Sam Rhine - Genetic Update Conferences - www.samrhine.com
Genetics of Common Human Traits and Diseases…..
Cloning and Stem Cells…..New Medical Applications
Basic Genetic Stuff Review:
I. CHROMOSOMES - CYTOGENETICS:
A. Metaphase Spread - first observation was in 1956 - confirmed chromosome number = 46
B. Karyotype - chromosomes cut out and arranged by size - from tallest to shortest
1. Autosomes - #1 thru #22
2. Sex Chromosomes - XX - Female; XY - Male
3. Chromosome Anatomy - Chromosome #5
a. Centromere - constriction
b. p-arm - short arm - placed up in the karyotype
c. q-arm - long arm - placed down in the karyotype
d. Telomeres - top and bottom of every chromosome
e. Chromatids - double arms of the chromosome - fuse with banding
f. Has #5 - Homo sapiens chromosome #5
4. Chromosome Identification - How do you tell them apart?
a. Chromosome Banding - unique sets of stripes on all the chromosomes
b. Permits individual chromosome identification = 'Bar Code"
c. International System of stripes and numbers
d. Ideogram - Idealized Diagram of banded chromosomes
e. Pinpoint Break Points…..1q23
f. Pinpoint Gene Locus (Loci) = address…..Rh - 1p34; UDGP - 1q21
h. High Resolution Banding - see more bands - Cystic Fibrosis - 7q31.2
C. Syndrome: a recognizable pattern of anomalies, a group of signs or symptoms,
that occur together and characterize a particular abnormality
D. Chromosome Syndromes: 1 in 160 live births / 50% of a miscarriages
MCA babies (Multiple Congenital Anomalies
1. Trisomy 16 - most common chromosome syndrome - always miscarries
2. Trisomy 21 - most common chromosome syndrome in live born babies
a. Down Syndrome - 1/800 - Dr John Langdon Haydon Down - 1866
b. Most common GENETIC cause of Mental Disability
c. Principle Features - Syndrome Diagnostic Criteria
d. Best of the whole chromosome syndrome children
e. Karyotype - Trisomy 21
f. Cause - Non-Disjunction of pair 21 on egg or sperm formation
g. Monosomy 21 - other possibility with NDJ of #21
h. Parents are usually fine - error in formation of egg or sperm
i. 90% Maternal NDJ / Increase of DS with increasing Maternal age
j. DSCR - Down Syndrome Critical Region at 21q22.1 = tripled for DS
3. Trisomy 18 - Edwards Syndrome - NDJ pair 18
4. Trisomy 13 - Patau Syndrome - NDJ pair 13
5. Monosomy X - Turner-Ulrich Syndrome - NDJ of XXs or XY
6. XXY Syndrome - Klinefelter Syndrome - NDJ of XXs or XY
E. Why does a baby with an extra chromosome have a diability?
1. Why MCA?
2. Why is Trisomy 21 best?
3. Principle of Duplicate Balance - Genes usually come in pairs
4. Trisomy 21 - 231 genes on chromosome #21 are in triplicate
a. Triple dose of all the proteins from the genes on chromosome #21
b. Leukemia increae
c. Fewer solid tumors
d. APP Inherited Alzheimer gene 21q21 - Down Syndrome all develop Alzheimer
e. DSCR-1 Gene tripled - deficient number of dendritic spines = MR
II MONOGENIC INHERITANCE - SINGLE GENE PAIR - MENDEL'S RULES of INHERITANCE
19th Century - Inheritance thought to be BLENDING - even mixture from both parents
A. Johann Gregor Mendel
1. Monk - Church of the Assumption - St. Thomas Monastery in Brno, Czech Republic
2. born: July 20, 1822 - died January 6, 1884
3. published work on peas - 1866 / forgotten / Rediscovered ~1900
4. "My time will come, people will see it one day, it doesn't matter that I will not be there"
5. Beginning of Particulate Inheritance - inheritance via particles called genes
Pairs of genes that…..1. Segregate and 2. Independently Assort
20th Century - Inheritance understood to be PARTICULATE
B. Monogenic Reference Sites:
1. OMIM - Online Mendelian Inheritance in Man - ~20,000 with code numbers
http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim
2. Genes and Disease - summaries of ~80 common monogenic conditions
http://www.ncbi.nlm.nih.gov/books/NBK22183/?depth=2
3. Code Numbers: 100000 = AD; 200000 = AR; 300000 = XL;
400000 = YL; 500000 = ML (mitochondrial)
C. AUTOSOMAL DOMINANT INHERITANCE - AD
One Parent Affected / One Parent OK / Passed to half the children / 50%
1. Brachydactly - first recognized AD in humans - OMIM = 112500 - multiple types
2. Huntington Disease - OMIM = 143100 - 4p16.3 - Late Onset - shows up in 40's or 50's
CAG Triplet Repeat Mutation - gene elongates every generation
Mutant HTT Huntingtin Protein - leads to loss of striatal neurons in brain
3. Neurofibromatosis - OMIM = 162200 - 17q11.2
Causes small benign tumors - neurofibromas - may be mild to very severe
4. Marfan Syndrome - OMIM = 154700 - 15q1.5
Tall; slender; long arms, legs and fingers; prone to aortic aneurysm
5. Alzheimer Disease - ~1% of cases inherited - APP = Amyloid Precursor Protein
APP gene > APP Protein > cleaved to become Amyloid Beta > accumulates
D. AUTOSOMAL RECESSIVE INHERITANCE - AR
Both Parents OK / Both Parents are Heterozygous Carriers / 1 in 4 / 25%
What does 1 in 4 mean - shuffle the four Aces - draw a card - Ace of hearts = aa
1. Cystic Fibrosis - OMIM = 219700 - 7131
Abnormal CFTR membrane protein - leads to abnormal cell secretions
Respiratory complications and infections - more common in Caucasians
2. Sickle Cell Anemia - OMIM = 141900 - 11p15.5 - Beta Globin Gene
Causes sickling of RBCs in situations of low oxygen tension
More common in individuals of African and Mediterrsnesn ancestry
3. Tay-Sachs Disease - OMIM = 272750 - 15q23 - Hexosaminidase A deficiency
Causes slow down hill deterioration from ~4 months to ~48 months
More frequent in Ashkenazi Jewish populations
E. X LINKED RECESSIVE INHERITANCE - XLR
Mother is fine but Carrier if a harmful recessive gene / Father is fine
Half the sons will be affected / half of the daughters will be carriers
1. Hemophilia Type A and Type B - OMIM = A - #306700 - Xq28 - Factor VII
B - #306900 - Xq26.3 - Factor IX
Blood clotting Factors deficient - sometimes called the 'Bleeders Disease'
2. Duschenne Muscular Dystrophy - OMIM = 310200 - Xp21.1
Most common type of Muscular Dystrophy
3. Fragile X Syndrome - OMIM = 309550 - Xq27.3 - bottom of long arm of X
Moderate to Severe MR / Autism in ~50% / long face / large ears / large jaw
CGG Triplet Repeat of Mutation in FMR1 gene - at Fragile Site on X chromosome
Most common Inherited Cause of Mental Retardation
Diminished number of Dendritic spines - Therapy CTEP inhibition of mGluR5
4. Happiness Gene - sex limited - only in females - low MAOA levels
X linked recessive deficiency that Lyonizes in females
Genome and Genes Review:
I. INTRODUCTION: Genome / Genes / Gene Control …..September 1, 2012
A. Genome: the sum total of all the genetic information for any biologic organism
1. DNA - double strand
2. RNA - single strand
3. Expressed as the total number of nucleotides
a. Human Genome: ~3,000,000,000 nucleotides pairs, ~20,000 genes
b. HIV Genome 9,749 nucleotides 9 genes
4. Human Genome:
~1.5% - 'Coding' DNA………carries DNA Code of 20,000 protein producing genes
~98.5% - 'Non Coding' DNA…'Junk' DNA
B. Gene:
1. 'Coding' DNA Genes - carry the genetic code to make a protein
a. sequence of DNA responsible for the production of a specific protein molecule
b. DNA double strand with promoter (on/off) region in nucleus
b. DNA transcribed into mRNA (transcript) in nucleus
transcript with genetic code, plus 5' and 3' UTRs - UnTranslated Regions
c. Transcript translated into protein at the ribosome - at endoplasmic reticulum
d. both Coding and Non Coding DNA segments within almost all Coding Genes
Coding Segments - Exons - part of the 1.5% Coding DNA
Non Coding Segments - Introns - part of the 98.5% Non Coding DNA
e. RNA Processing - occurs in the nucleus - at the Spliceosome
Remove the Introns / Splice the Exons together
2. 'Non Coding' Genes - carry a code to make RNA only
a. sequence of DNA responsible for the production of a specific RNA molecule
b. produce ~500 small non coding RNAs - microRNAs - negative gene control
3. Coding and Non Coding DNA in Coding Genes:
a. EXOME - sum total of all the Coding DNA in all the Exons - 1.5%
b. INTROME - sum total of all the Non Coding DNA in all the Introns - 98.5%
c. Exome plus Introme = ~30% of the genome, therefore ~70% 'Junk'
d. 500 Non Coding microRNA genes in the 70%
e. Most of the microRNA genes are in the 'Junk' - but some are in the introns
microRNA gene in an intron - 'Gene within a Gene' - mirTRON
f. mirTRON - Non Coding DNA gene exists with an Intron of a Coding DNA gene
g. Total Number of Human Genes: ~20,500…..20,000 Coding + 500 Non Coding
h. Summary - Coding DNA Genes contain both:
Coding DNA (exons) and
Non Coding DNA (introns)
Non Coding DNA Genes contain:
Non Coding DNA only
C. GENE CONTROL = GENE REGULATION - ON / OFF MECHASNISMS
1. Transcription Factors - turn transcription ON and OFF
a. attaches to the Promoter
b. promoter acts as 'Docking Site'
c. TF Activators - bind to promoter and turns genes ON
d. TF Repressors - bind to promoter and turns gene OFF
e. Enhancers - can also bind to DNA and enhance protein output
2. microRNA = miRNA - negative regulators - turn genes OFF
a. microRNA, ~22 nts, complementary to and binds to 3' UTR of transcript
b. helps usher RISC (RNA Induced Silencing Complex) to the 3' UTR
c. RISC blocks the ribosome > blocks translation > turns gene off
d. referred to as miRNA 'Gene Silencing'
e. microDNA - newly discovered type of normal human cellular DNA
small circles of non-repepitive DNA, 200-400 bp in length
widespread in all human somatic cells
produced by chromosomal microdeletions
3. Epigenetics - 'Epi' means upon / on top of / above and beyond the DNA
a. Chromatin - epigenetic control mechanism acts on chromatin
DNA (Genome) interacting with Histone Proteins
DNA / Histone Complex
b. Histone Proteins: H1, H2A, H2B, H3, H4
NCP - Nucleosome Core Particle - octomer: 2-H2A, 2-H2B, 2-H3, 2-H4
Nucleosome - DNA wrapped around the NCP
Nucleosome Fiber - strand of multiple nucleosomes
DNA…..'Never Acts Alone'
c. Gene Contol: the Degree of Chromatin Compaction
i. Methylation of Cytosine in the DNA of Chromatin at CpG Islands
add methyl groups - compact = 'Closed' chromatin = OFF
lose methyl groups - loose = 'Open' chromatin = ON
ii. Acetylation of Histone Proteins = 'Open' chromatin = ON
d. Methylation and Acetylation
Epigenetic Marks on the Chromatin
Remodels the Chromatin Architecture
e. Enzyme Controlled Mechanism:
Methylation Enzymes: DNMT - DNA Methyl Transferase
de novo DNMT-3
maintainence - DNMT-1
Acetylation Enzymes:
HAT Histone Acetylase
HDAC Histone DeAcetylase
f. Epigenome
Chromatin modified - DNA sequence does not change - 'above & beyond'
Genome - 3,000,000,000 nucleotides of DNA
Epigenome - Chromatin modifications - determines all of our phenotypes
Modification is an ongoing, life-long process, affected by the environment
Identical twins - two persons who are genetically identical
but may not be epigenetically identical > different phenotypes
GENOME - stable - does not change
EPIGENOME - fluid - changes all the time
Epigenetic modifications can be passed through the gem line!!
D. ENCODE - ENCyclopedia Of Dna Elements - new information as of September 5, 2012
1. International Consortium
2. 32 Research Institutions
3. 442 Consortium members
4. 10 Year Genome Annotation Research Project
5. 30 Coordinated Research Papers released Sept 5, 2012
6. 4 Major Journals: Nature, Science, Genome Research and Genome Biology
7. New Genome Findings:
a. many non coding parts of the genome…..the 'Junk'
contain 'Docking Sites' where control proteins effect gene
expression of both nearby and distant genes…..How Many?
2,890,000 - newly discovered Docking Sites…..in the 'Junk'
~200,000 active in any given cell at any one time
8. Gene Switches do not turn genes ON /OFF - they are 'Dimmer Switches'
9. Also in the 'Junk':
a. sncRNAs - small non coding RNAs:
20 to 200 nucleotides - microRNA,, rRNA, tRNA - ~500
b. lncRNAs - long non coding RNAs:
200 to 1000s of nucleotides - control Coding genes - ~9,500
10. 80% of the genome nucleotides now have a biochemical function!
80%.....going to be 100% soon!
11. Total number of genes in the Human Genome? ~30,000
20,000 Coding Genes + 10,000 Non Coding Genes = 30,000
Genetics of Common Human Traits and Diseases…..
and their Multifactorial / Polygenic Origins
INTRODUCTION: GENOMIC MEDICINE - NEW ERA of HUMAN GENETICS
A. OLD: Genetic Medicine - the use of knowledge about single genes to improve
the diagnosis and treatment of single gene diseases…..~20,000
B. NEW: Genomic Medicine - the use of knowledge about the entire GENOME
1. plus NONGENOMIC factors that effect health and disease;
2. new diagnostic and therapeutic approaches to help
3. understand COMMON MEDICAL conditions
4. by studying POPULATIONS of people
5. Genomic Medicine - there is no 'Normal'…..No Normal human genome
a. 'Variants' - millions of differences among individuals in a population
b. 'Mutation' - DNA variant that is pathologic / causes disease
"We are all Mutants"
6. Person to Person Genomic Sequence - 99.6% identical DNA Sequences
0.4% different DNA Sequences
a. 0.4% different = 24,000,000 nucleotides in the genome
b. 24,000,000 variants in DNA sequence between you and any other person
C. CLASSIC GENETIC CLASSROOM: Genetic Medicine
1. Cytogenetics - Chromosomes: