human genetics lecture #1 march 24,...
TRANSCRIPT
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Bio 5491 - Advanced Genetics
Human Genetics Lecture #1
March 24, 2020
Cristina de Guzman Strong, Ph.D.
Department of Medicine
Dermatology/Pharmacogenomics
Center for the Study of Itch
McDonnell Basic Sciences 770
362-7695
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Human Genetics
• Karyotype
• Genetic Variants
• Mendelian Diseases
• Penetrance/Expressivity
• Human Genome Project
• GWAS/Next-Gen
sequencing (Exome)
• Undiagnosed Diseases
• Epigenetics/ENCODE
• Variants in Regulatory
Elements
• Copy number variation
diseases
• Mitochondrial genetics
• Human-specific variation
• Future
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The relationship between natural
DNA sequence variation(s) and
human phenotypic traits
What is Human Genetics?
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What is different about Human Genetics?
• Trinucleotide repeat diseases…….anticipation.
• Imprinting……..uniquely mammalian.
• Extensive sequence variation leads to
common/complex disease
1. Common disease – common variant hypothesis
2. Large # of small-effect variants
3. Large # of large-effect rare variants
4. Combo of genotypic, environmental, epigenetic
interactions
• One can study complex behaviours and cognition.
Greg Gibson, Nature Review Gen 2012
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Human Genome (Karyotype)
22 autosomes/ XY sex chromosomes
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Human genome is ~41% GC, but that is non-randomly
distributed. Dark G-bands are lower GC (and lower
gene content)
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Genetic variation: Single Base Pair
– SNP (single nucleotide polymorphism) -
Freq > 0.01
– Alleles with Freq < 0.01 – called rare
variants OR SNVs
– Can also be 1 insertion or 1 deletion,
“indel”
– Mutations: usually, really RARE. Alter
protein function or regulation. Simple
Mendelian Trait. Can cause disease
C
T
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Understanding the SNPMajor vs. Minor Allele
• Referring to coding OR non-coding
region
• Nomenclature – rs”X” (SNP)
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Looking up a SNP
C
T
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Looking up a SNP C
T
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Types of Coding Mutations
p.K867* p.K867R p.K867T
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Courtesy of Laura Elnitski
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Ars et al., HMG 2000
Example of Nomenclature
(NF1)
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Resource for Sequence Variant Calling (2016)
• http://varnomen.hgvs.org
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http://exac.broadinstitute.org
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gnomAD Browser Populations
GRCh37/hg19 genome build
Gencode Version19, VEP version 85
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Genetic Variation: Copy Number
Insertion/deletions of small number of bp (indels): – Polymorphism - also known as copy number
variation (CNV)
– Indels in coding region – frameshift mutation if less than 3 bp
– Repeat sequences: di (TG), tri, or tetra –microsatellites
Larger repeats: VNTRs (variable number of tandem repeats), minisatellites - used for forensics
Deletions or duplications of larger blocks of DNA encompassing one or more genes (Williams or DiGeorge Syndrome)
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Larger repeats: VNTRs (variable number of tandem repeats), minisatellites - used for forensics
Genetic Variation: Copy Number
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Description of diseases and mutations
Human mutation database : http://www.hgmd.org
• Online Mendelian Inheritance in Man (McKusick):
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OM
IM
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Characteristics of
Simple/Mendelian diseases• >20,000 Mendelian traits described in OMIM (Online
Mendelian Inheritance in Man)
• Freq usually < 1/10,000
• Most mutations: Loss of function and recessive phenotypes, e.g. inborn errors of metabolism
• Dominant mutations: Cause disease due to 50% of protein product (haploinsufficiency) or dominant negative effect
• Some dominant mutations lead to “gain of function” -e.g. expanded polyglutamine repeat leading to abnormal aggregate (triplet repeat diseases)
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Thompson & Thompson, Genetics in Medicine (5th)
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Basic Mendelian pedigree patterns
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Example of Mendelian disorder: Waardenburg Syndrome
(PAX3: Deafness in association with pigmentary anomalies
and defects of neural crest-derived tissues).
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Loss of function mutations in PAX3 gene:
Type 1 Waardenburg syndrome
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Penetrance - the frequency of
expression of an allele when it is present
in the genotype of the organism
Example: if 9/10 of individuals
carrying an allele express the trait, the
trait is said to be 90% penetrant
Expressivity - variation in allelic
expression when the allele is penetrant.
Example: For polydactyly, an extra
digit may occur on one or more
appendages, and the digit can be full size
or just a stub. Modifier genes can affect penetrance, dominance, expressivity
Variable penetrance versus
variable expressivity
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Neurofibromatosis ( NF1)
• Mutations in neurofibromin
gene
• Reduced penetrance
• Wide range of symptoms –
variable expressivityNature 455, 1061-1068(23 October 2008)
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Somatic Mosaicism and Related Syndromes
• Often involve trisomies – nondisjunction event
• Syndrome severity related to percentage of cells
with aberrant genotype
Klinefelter (47,XXY/46, XY)
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http://www.slideshare.net/medik.cz/practical-6-07
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Ichthyosis with confetti
Revertant mosaicism
Choate et al., Science 2010
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How did we get here?
• The revolution in human genetics has been driven by
advances in genomics, DNA sequencing and
polymorphism detection.
• ~1,200 “simple” Mendelian trait loci have been cloned,
mostly by genetic linkage analysis and positional cloning.
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Courtesy of Eric Green
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Courtesy of Eric Green
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Post HGP
Goal: Identify genetic variation to disease by finding
haplotypes of human genome, n = 269 individuals,
4 populations (YRI, CEU, CHB, JPT), array based methods
Haplotype: Specific Allele defined by set of SNPs that are inherited
together
A T GG
Tagging SNP
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sequence about
2,000 unidentified
individuals from
20 populations
around the world
1000 Genomes Project
Capture minor
allele frequencies
as low as 1%
RARE
VARIANTS
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Post HGP
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Published Genome-Wide Associations
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1% of the genome – 30MbFrom Nimblegen
Targeted Capture for Exome Sequencing
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Slide courtesy of Elliott Margulies
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Exome sequencing – XIAP
Whole Bone Marrow Transplant
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Slide courtesy of Eric Green
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Slide courtesy of Eric Green (modified)
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Slide courtesy of Eric Green
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Slide courtesy of Eric Green
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Hon, Hawkins, Ren review (Human Molecular Genetics 2009)
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Calo & Wysocka, Mol Cell 2013
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http://www.nature.com/encode/#/threads
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M
a
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Mutations in regulatory regions
– Altered TF binding to promoter or enhancer
e.g. sonic hedgehog enhancer
– Splice site alterations (e.g. some beta thalassemias)
– Altered mRNA stability (e.g. in AAUAA)
– Altered micro RNA binding leading to altered protein translation
Sequence variants in SLITRK1 are associated with Tourette's syndrome. Science 2005, 310.
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Nature March 23 2011 Advance issue
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Copy Number (Structural)
Variation
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Structural variation of the
genome
kilobase- to megabase-sized
deletions,
duplications,
insertions,
Inversions
complex combinations of
rearrangements.
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11_19_2.jpg
(Smith-Magenis
syndrome)
DiGeorge Syndrome
Velocardiofacial
syndrome
CNVs due to non-allelic recombination between
low-copy repeats (LCRs) that lead to human
disease
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Examples of contiguous gene
syndromes• Xp:
– Successively large deletions remove more
genes and add more diseases
• 11p12:
– WAGR (Wilm’s tumor, Aniridia, Genital and/or
urinary tract abnormalities, Mental retardation)
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Segmental aneuploidy
• Phenotype in heterozygotes depends on only a subset
of deleted genes that are dosage sensitive
• De Novo microdeletions, frequently flanked by long
repeats (often transcribed hence open chromatin -
more recombination prone)
46, 5p- Adapted from Figure © 2010 PJ Russell, iGenetics 3rd ed.
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Williams syndrome - example of
segmental aneuploidy (1.6Mb deletion at
7q11.23/~ 20 genes)
1/20,000 births
Growth retardation
Hypercalcemia
Supravalvular aortic stenosis (elastin)
Moderately mentally retarded
Highly sociable, often musical, defect in visuospatialconstructive ability
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Deletions identified in
Williams syndrome
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Chromosomal Microarray
(CMA)
Usrey et al., Case Reports in Genetics, 2014
15q11.2 BP1-BP2 microdeletion
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Current knowledge of of CNV
(copy number variation) in the
human genome
http://dgv.tcag.ca/dgv/app/home
Inversions: 3164
Total CNV loci: 552,586
Number of studies: 72
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CNV affecting one human phenotype: Ability to digest starch:
Diet and the evolution of human amylase gene copy number variation
Perry et al. Nature Genet. Nature Genetics 39, 1256 - 1260 (2007)
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Different types of mechanisms
leading to SVs/CNVs
• Non-allelic homologous recombination
(NAHR)
• Non homologous end joining (NHEJ)
• Transposon insertion (e.g. L1)
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Gu et al. PathoGenetics 2008 1:4
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Genomic rearrangements in
the genome are likely to be
more common than expected
5% of human genes are found in interspersed
duplicated copies
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Recent examples of large
rearrangement polymorphisms in the
human genome
• Sebat et al. Large-scale copy number polymorphism in the human genome.
Science 305:525-8 (2004)
• A common inversion under selection in EuropeansStefansson et al. Nature Genetics 37, 129 - 137 (2005)
900kb
Chromosome 17q21
H2
H1
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A common inversion under selection in Europeans
Stefansson et al. Nature Genetics 37, 129 - 137 (2005)
20% chromosomes
900kb
CRH1 MAPT
CRH1: corticotropin releasing hormone receptor 1
MAPT: microtubule associated protein tau
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Genomic architecture,
rearrangements and marker
genotypes at 17q21.31
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Fragile X – trinucleotide repeat
•Most common inherited form of mental retardation
•Due to instable CGG repeat at FMR1
•All full mutations derive from premutation (56-200 repeats)
•Expansion through female meiosis
•Severity correlates with CGG repeats
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Rare L1 insertions as a cause
of disease
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AKA: Kpn1 element
~5kb. Relic of retrovirus
3 distantly related LINE families are found in
the human genome, but only LINE1 is
active.
Human genome: ~515,000 copies of LINE1
(L1), ~365,000 L2, and ~37,000 L3 (most
are truncated or rearranged)
Only ~30-60 are active
In mouse, ~3,000 are active.
LINEs (long interspersed repetitive elements)
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Occasionally lead to genetic disorder: Reported in Duchenne
muscular dystrophy, type 2 retinitis pigmentosa,
thalassaemia, chronic granulomatous disease, and
hemophilia A (2/140 patients) - insertion into factor VIII.
Prak & Kazazian. (2000) NRG. 1: 134-144
L1 Insertions
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Prak & Kazazian. (2000) NRG. 1: 134-144
In addition to duplicating themselves, L1s can carry with
them genomic flanking sequences that are downstream of
their 3UTRs.
L1 elements also cause Transduction.
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Mitochondrial genetics
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Mitochondrial inheritance gives
matrilineal pedigree pattern
• Matrilineal inheritance
• Sperm mtDNA is actively degraded
• Mitochondria present in thousands of copy per somatic cell
• Normal individuals: ~99.9% of molecules are identical (homoplasmy)
• New mutation leads to heteroplasmy
• In some patients with mitochondrial disease every patient carries causative mutation (homoplasmy)
• In some patients there is heteroplasmy.
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The mitochondrial genetic bottleneck
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Mitochondrial genome
• Cytoplasmic organelle
• Small genome (~16kb)
• 1/200,000 size of nuclear genome
• Sequenced in 1981 (Anderson et
al.)
• 93% is coding
• ~ 1,000 copies per cell
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Organ systems and symptoms
of mt diseases
• Multisystem disorders with large range of symptoms:
• Brain, heart, skeletal muscle, kidney and endocrine systems can be affected (sometimes there is a threshold effect)
• Symptoms: forms of blindness, deafness, movement disorders, dementias, heart disease, muscle weakness, kidney dysfunction, endocrine disorders (including diabetes)
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Functions of the 37
mitochondrial genes• 13 of mitochondrial peptide
subunits in mitochondrial respiratory-chain complex(OXPHOS)
– Remaining > 67 OXPHOS subunits are nuclear encoded
• rRNAs: 2
• tRNAs: 22; Located between every 2 rRNA or Protein coding genes
• Third base wobble
• All factors involved in maintenance,replication & expression of mtDNA are Nuclear encoded
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Example of moderately severe
tRNA mutations
tRNA Lys :
A8344G (Frequent)
T8356C
G8363A
G8361A
MERRF (Myoclonic Epilepsy and Ragged-Red Fiber Disease)
Onset: Late adolescence - Early adult
Level of mutant heteroplasmy + age of patient influence severity of symptoms
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Mitochondrial DNA and human evolution: Nature
325, 31 – 36 (1987)
Rebecca L. Cann*, Mark Stoneking & Allan C. Wilson
Mitochondrial DNAs from 147 people, drawn
from five geographic populations have been
analyzed by restriction mapping. All these
mitochondrial DNAs stem from one woman
who is postulated to have lived about 200,000
years ago, probably in Africa. All the
populations examined except the African
population have multiple origins, implying that
each area was colonized repeatedly
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J lineage often seen with Leber’s hereditary optic
neuropathy (LHON) patients
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Map of sites with ages and postulated early and later pathways associated with modern
humans dispersing across Asia during the Late Pleistocene.
Christopher J. Bae et al. Science 2017;358:eaai9067
Published by AAAS
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February 2011