Sam Rhine - Genetic Update Conferences -
-GWAS and Stem Cells Revisited -
Genetics of Common Human Traits and Diseases…..
their Multifactorial / Polygenic Origins
- NEW ERA in HUMAN GENETICS…..the OLD ERAS…..the TWO BIG SECRETS
BOX 1 - Cytogenetics and BOX 2 - Monogenic
‘Genetic Medicine’ - use our knowledge about chromosomal syndromes (6100)
and single gene disorders (23,000) to improve the diagnosis
and treatment of our patients
Box 1 and Box 2…..Two BIG SECRETS!
B. SECRET #1 - Most of those 29,000 Syndromes are very rare
1. BOX 1 - Cytogenetics: Chromosome Syndromes…..Padlocked for centuries - 1956!
a. Down Syndrome Trisomy 21(1/800)
b. Patau Syndrome Trisomy 13(1/10,000)
c. Edwards SyndromeTrisomy 18(1/6000)
d. Klinefelter SyndromeXXY(1/500 males)
e. Turner SyndromeMonosomy X(1/5000 females)
EASY to Understand - via Karyotype - but most syndromes are very RARE
2. BOX 2 - Mendelian: Monogenic Traits…..Padlocked for Centuries - 1865 / 1903!
a. AR - Sickle Cell Anemia / Cystic Fibrosis / Tay-Sachs Disease
b. AD - Huntington Disease / Neurofibromatosis / Marfan Syndrome
c. XL - Fragile X Syndrome / Hemophilia / Duchene Muscular Dystrophy
d. AR, AD, XLR or MITO - Retinitis Pigmentosa
EASY to Understand - via Punnett Square - but most conditions are very RARE
3. Why don't you genetics people study the genetics of…..Common Conditions:
Adult Type 2 Diabetes / Macular Degeneration / Hypertension
High Cholesterol / Heart Attack & Stroke / Tumors & Cancer
Bi-Polar Disorder (Manic/Depressive) / ADHD - Attention Deficit / Alzheimer
Alcohol Dependency / Autism Spectrum - ASD / Epilepsy / Asthma / etc.
…..COMMON DISEASES…..but COMPLEX GENETIC TRAITS
4. Why don't we study the genetics of …..Autoimmune Diseases:
Type 1 Diabetes (insulin dependent) / Rheumatoid Arthritis / Multiple Sclerosis
Lupus Erythematosis / Scleroderma / Crohn's Dx / Grave'sDx / Psoriasis
…..COMMON DISEASES…..but COMPLEX GENETIC TRAITS
C. SECRET #2: There has always been a THIRD BOX…..that was ignored for many decades!
Padlocked for centuries…..April 25, 2003-Human Genome Project Completed
1. MULTIFACTORIAL - Box 3 - Complex Genetic Traits - COMMON DISEASES
the KEY to the New Era of Human Genetics…..the HUMAN GENOME
the Most Important Box! - the ‘New Era’ in human Genetics
2. NEW ERA in HUMAN GENETICS: ‘Genomic Medicine’
Use our knowledge of the entire GENOMEplus ENVIRONMENTAL factors
inPOPULATIONS of people…..to understand COMMON MEDICAL conditions
a. ‘Genetics of Common Diseases’
b. NO 'Normal'…..no normal human genome
c. 'Variants' - millions of differences among individuals in a population
SNPs - small variants and CNPs - large variants
d. 'Mutation' - DNA variant that is pathologic - causes genetic disease or cancer
"We are all Mutants" - ~60 new mutations per generation
Person to Person Genomic Sequence - 99.6% identical DNA Sequences
0.4% different DNA Sequences
0.4% different = ~24,000,000 nucleotides variants in the genome
~24,000,000 variants in DNA sequence between any two people.
3. 'COMMON DISEASES / COMMON VARIANTS HYPOTHESIS'
a. Mid 1990s - Hypothesis to try to explain Common Diseases
b. Persons with the same COMMON DISEASE…..
would have a unique set of DNA VARIANTS in COMMON
c. Common - DNA change found in 1% of the population
d. Quantitative Human Traits: Traits that are easily measured -easily quantified
Continuous Distribution in a Population
Most Common Diseases are Part of a Quantitative Trait
4. MULTIFACTORIAL HUMAN CONDITIONS - Box 3
a. BIOLOGIC BASIS of COMMON DISEASES
b. QUANTATATIVE HUMAN TRAITS–
easily measurable traits - easy to quantify:
continuous distribution in a POPULATION
Height, Weight, Finger Print Ridge Count,
Blood Pressure, Blood Glucose Level, IQ, etc.
Human Quantitative Traitsin a general population…..
normal distribution - bell shaped curve
Low Average High
*COMMON DISEASES are part of a QUANTATIVE TRAIT*
c. VARIABLE EXPRESSION in DISEASES - from very mild to very severe
d. COMMON DISEASES - known to have a GENETIC COMPONENT
run through families
twin studies - compare MZ (identical) v. DZ (fraternal)
no Mendelian inheritance pattern…..AR, AD, XLR - not part of Box 2
chromosomes are fine - not part of Box 1
e. POLYGENES - POLYGENIC - many pairs of gene involved
ie: human height…..predicted to be ~700 polygenes involved
f. ENVIRONMENTAL FACTORS interact with the polygenes – play a significant role
HERITABILITY: H - the proportion of Phenotype variation for a
particulartrait that is strictly due to Genetic
differences in a certainpopulation at a certain time
HeightH = ~80%E = ~20%
Cystic Fibrosis H = ~90%E = ~10%
Adult II DiabetesH = ~55%E = ~45%
HIV / AIDSH = ~5%E = ~95%
5. HUMAN QUANTATIVE TRAITS…..Locating Polygenes on a Chromosome
IF we could find one of the polygenes for a quantitative trait
a. locate it's QTL - Quantitative Trait Locus - e.g. 6p24.2
(chromosome #6, short arm (p), band region 2, subregion4.2)
b. then check the genes at 6p24.2 from human genome map database
c. relatethatpolygene to the gene function - what does that gene do?
d. how could that gene contribute to that quantitative trait?
7. Flipping Pennies Model…..within a Normal Curve in a Population
a. each penny represents one polygene for a quantitative trait - height
ten polygenes (actually ~700) …..five from Mom and five from Dad
b. Height: Head = Tall polygene / Tail = Short polygene
c. Polygenes - Additive or Cumulative - NO Dominant Recessive
d. Reassortment - the mixing of genes and genetic material from the parents
into new combinations of genes in their offspring
d. This Means: Two parents of average height…..
WILL USUALLY have an average height children - most likely - near the Mean
BUT…..two average height parents can have a very tall child
OR……two average height parents can have a very short child
WHY?…..Genetic Reassortment:
that is how polygenes work…..all the polygenes reassort every generation
yieldingpotentially thousands of new and unique possibilities
e. Polygenes and Medical Conditions - Add THRESHOLD effect to the curve:
Blood Pressure:
Most people have average blood pressure
High Blood Pressure - cross threshold - Cardiac Risk
Blood Glucose Level:
Most people have average blood glucose levels
High Blood Glucose- cross the threshold - Diabetes
Neuronal Synaptic Pruningin Early Development:
Most people have the average number of synaptic connections
Less Pruning = Excessive Connections - cross threshold - Autism (ASD) Extra Pruning = Fewer Connections - cross opposite threshold
f. GENOME + ENVIRONMENT
Genetic Predisposition - via polygenes
Environmental Factors - trigger to push you across the Threshold
g. TWO perfectly NORMAL parents…..from the middle of the normal curve
Can have an AFFECTED child at one extreme or the other!!
WHY? Because of the polygene Reassortment every generation
D. QUANTATIVE TRAITS and POLYGENES in COMMON DISEASES:
What we do NOT know…..
a. How many polygenes for a particular common disease or trait?
b. Where are the polygenes located - their QTLs = chromosomaladdress
c. What do those genes do - what is the function of that one gene?
d. One day in the future - PREVENT thatCOMMON DISEASE!
…..Modify the polygenes in such a way so that we could
…..Nobody ever again Crosses the Threshold!
E. What would it take to find the Polygenes for Common Diseases?
1. GENOME: The sum total of all the genetic material for any biologic organism,
may be DNA or RNA, expressed as the total number of nucleotides.
Large genome: Human (DNA) > 3,000,000,000 nts / ~35,000 genes
Small genome: HIV virus (RNA) 9,749 nts / 9 genes
Loblolly Pine Tree - >23,000,000,000 nucleotides
1. HGP - Human Genome Project - Director: Dr. Francis Collins
Largest ever Scientific Endeavor!
15 Year International Cooperative effort - 20 Countries - mainly US + UK
Began: October 1, 1990 - projected completion date: Sept. 30, 2005
Actual Completion Date: April 25, 2003 - Double Helix Anniversary April 25, 1953
How many human genes? > 23,000 coding genes/ ~12,000 non-coding genes
'Rough Draft' - June 26, 2000 - US / British joint announcement
1600 Pennsylvania Avenue in DC / 10 Downing Street in London
Human DNA - we are all 99.6% Identical DNA Sequence…..0.4% different
Same among and between all international people groups
No DNA / Genetic basis for the term 'Race'
Rough Draft Published: Nature - February 15, 2001 / Science - February 16, 2001
"To determine our DNA Sequence is to achieve an historic step
forward in Human Knowledge"
Genome Magazine - FREE subscription -
2. SNPs and CNPs
a. SNPs - Single Nucleotide Polymorphisms = SNVs - Single Nucleotide Variant
"snip" - found in >1% of the population = common
how many SNPs in the average person? ~3,750,000
b. CNPs - Copy Number Polymorphisms = CNVs - Copy Number Variants
"cnip" - found in >1% of the population = common
c. We are all 99.6% identical in our DNA sequences
d. Differences that cause common diseases - must be in 0.4% where we are different
SNPs = SNVs - Small Scale variants - ~80% of the 0.4%
Change one nucleotide…..A > T; G > C
CNPs = CNVs - Large Scale variants - ~20% of the 0.4%
Add or Lose 1 kilobase up to 5 megabases - add or lose a gene
2 copies of a gene > 1 copy or 2 copies of a gene becomes > 3
SNPs & CNPs - Common - Normal Variants in the population
e. How do we find the SNPs? Search for groups of SNPs - Haplotypes
Haplotype - Sets of nearby SNPs - located close together on a chromosome
HAPMAP - Haplotype Map - find the addresses of the SNP loci
Hapmap I 2005 - 1,000,000 most common SNPs
Hapmap II 2006 - 10,000,000 SNPs
Hapmap III 2010 - 1,440,616 SNPs for detailed studies
Makes Possible: Routine, Affordable SNP & CNP testing
Average Person: 1 SNP every ~800 bp = ~3,750,000
f. HYPOTHESIS: COMMON DISEASES / COMMON VARIANTS…..OR
COMMON DISEASES / COMMON SNPs
F. GWAS - GenomeWideAssociation Studies
1. Evaluate the entire genome of thousands of people, in a population,all at one time
2. See if any unique set of SNPs might be Associated with a particular Common Disease
3. GWAS Example: T2D = Type 2 Diabetes - usually adult onset
a. Experimental Group: 2500 people - medically confirmed DO have T2D
b. Control Group: 2500 persons - medically confirmed - DO NOT have T2D
c. Scan their 5,000 genomes and check to see which SNPs variants are present
d. Question? Do the 2500 persons with T2D have a unique set of SNPs
in Common that persons without T2D DO NOT HAVE? YES
e. AND…..we know the QTLs of those unique SNPS…..
one unique T2D SNP is located at 10p12.3
one of the polygenes for T2D must be located at 10p12.3 - Candidate Gene
f. go to Human Genome Map - to 10p12.3 - see which genes are there
g. attempt to link that SNP to a known gene Function
4. We have TESTED the CD/CV HYPOTHESIS and it is VALID
COMMON DISEASE / COMMON VARIANTS HYPOTHESIS = VALID
G. GENOMICS of COMMMON DISEASES - MIT & Harvard - Sept 6 - 9, 2008
'The Beginning of the New Genetics'
GWAS STUDIES:
1. T2D - Adult Onset Type 2 Diabetes
a. 18 SNPs = 18 Polygenes - 18 QTLs / today = 53
b. QTLs connected to glucose metabolism pathway genes…..300 total
2. T1D - Juvenile Onset Type 1 Diabetes - autoimmune disease
a. 18 previous SNPs + 14 newSNPs = 32 Polygenes / QTLs / today = 45
b. QTLs connected to HLA - immune system genes
3. Inflammatory Bowel Disease - Crohn's and Ulcerative Colitis
a. Crohn's Disease - 32 SNPs - 32 QTLs / today = 71
b. Ulcerative Colitis - 10 SNPs - 10 QTLs / today = 47
4. GIANT Studies - Genomic Investigation of ANthropormorphicTraits
GWAS for BMI, Obesity, Height, Weight, Adiposity
a. Obesity - 6 SNPs = 6QTLs - BMI and Risk of Obesity Genes / today = 34
9 SNPs = 15 QTLs - Hypothalmic Weight Control Axis in brain
Obesity is a polarizing polygenic trait with thin habitus
b. Height - H = 80% - 180 SNPs = 180 QTLs - only 20% of H - 700 total?
Single Gene Mutation - override 700 polygenes effect - achondroplasia
5. Blood Lipids - major indicator of heart disease
100,000 persons tested - 95 distinct SNP and CNP variants
59 new - never found before
6. SNPs and I.Q. - g = general cognitive ability - Scientific American - Oct 2008
7. SNPs and Human Personality Traits:
Neuroticism / Extraversion / Openness /
Agreeableness / Conscientiousness / Music Ability / Leadership Skills
Leadership Skills……….All Human Behaviors polygenic/multifactorial??
8. SNPs and Human Facial Appearance - VisiGen - International Visible Trait Genetics
a. 5 polygenes found that affect human facial shape
b. 24 polygenes for eye and hair color - Forensic - facial ID from blood SNPs
c. Hope to identify victims / perps face from DNA in blood samples at crime scenes
- Five major psychiatric disorders with shared risk effects; 60,000 person GWAS
a. ASD - Autism Spectrum Disorders; b. Schizophrenia;
c. Bipolar Disorder; d. Major Depression; e. ADHD
These five conditions have a group shared SNPs…..
2 SNPs were for genes affecting calcium channels –might lead to therapy?
10. GWAS - Big Questions…..
a. ONLY ~12% of GWAS SNPs are located in coding DNA gene regions
b. ~40% of GWAS SNPs are in non-coding introns
c. ~49% of GWAS SNPs are in intergenic regions
d. may indicate intronic or intergenic gene control elements
e. "Missing Heritability"
H. CNPs = CNVs - Large Scale variants - ~20% of the 0.4%
Add a gene or Lose a Gene: Add or Lose from 1 kilobase up to 5megabases of DNA
1. Normal - 2 copies of a gene / CNP = 1 gene copy or 3 gene copies, etc.
2. Large Scale Variation - add or lose a whole gene or genes
3. INDELS: INsertions / DELetions or Rearrangements
a. MAY be INHERITED…..passed from the parents , or
b. MAY arise DE NOVO…..mistake in meiosis - not passed from parents
‘Genetic but not Inherited’
c. Copy Number Variant - three instead of two, or one instead of two
d. Most Common Example - Down Syndrome - all genes on chromosome #21 - x3
4. Epilepsy / HIV / Heart / Schizophrenia / Tourette / Obesity / Autism
I. AUTISM EXAMPLE -Autism Spectrum Disorders
1 in 68 children.....1 in 42 males.....Males : Females = 4 : 1
1. Spectrum - from very mild to very severe effects
2. may be Autism only - Simplex Family - one child with autism
Multiplex Family - two or more children w/ autism
3. maybe a Syndrome: Fragile X, Rett, Tuberous Sclerosis, Angelman
4. Many forms of Autism = Many different causes
Neurodevelopmental disorder characterized by:
Social Impairments, Cognitive Impairments
Communications Difficulties, Repetitive Behaviors
Can occur in any ethnic, socioeconomic and age groups.
some children with autism appear normal before age 1 or 2 thensuddenly 'regress'and
lose languageskills they had previouslygained - this is the ‘Regressive’ type of autism.
1 2 3
GWAS RESULTS: GWAS Trios - normal mother and normal father with autistic child
1. Children with autism carry a higher load of rare CNPs
2. Some inherited from parents as polygenes - others having arisen de novo
3. de novo CNVs account for 5-8% of simplex cases - paternal age effect
4. Recent Information - perhaps the main cause of ASD are “Ultra-Rare” mutations of
genes that are classified as “Vulnerable” genes which harbor an LGD - “Likely Gene
Disruption” - and the LSD mutations can occur de novo – genetic but not inherited.
PNAS - on line, September 23, 2015
5. Similar results Mental Retardation - numerous de novo mutations with Exome Trios
6. Examples of CNVs and Reciprocal Variants, +1 gene v -1 gene - Phenotypic Opposites
Obesity <1 - Underweight >1
Macrocephaly < 1 - Microcephaly > 1
Autism < 1 - Schizophrenia > 1
MUTATION and HUMAN DISEASE - Science (special issue) - September 25, 2015
J. SNPs (SNVs)and CNPs (CNVs) associated with:
Migraines / Fatty Liver Disease / Glaucoma / Narcolepsy / Alzheimer Disease
Scleroderma / Intracranial Aneurysms / Essential Tremor / Epilepsy
Osteoarthritis / Osteoporosis / Restless Leg Syndrome / Tobacco Dependency
Cerebral Palsy / Attention Deficit Hyperactivity Disorder / Psoriasis
Asthma / Voter Turnout / Criminal Behavior?.....one Indy family…..50 convictions!
K. All GWAS results available at One Web Site:
L. Early Genetics…..1800's - 19th Century - Inheritance = BLENDING
Blending of Characters of Mother &Father
Beginning in 1900's - 20th Century - Inheritance = PARTICULATE
Particles called genes - Mendelian Inheritance
Box 3 - 21st Century - BLENDING of PARTICLES called POLYGENES
from Mother and Fatherreassort every generation
M. DEPENDENCY STUDIED
1. SAGE - Study of Addiction Genetics and Environment
2. COGA - Collaborative Study of Genetics of Alcoholism
3. FSCD - Family Study of Cocaine Dependence
4. COGEND - Collaborative Genetic Study of Nicotine Dependence
N. TCGA - THE CANCER GENOME ATLAS - discover all human predisposing SNPs
1. Prostate Cancer - 45 predisposition SNPs
2. Breast Cancer - 29 predisposition SNPs…..Hereditary Breast & Ovarian Cancer
3. Colorectal Cancer - 20 predisposition SNPs
4. Lung Cancer - Tumor cells contain up to 50,000 SNPs…..Cancer Causing Mutations!
O. HUMAN MICROBIOME PROJECT - sum total of all the microbes of human body
“the Other Genome” - Major Environmental Factors
1. 800,000,000,000,000 - Cells in Human Body…..American Academy Microbiology
80,000,000,000,000 - Human Cells…..~220 different types
720,000,000,000,000 - Human Microbiome - Bacteria, Fungi, Protozoa-Live in Us and On US
>2,000 different species - weighs ~2 ½ pounds
2. You think you are ONLY human…..You better think again!
Human Microbiome holds the key to many future medical treatments
3. “Instead of declaring war on microbes, we need to think in the context of microbial
ecosystemswithin our bodies. Figuring out how to encourage good microbes to thrive,
while eliminating the bad ones will be of increasing future importance.”
“We are all surrounded by our own personal microbial cloud…..24/7”
4. “We are the Sum of Our Parts”
5. Personal Microbiome Evaluation - $99: * *
6. MULTICACTORIAL = GENOME + ENVIRONMENTAL EFFECTS
P. OPEN TREE of LIFE: the first comprehensive genomic tree of life
You can check how closely related you are to any other biologic organism
Q. THE '1000 GENOME PROJECT' - began in January 2008 -
1. Collaboration among US, UK, China, Germany and nine other countries
2. Produce an extensive international catalogue of human genetic variation - SNPs & CNPs
3. Goal was to sequence at least 1000 persons to provide a resource for almost all human variants
4. Evaluated 2,504 total genomes from 26 people groups from six continents - form the basis for
ethnic group comparisons and tracking people groups
5. Project Completed - Nature (cover article) October 1, 2015
R. YOUR PERSONAL TOTAL GENOME EVALUATION
1. 'The Language of Life' - book by Dr. Francis Collins - Director of NIH
2. Construct Family History / Pedigree Online via HHS -
3. Faster and Cheaper in the Future…..Whole Genome: 2015 - $1000 / 2020 - $100
4. - can check anyone today for ~35 medical conditions for $199!
S. YOUR PERSONAL DNA CHIP
1. 'Genomic Era of Medicine' - 'Personalized Medicine' or ‘Precision Medicine’
2. Pharmacogenetics - Personalized / Precision Prescriptions and Cancer Therapy
3. GPP - your personal Genetic PredispositionsProfile - your Medical Future
a. Do you want to know? b. Who else should know?
c. Who pays? Insurance? d. Who else should have access?
e. Where will you keep the information? f. Who will explain it?
4. GINA - Genetic Information Nondiscrimination Act passed in 2008
5. Massive Parallel Sequencing - Next Generation Sequencing
Chromosome Evaluation without Karyotyping via unique chromosome fragments
6. Prenatal Diagnosis and SNP / CNP evaluation of the unborn?
c f DNA = cell free DNA in mother’s blood at 8 weeks of pregnancy
Your unborn baby is:
a. XY - boy
b. height SNPS - he will be about 6'2"