LECTURE 1 INTRO TO GENETICS 20 genetic disease classic Medical genetics single gene early onset pediatric 80 genetic susceptibility common gene variation and environment delayed onset adult Pedigree Children siblings parents Nuclear family age date birth health status age date death cause of death Proband individual who brings pedigree to your attention does not necessarily have to be affected General Info DNA RNA Protein Function Changes in environment Both have common DNA variants o Change in gene transcription profile o Change in protein profile SNP single nucleotide polymorphism single nucleotide difference Human genome 3 000 Mbp o 25 000 30 000 genes o Exons contain 1 5 of DNA o Gene distribution is uneven o Knowing the sequence of the genome makes it easy to locate genes and variants quickly NCBI Human Genome Sequence Components o Human DNA sequence o Human mRNA transcriptome o Variations o Usable database The ENCODE project encyclopedia of DNA elements project to discover all functional elements in human genome and release the information to the public o Genes can give many different proteins via splicing post ENCODE Advancements in Technology 1990 radioactive methods 3Kbp per day 1998 ABI Prism 300Kbp per day 2009 Helicos Genetic Analysis 21 28Gbp per run o While costs and speed have gone down dramatically for sequencing the costs for analysis are still very high Variation and Disease Everyone has 5 50 significant genetic flaws all diseases have some genetic component susceptibility o Down up regulate expression o Directly affect protein function structure o Alter mRNA splicing processing stability o Genetic disequilibrium with an unknown functional SNP Homocysteine intermediate product in protein catabolism removed via Remethylation to methionine Transulfuration to cysteine o Rs1801133 C T substitution at nt 677 Alanine valine substitution at codon 222 Altered protein T allele is thermolabile reduced activity increased plasma homocysteine Increased coronary heart disease cleft palate thrombosis o o o o Increased risk with increased affected relatives Increased risk with genetics Increased risk with living in SE USA Increased risk with decreased folic acid intake Pre perinatal folic acid therapy reduces frequency of NTDs SB and anencephaly Big Variations pathogenic variation causes big change in gene function single gene abnormalities dominant recessive chromosomal disorders trisomy deletions not common less than 1 1000 Small variations polymorphic variation small moderate changes diseases and conditions with genetic susceptibility common 1 2 1 100 Websites for Info NCBI national center for biotechnology information o Public databases research in computational biology software tools for analyzing genome data disseminates biomedical info for the better understanding of molecular processes affecting human health and disease Pubmed online catalogue of published papers OMIM online mendelian inheritance in man information on genetic diseases o Systematic arrangement classification of diseases SNP common variants Gene information on genes map viewer Gene Cards database on human genes products and involvement in disease o Concise info about functions of all human genes that have an approved symbol and other selected genes LECTURE 2 CYTOGENETICS 1 Intro to Cytogenetics Involves the study of chromosomes both the number and the structure are analyzed by conventional techniques G banding Molecular Cytogenetics FISH and microarrays have extended capabilities of identifying abnormalities Constitutional studies chromosome abnormalities present at birth o Prenatal Diagnosis CVS Amniocentesis Products of conception villi o Postnatal Diagnosis peripheral blood skin biopsy Tissues appropriate for conventional cytogenetic study That can undergo cell division during mitosis is best Chorionic villi amniotic fluid peripheral blood lymphocytes skin fibroblasts bone marrow After culturing in vitro a proportion of cells are arrested in mitosis and are then harvested for chromosome analysis o MOST COMMON tissue used to search for a constitutional abnormality is peripheral blood After harvesting the cell preparations are dropped onto glass slides and stained For most chromosome analysis a G banding technique is utilized for staining Each chromosome has a unique G banding pattern that is constant from individual to individual ISCN International System for Cytogenetic Nomenclature P short arm Q long arm Centromeres p10 and q10 Telomeres 6 bp sequence repeat at ends of chromosomes pter qter Band numbers increase as move from the centromere to the telomere A single G band typically contains more than 3 MB of DNA Therefore most constitutional chromosome abnormalities are associated with multiple congenital anomalies Therefore deletion of a single gene cannot be detected by G banding Clinical findings in Down Syndrome Recurrent respiratory infections GI tract anomalies increased risk for leukemia mental retardation Alzheimer s Pregnant women in 19 weeks gestation showing abnormal findings FISH is done because it is faster Fluorescence in situ hybridization FISH get results in 24 hrs G banding takes a week for culture of amniotic fluid disease o Phenotype Mapping for Down Syndrome APP amyloid beta precursor RUNX1 leukemia Dyrk neurogenisis Probe DNA label with fluorescent due and denature and hybridize Down Syndrome can also result from structural chromosomal abnormalities Trisome 21 o 95 due to meiotic nondisjunction o 4 due to Robertsonian translocation o 1 due to mosaicism In general TRANSLOCATIONS may be classified as BALANCED or UNBALANCED Balanced no net gain loss of essential genetic info Unbalanced net loss or gain of essential genetic material Carriers of balanced translocations are typically phenotypically normal but are at risk for generating gametes with unbalanced translocations LECTURE 3 CYTOGENETICS 2 Gain of an extra sex chromosome XXY and XYY 1 1000 males XXX 1 1000 females Most do not cause clinical suspicion in the newborn period 47 XXY 6 yr old presenting with behavior issues 15 hr old presenting with gynecomnastia large mammary glands in men 30 yr old male presenting with history of infertility Taurodontism enlarged pulp chamber at expense of roots in the molar teeth Micro deletion Syndromes Involve the loss of a very small amount of material from the chromosome Typically associated with a specific clinical syndrome Can be very difficult to detect by G banding therefore typically