent. B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 10 of 25

11 Chromosome 15q11-q13 Prader Willi Syndrome 3 etiologies Angelman syndrome Prader Willi syndrome 70-75% 25-29% < 1% Prader Willi Syndrome Array-based Comparative Genomic Hybridization Patient DNA Genomic Clones Initial Screening Test Sporadic Sporadic Could carry 50% risk for recurrence Control DNA Pinkel et al., Nat Genet (1998), 20(2): Slide courtesy of Christa Martin, PhD NORMAL Only detects unbalanced rearrangements Patient DNA Control DNA Array-based CGH Genomic Clones Loss: ratio < 0.8 Normal: ratio Gain: ratio > 1.2 Emory Array Formats and Characteristics EmArray 60K: 60,000 oliognucleotides, covers 75 kb whole genome and 400 targeted region. List price: $1,695. EmArray 180K SNP: 180,000 oligos, covers areas of 25 kb whole genome and absence of heterozygosity for UPD and areas of common descent [consanguinity]. List price: $1,995. Array image from UCSF website B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 11 of 25

12 Turner synd. (45,X) Normal (46,XX) 47,XXX Small (200 kb) Heterozygous deletion of 7q35 Chr. 7 22q11.2 Region and FISH oligo probe coverage on EmArray 3 Mb DGS region FISH probe (~100 kb) used for testing only covers this gene Prevalence ~1:2000 live births EmArray Results - ABNORMAL Limitations of Standard array CGH technologies Trisomy 21 Notice majority of oligos are shifted to the right, outside of the green line Cannot detect low-level mosaicism (<20-30%) Cannot detect balanced translocations Cannot detect structural variants (inversions) 21 Chr 21 B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 12 of 25

13 Limitation: Microarray will not detect Balanced Structural Abnormalities 4p+ and 11q- (This was not detected on prenatal chromosomes) 4pter-p16.1 gain: 8.3Mb 11q23.2-qter loss: 15.6Mb 4p duplication: prominent glabella, depressed nasal bridge, bulbous nose, short neck, low hairline, growth and mental retardation, parents at risk for balance carrier status 11q deletion: Jacobsen syndrome, ocular hypertelorism, large, carp shaped mouth, cardiac defects, ParisTrousseau (neonatal thrombocytopenia) Patient MH: Single ventricle cortriatrium hypoplastic aorta Indications for Microarray Use As an alternative to routine chromosomes or FISH Routine chromosomes abnormal detection rate is 5% Microarray abnormal detection rate is 18 to 20% Assess the size and gene content of unbalanced chromosomal rearrangements To test for cryptic deletions/duplications in individuals with apparently balanced translocations and a clinical phenotype Chromosome to genes Testing strategies for Mendelian Diseases: Biochemical testing Gene Sequencing The human genome is made up of 3 billion ( ) bases of DNA The four letters of the DNA alphabet A, C, G, and T are used to carry the instructions ti for making an organism. The order (or sequence) of these letters holds the code for the building blocks (20 amnio acids) used in various combinations to make genes which in turn produce our proteins, for example keratin in hair and hemoglobin. B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 13 of 25

14 Modes of Inheritance Autosomal: non-sex determining chromosome (one of the first 22 in humans) Autosomal mutations effect males and females equally! Types 1. Autosomal Dominant 2. Autosomal Recessive Autosomal Dominant Transmitted from parent to child or can occur as new mutations Affected person has a 50% chance of passing trait Tend to occur in every generation Examples: Achondroplasia Marfan Syndrome Nuerofibromatosis Type I Autosomal Dominant Myotonic Dystrophy Congenital: Appears at birth - is most severe Juvenile: Appears after birth and in teen years Adult: Appears in the late 20's to early 40's Late Onset: Appears later after 40's and generally mild Incidence 1:8000 Incidence of the congenital form 1:100,000 B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 14 of 25

15 Myotonic Dystrophy Characterized by muscle stiffness and progressive dystrophic changes leading to muscle weakness and atrophy Myotonia is defined as hyperactivity of the muscle cell membrane The problem lies in the inability of the muscles to relax once contracted Genetic Mechanisms of Myotonic Dystrophy Caused by an excessive number of CTG trinucleotide repeats of one allele on Chr 19 (q13.2q13.3) Unaffected persons have from 5-34 repeats Congential Myotonic Dystrophy one allele has over 2000 repeats DNA test ~ $ (Normal CTG repeat size is 5-34): Congenital Myotonic Dystrophy This form is evident prenatally Diminished fetal movements Polyhydramnios Occurs in 50% of offspring of myotonic mothers (never fathers) Affected mother may be minimally affected and often undiagnosed Prevalence 1 in 100,000 (1 in 3,500 in Sweden) Neonatal Signs of Myotonic Dystrophy Diminished cry Poor suck reflexes Severe hypotonia weak muscle tone and floppiness Severe respiratory compromise likely to be ventilator dependent Extensive facial weakness Moms have hypotonic facies SM: 1 month old Hispanic Congenital myotonic dystrophy Floppy in delivery room Apnea intubated in DR Ventilated for 1 month Hypotonic facies Open mouth Tented upper lip Poor tone Poor movements Test Results: Allele 1: 5 repeats Allele 2: 2400 repeats B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 15 of 25

16 SM: Congenital myotonic dystrophy Myotonic dystrophy Shake hands - affected person will grasp but have difficulty releasing grip Mom s grip and release Hypotonic facies in mom Mental retardation: mom was in 5 th - 11th grades in USA and still does not speak English CHARGE syndrome Colobomas 80-90% iris or retina Heart 75-80% Aortic Valve stenosis, coarctation, IAA, TGA Atresia Choanae 58% Retardation of: Growth (70%) Development 100% Genital hypoplasia in males 75% Ear anomalies and deafness 90% CHARGE syndrome: Square face with asymmetry Cleft lip and palate (30%) CHARGE syndrome Ears Normal ear Typical CHARGE syndrome ear Deficient upper helix triangular crus absent lobes Posteriorly rotated Triangular Crus Underdeveloped Upper helix Over folded Upper helix Moderate to severe hearing loss B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 16 of 25

17 CHARGE syndrome Inheritance: usually sporadic however, once it occurs. it is Autosomal Dominant (50% risk for recurrence) in the affected individual Some presentations can be very mild be sure to evaluate parents for subtle physical signs and for hearing impairment CHARGE syndrome Consider CHD7 testing if positive, prenatal testing could be offered to future pregnancies Sequence analysis/mutation scanning of the CHD7 coding region detects mutations in approximately 60% - 65% of individuals with Charge syndrome Cost: $3600 Congenital Central Hypoventilation Syndrome (CCHS) Generalized autonomic nervous system dysfunction/dysregulation (ANSD) Characterized by adequate ventilation while the affected individual is awake and by hypoventilation during sleep Subset with altered neural crest-derived structures (i.e. Hirschsprung) and tumors of neural crest origin including neuroblastoma, ganglioneuroma etc. Can present in newborn, childhood or adulthood. Congenital Central Hypoventilation Syndrome (CCHS) 92% of affected individuals have a PHOX2B polyalanine repeat expansion of repeats 8% of affected individuals need the entire gene sequenced to detect deletions or point mutations ~5% of parents are mosaic for the mutation and have a 50% risk for recurrence in every future pregnancy Autosomal Dominant 50% recurrence risk CCHS: Congenital Central Hypoventilation Syndrome 2006 Son born by IVF with mom s egg and dad s sperm Central Hypoventilation Hirschsprung Labile blood pressure CCHS: Congenital Central Hypoventilation Syndrome Mom had Hirschsprung Disease No issues with respiratory deficiency or anesthesia Mom was mutation positive in blood (with brain spairing???) Mom unconvinced about mosaicism - used frozen embryo for next pregnancy Second Affected Son B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 17 of 25

18 Autosomal Recessive Autosomal Recessive Both parents are carriers Ethnic background is significant Increases with consanguinity Usually not seen in every generation Examples: Sickle Cell Cystic Fibrosis Spinal Muscular Atrophy Are you a carrier of a recessive disorder? Spinal Muscular Atrophy 2 nd most common AR disorder after CF Type 1: Werdnig-Hoffman 7/100,000 live births Autosomal Recessive Hypotonia Facial weakness minimal DTRs decreased or absent Tongue fasciculations SMN1 gene mutation degeneration or loss of motor neurons in the anterior horns of the spinal cord Types II and III - later ages of onset NBS: Prevention! Untreated and Treated PKU Newborn Screening: It s Not Just the PKU Test! Occurring in ~1 in 10,000 babies born in the U. S Can cause mental retardation, organ damage, and unusual posture if untreated Treatment of PKU is the elimination of phenylalanine from the diet B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 18 of 25

19 Newborn Screening:Tandem Mass Spectrometry [TMS] Amino Acid Profile Acylcarnitine Profile Organic Acids (parital) NBS: HRSA/ACMG/MOD/AAP: 2004 Genetics in Medicine. Vol 8. May disorders on a Uniform Panel 9 Organic Acidemias 5 Fatty Acid Oxidation Defects 6 Amino Acidopathies 3 Hemoglobinopathies 6 Others: CH, CAH, Galactosemia, Cystic Fibrosis, Hearing 25 additional Reportable Disorders found by TMS Modes of Inheritance Cont X-Linked- mutations in genes on the X chromosome Georgia Newborn Screening State Specific Web Sites Have Valuable Information X-linked dominant fathers cannot pass X-linked traits to their sons Can be lethal in males X-linked recessive fathers cannot pass X-linked traits to their sons Males are more frequently affected than females Rarely have affected females X-Linked Dominant in Males X-Linked Dominant in Females B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 19 of 25

20 X-Linked Dominant - Fragile X expansion of a CGG tandem repeat in the FMR1 gene Males: Average IQ < 50 ADHD/ Autism spectrum Post pubertal macroorchidism Large ears & dysmorphisms Avoidance of eye contact Females (milder): ADD Learning disabilities Personality disorders Premature ovarian failure (20%) Fragile X Mental Retardation 1 (FMR1) CpG Transcription Island Translation (CGG)n 5 3 ~44 repeats Common ~45-54 repeats Intermediate ~ repeats > 200 repeats, methylated Premutation Full mutation Male Female 1/25 1/12 1/800 1/250 1/4000 1/4000 X-Linked Recessive in Males X-Linked Recessive in Females Example of X-Linked Recessive Hemophilia A (Xq28)- decreased production of Factor VIII, required for normal clotting B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 20 of 25

21 Gene Therapy The Tsar in Waiting: Alexis Copyright restrictions may apply. Inserting a gene into the patient s cells instead of using drugs and surgery Replacing a mutated gene Knocking out a mutated gene Introducing a new gene to fight a disease Promising option but remains risky and still under study for safety and efficacy Current use for treatment of diseases with no other cures Gene Therapy A way to correct disease by altering the gene Would allow a person with hemophilia to make their own factor May still need infusions after serious injury or surgery Use a virus to introduce a working copy of the gene into a person s cells May need to be repeated multiple times Would not correct the mutation in the patient s sperm (or egg) cells Challenges to Gene Therapy Finding the right vector Most research done on adeno-associated viruses (AAV) Targeting g of the correct cells (ie liver, lung) Getting corrected gene to produce sufficient quantities of the factor Avoiding rejection by the body Need to reduce the immune response Need to curtail the production of antibodies Example of X-Linked Recessive Molecular Information for DMD Duchenne muscular dystrophy (Xp21.2)- decreased production of dystrophin, required for normal muscle activity Females are rarely affected by these forms of muscular dystrophy Huge gene with 79 exons spanning at least 2,300 kb Majority of mutations are deletions (60%) or duplications (6%) The remainder are point mutations resulting in premature translation termination B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 21 of 25

22 DMD Gene Multifactorial conditions: Caused by a combination of genes and environmental effects Isolated Heart defects Isolated Cleft lip +/- palate Isolated Spina bifida Some functional protein Multifactorial Conditions Cleft Lip/ Cleft Palate Babies can be born with both cleft lip and cleft palate Males are affected more frequently than females. Occurs more frequently in Asians, American-Indians, and African Americans Multifactorial Conditions Spina Bifida is the most common of a group of birth defects called neural tube defects (NTDs) affects the backbone and, sometimes, the spinal cord B vitamin folic acid- can prevent some neural tube defects (including spina bifida) Prevention - Folic Acid Revolution Prevention Folic Acid All women of reproductive age need 400 micrograms of folic acid daily Women who have had a neural tube defect need 4000 micrograms while planning and during a pregnancy 4000 micrograms of folic acid a day from folic acid only pills --needs a prescription Folic acid also thought to be helpful for cleft lip and or palate and congenital heart defects Need to start at least 3 months prior to conception for best effect B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 22 of 25

23 Teratogens and Environmental Maternal PKU Powerful Teratogen Diabetic Embryopathy: Caudal regression clubbed foot CHD Pre-hallucal polydactyly Microcephaly, Coarc Aorta, Multiple VSDs Environmental causes of Birth Defects What s on the horizon???? Amniotic Bands Oblique facial cleft 2007 J. Craig Venter Decoded a full diploid genome his and James Watson s 1990 Human Genome Project goals included: determine the sequences of the 3 billion chemical base pairs that make up human DNA ***It took 13 years and 2.7 billion dollars It took 3 months and $300,000 each B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 23 of 25

24 HGP What are they finding? In the 3 billion base pairs there are: 21,000 Protein coding genes 15,000 will be linked to diseases 2,500 are known to cause disease today In spite of Microarrays, Targeted Gene sequencing and Gene Panels still many rare genetic disorders cannot identify. What if you could sequence ALL the EXONS of a child, and compare the sequence to the all the exons in the human genome sequence. Whole Genome Sequencing (WGS) & Whole Exome Sequencing (WES) is in clinical practice Children s Hospital of Wisconsin & Medical College of Wisconsin offers whole genome sequencing: Nature 478, (2011) News Feature Human genetics: Genomes on prescription Brendan Maher 48 patients evaluated for the programme, 17 have been accepted, and their families have gone through six hours or more of genetic counseling before sequencing. Insurance companies have agreed to foot the bill for at least two of the cases. Next Generation Sequencing Genome vs. Exome Genome vs Exome sequencing What is the exome? Human Genome: 20K to 25K genes Genes Genes composed of exons that code for AA of a protein Introns are spacer regions that are spliced out Can interpret a change in AA sequence such as an Arg to a stop codon As of September 2014 Whole exome sequencing for $5,000 Illumina close to $1,000 TAT ~15 weeks Goal: to be able to do individual genomes for under $1,000 B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 24 of 25

25 WES to identify known disease gene What about using genetic information to discriminate? Freeman Sheldon syndrome AD disorder caused by mutations in MYH3. WES of 4 patients with Freeman Sheldon syndrome Identified mutations in MYH3 in all 4! Genetic Information Nondiscrimination Act of 2008 (GINA) What GINA covers Protects people from discrimination by health insurers and employers on the basis of DNA information What GINA does NOT cover Life Insurance, Disability insurance and Long-term care insurance Military Personnel Resources on the Web On-line Mendelian Inheritance in Man (OMIM) Or Google OMIM Genetic Conditions and Rare Conditions Support Groups For updated summaries for specific genetic diseases click on Gene Reviews box at top of home page and then type the disease name in the search window Emory Genetics Laboratory for tests and forms Other states will have similar labs and genetic services B3: GENERAL GENETICS AND NEW TECHNOLOGIES IN TESTING Page 25 of 25