Genetics in Human and Animal Medicine Flashcards
what is a karyotype?
the set of chromosomes found in a particular species
what is a diploid karyotype?
having 2 copies of each chromosomes
what are the 2 types of chromosomes?
autosomes and sex chromosomes
what are autosomes?
chromosomes which are diploid in all individuals of a species regardless of sex
what are sex chromosomes?
chromosomes which confer sexual traits and are different between males and females
which are the heterogametic sex in mammals?
males
what is the heterogametic sex?
the sex with 2 different types of sex chromosomes
how many chromosomes do humans have?
22 pairs of autosomes, 1 pair of sex chromosome
how many chromosomes do dogs have?
38 pairs of autosomes and 1 set of sex chromosomes
what are centromeres the site of?
spindle attachment during mitosis and constriction between the 2 sister chromatids in G2 cells
what are sister chromatids?
the 2 replicated chromosomes present in G2 of the cell cycle
what is a chromosomal arm?
the region from the centromere to the end of the telomere
which is the p-arm?
the shorter of the 2 chromosome arms
which is the q-arm?
the longer of the 2 chromosome arms
what percentage of the genome is non-coding?
98%
what does non-coding mean?
doesn’t encode protein-coding gene exons
what is the reference genome?
a completely sequenced genome isolate that is used for reference for genetic studies
how many chromosomes and chromatids will a human cell in G1 have?
46 chromosomes, 46 chromatids
how many chromosomes and chromatids will a human cell in G2 have?
46 chromosomes and 92 chromatids
what is a locus?
a position in a genome
what are alleles?
variant sequences at a particular locus
when are 2 loci considered linked/under linkage disequilibrium?
if they are frequently inherited together
what are the 5 classes of genome variation?
SNVs, indels, structural variants, transposable element insertions, cytogenetic variation
what are SNVs?
single nucleotide variations
what are indels?
small insertions and deletions
what are SNVs also known as?
point mutations or substitutions
when are SNVs termed SNPs?
if they occur in the germline and are variable within individuals in a population
what are SNPs?
single nucleotide polymorphisms
what are the 6 types of SNV?
2 transitions and 4 transversions
what do transitions involve?
only purines/pyrimidines respectively
what do transversions involve?
purines -> pyrimidines or vice versa
what 3 cellular DNA repair pathways repair the majority of incipient SNVs?
NER, BER, MMR
what is NER?
nucleotide excision repair
what is BER?
base excision repair
what is MMR?
mismatch repair
what does NER primarily repair?
helix distorting damage
what does BER primarily repair?
small, non-helix-distorting lesions
what does MMR repair?
base-base mismatches
what can SNVs be caused by?
exogenous or endogenous mutational processes
what are exogenous mutational processes?
those that involve exposure to exogenous agents
what are endogenous mutational processes?
processes that derive from mutational activities that naturally operate within the cell
what mutation is present in 60% of human malignant melanomas?
BRAF V600E
what does the BRAF V600E mutation cause?
activation of the cell cycle without growth factor binding to RTK
SNV mutation in what gene causes phenylketonuria?
PAH, the gene encoding phenylalanine hydroxylase
what causes xeroderma pigmentosum?
mutations, often SNVs, in components of the NER pathway causing extreme sensitivity to UV light and accumulation of SNVs in sun-exposed cells
where does polymerase slippage often occur?
at simple repeat tracts called microsatellite/STRs
what does polymerase slippage cause?
indels
what are STRs?
short tandem repeats
what are microsatellite length alleles?
alleles present at simple repeat tracts characterised by different lengths of repeat tract loci
what is the causative mutation in trinucleotide expansion diseases?
simple repeat indels
what sort of disease is Huntington’s?
trinucleotide expansion disease
do all indels occur at repeat regions?
no
what do structural variants in DNA often involve?
dsDNA breakage repaired by HR or NHEJ
what are structural variants in DNA?
large scale genomic rearrangements that lead to juxtaposition of DNA that wasn’t previously connected
what are the 2 types of structural variants?
interchromosomal or intrachromosomal
what is involved in inter-chromosomal structural variants?
2 chromosomes
what is involved in intrachromosomal structural variants?
different parts of the same chromosome
what are balanced structural variants?
ones that don’t lead to an overall gain or loss of DNA from the cell
what are unbalanced structural variants?
ones that introduce additional DNA or cause DNA to be lost from the cell leading to copy number variants
what is the Philadelphia chromosome?
a translocation between human chromosomes 9 and 22, type of balanced structural variant
what disease is the Philadelphia chromosome frequently observed in?
chronic myeloid leukaemia
what are transposable element insertions?
virus-like sequences that copy themselves and transpose around the genome
what genes do autonomous transposable elements encode?
genes required for transposition such as reverse transcriptase
what type of transposable element are LINE elements?
autonomous
what do non-autonomous transposable elements use to support transposition?
transposition proteins encoded by autonomous elements
what type of transposable element are SINE elements?
non-autonomous
what is the merle phenotypes an example of?
a transposable element insertion
what is the function of transposable elements in the genome?
no function, they are parasitic elements
what is involved in cytogenetic variation?
the gain or loss of 1 or more entire chromosomes leading to aneuploidy
what does whole genome duplication lead to?
tetraploid cells and additional aneuploidy
what does whole genome duplication frequently occur in, and via what process?
cancer cells, via endoreduplication
how does the spindle assembly checkpoint prevent aneuploidy?
prevents progression through mitosis if chromosomes aren’t correctly attached to spindle apparatus
how is genome variation detected?
by whole genome sequencing
how can copy number variants be identified by whole genome sequencing?
by identifying differences in the number of reads mapping to the reference genome
what are the 2 cell types the body is composed of?
germline cells and somatic cells
what are germline cells?
gametes (sperm and egg cells) or their precursors
what are somatic cells?
the cells of the body that cannot contribute to the next generation
what is germline variation?
genetic variation that occurs in the germline and is inherited
what is the germline lineage?
the lineage of cells that contributes to the production of gametes
what does the germline lineage begin with?
the fertilised egg
how many cell divisions occur before the specification of primordial germ cells?
10
what are primordial germ cells (PGCs)?
embryonic cells committed to the germline lineage
what leads to formation of a germline mosaic?
if a variant occurs in the 10 cell divisions prior to PGC specification
what is a germline mosaic?
when a subset of somatic and germline cells contain a variant
where do the primordial germ cells migrate to?
the developing gonads (testes/ovaries)
what happens to germ cells in the male at puberty?
cell division recommences
how many times per year do male spermatogonial stem cells (SSCs) divide per year in humans?
23
how many more divisions do committed sperm cells undergo to become mature?
4
what happens in the female at puberty?
menstrual cycles commence and 1 oocyte completes maturation and is ovulated each month
how many divisions will the germline cells of adult women have undergone?
30
how many divisions will the germline cells of a 30 yr old adult man have undergone, assuming he entered puberty at 15 yrs?
383
which is more vulnerable to acquiring variants, the male or female germline?
the male as it undergoes more division
how many germline SNVs are introduced via the male germline?
70-80%
what is the number of de novo germline SNVs dependent on?
the father’s age at conception
what germline are most cytogenetic variants introduced via?
the female germline
what does the number of cytogenetic abnormalities appear to be due to?
segregation errors
what percentage of gametes derived from the SSC will a variant be present in if a de novo germline variant occurs in the SSC?
50%
how many de novo variants will each sperm have?
50-100
how much DNA is shared between identical twins?
100%
how much DNA is shared between full siblings?
50%
how much DNA is shared between grandparent + grandchild?
25%
how much DNA is shared between aunt/uncle and niece/nephew?
25%
how much DNA is shared between first cousins?
12.5%
how many positions do the genomes of 2 unrelated individuals differ at?
around 3 million
what are common variants shared between?
populations
what are rare variants unique to?
families or individuals
what is genetic drift?
the change in the frequency of alleles in a population due to chance
when is genetic drift particularly important?
when populations are small and chance fluctuations can have a large effect
when do genetic bottlenecks occur?
when a population is drastically reduced in size
when do founder effects occur?
when a small number of individuals leave a population and found a new colony
what has caused the high frequency of some disease alleles in breed dogs?
genetic bottleneck and then genetic drift
what is an example of founder effects?
the Amish population
what is natural selection?
a change in allele frequencies due to a change in fitness
what 2 types of variants can impact the cell?
coding and non-coding/copy number
what do coding variants lead to?
a change in the amino acid composition of the protein product
what do non-coding variants/copy number variants lead to?
changes in the amount of protein product produced
what variant types can coding variants cause?
missense, nonsense, in-frame insertion or deletion, frameshift, splicing, gene truncation via rearrangement, fusion gene
what happens in a missense variant?
causes a single amino acid to be switched from 1 to another via an SNV variant
what happens in a nonsense variant?
causes the introduction of a premature stop codon via an SNV variant
what happens in an in-frame insertion or deletion?
indel variant of 3bp or multiple of 3bp causes insertion or deletion of 1 or more amino acids
what happens in a frameshift variant?
indel or other type of insertion/deletion variant inserts or deletes a number of bases that isn’t a multiple of 3 - changes reading frame, leads to premature termination of protein
what happens in a splicing variant?
causes a change to splice donor or splice acceptor site which causes abnormal splicing such as exon skipping
what happens in a gene truncation variant via rearrangement?
structural variant leads to gene truncation
what happens in a fusion gene variant?
structural variant brings 2 genes together, they splice together to forma a novel in-frame fusion gene
what are examples of non-coding variants?
variants in promoters, enhancers, 5’ or 3’ UTRs, non-coding RNAs such as miRNAs, copy number variants, cytogenetic variants
what do dominantly acting variants do?
generate a phenotype when present in at least 1 copy in the cell regardless of the number of additional chromosomal copies
what do recessive variants do?
generate a phenotype only when the variant is carried by all chromosomal copies present within the cell
what is co-dominance?
where the impact of both alleles is visible in the heterozygous phenotype
what is positive selection?
selection acting on a phenotype to increase allele frequency in a population
what types of fitness advantage are there?
adaptive, selfish, artificial
what is an adaptive fitness advantage?
one that enhances individual’s adaptation to environment
what is a selfish fitness advantage?
one at the level of the cell rather than the level of the individual
what is artificial fitness advantage?
one caused by human intervention (like dog breeding)
what does negative selection do?
acts on a phenotype to reduce allele frequencies in populations
what is balancing selection?
an interaction between positive and negative selection which acts to maintain several alleles in population
what can most diseases be broadly categorised into?
single mutation, complex genetic, infectious, cancer
what are single mutation diseases?
diseases that arise due to a single mutation
what are complex genetic diseases?
diseases that don’t have a single genetic cause
what do infectious diseases develop due to?
exposure to an infectious agent
what does compound heterozygosity involve?
2 mutations in the same gene
what are de novo mutation diseases?
diseases that occur due to inheritance of a newly-arising germline variant
what are de novo mutation diseases that are passed on to offspring known as?
autosomal dominant/sex-linked/mitochondrial inherited diseases
what are many miscarriages likely due to?
de novo mutations that are incompatible with embryonic development
when do autosomal dominant diseases with severe phenotypes in humans tend to onset?
in adulthood as otherwise wouldn’t be inherited
what are examples of autosomal dominant diseases in humans?
Huntington’s disease and polycystic kidney disease
what are compound heterozygotes of autosomal recessive inherited diseases?
affected individuals that inherit 2 different faulty copies of the same gene (each carries distinct disease allele at different locus)
what are recessive lethal alleles?
alleles that are incompatible with fetal development in the homozygous state
which individuals are at a significantly higher risk of autosomal recessive disease?
those with a family history of consanguinity
what is reduced penetrance?
when different individuals harbour the same disease genotype and only some individuals develop the disease
what can cause reduced penetrance?
accumulation of somatic mutations, mosaicism, variable copy number of disease haplotype, epigenetic and environmental factors
what is variable disease severity/expressivity?
when individuals with the same disease develop less severe symptoms
what is an example of variable disease severity in dogs?
double merle phenotype
what causes the double merle phenotype of dogs?
inheriting 2 copies of a SINE element insertion in the SILV gene
what does gene therapy involve?
delivery of normal copies of genes directly to target cells in individuals affected with genetic diseases
what are the gene copies normally packaged into in gene therapy?
non-integrating viruses
what is mosaicism used to refer to in the context of disease?
the situation when a de novo disease mutation arises during embryonic development
what is a germline mosaic individual?
when a de novo mutation disease is present in a subset of germline cells and a subset of somatic cells
what does transmission frequency depend on in germline mosaic individuals?
the proportion of germline cells which carry the mutation
what is a clone?
a set of cells with a common origin (common ancestor)
somatic evolution of cancer?
occurs when a somatic cell of the body acquires a set of somatic mutations that cause that cell to acquire a selective advantage relative to other somatic cells
what sort of evolution is cancer an example of?
selfish evolution
what is the role of somatic cells from an evolutionary perspective?
to nourish and optimise the germline in order to maximise genetic contribution to the next generation
why is the evolution of cancer usually self-destructive?
the continued growth and survival of the cancer is not compatible with continued survival of the host upon which the cancer relies for nutrients and support
what are neoplasms?
all abnormal clonal cell growths in the body
when are neoplasms known as benign tumours?
if they remain localised, respect tissue boundaries and don’t have potential to invade host tissues
when does a neoplasm become malignant tumours?
when it disrupts tissue boundaries and invades host tissues or has the potential to
what is cancer?
a malignant clone of cells which arises when a somatic cell follows a programme of selfish positive selection maximising the fitness of the cell instead of the cell body
how many somatic mutations do somatic cells get per cell division?
2-10
what are neutral somatic mutations known as?
passenger mutations
what are passenger mutations?
somatic mutations with no effect on the cell
what are driver mutations?
somatic mutations that confer the cell with phenotypes that confer a selective advantage in terms of proliferation and survival
what phenotypes do selfish positive selection act on?
phenotypes that confer a growth or survival advantage to the cell
how are somatic mutations in cancers discovered?
by whole genome sequencing- any genetic variant not found in normal DNA is considered somatic mutation
how many somatic mutations do most human cancers have?
between 1000 and 30000
how are driver mutations in cancers discovered?
by searching for the same mutation occurring in independent cancers from different patients
what is the most common driver mutation in BRAF V600E?
an SNV which causes a missense mutation
how many driver mutations do most cancers have?
between 1 and 10
how many cancer genes are known in humans?
743
what is a cancer gene?
a gene known to harbour driver mutations in human cancer
what are oncogenes?
dominantly acting cancer genes where mutation of 1 copy is sufficient to trigger the selective advantage
what are 2 examples of oncogenes?
KRAS and BRAF
what is BCR-ABL1?
a dominantly-acting fusion gene created by the Philadelphia chromosome mutation
what mutation creates BCR-ABL1?
Philadelphia chromosome mutation
what is MYC?
a dominantly acting cancer gene
what are double minutes?
tiny circular DNA elements created by unbalanced structural variants
what can double minutes lead to?
massive copy number amplifications
what are tumour-suppressor genes?
recessively-acting cancer genes where both copies must be lost in order for selective advantage to be gained
what are 2 examples of tumour-suppressor genes?
CDKN2A and PTEN
what is CDKN2A also known as?
p16/ARRF
what is TP53?
a (usually) recessively acting cancer gene
what is PTEN?
a recessively acting cancer gene
what cancers are the most common in humans?
carcinomas
what cancers are relatively common in dogs and rare in humans?
sarcomas
what cells are carcinomas derived from?
epithelial
what tissues are sarcomas derived from?
connective tissue
how can cancer therapies lead to therapy resistant cancers?
therapy imposes a selective pressure on cancers- if resistance mutations are present these will be strongly positively selected
what is an example of a therapy resistance mechanism in ovarian cancer?
the reversion of BRAC1/2 mutations to wild-type in PARP inhibitor resistant ovarian cancer
what are transmissible cancers?
cancers that survive beyond the deaths of their original hosts by transmission of living cancer cells between hosts
how many known transmissible cancers are there?
14
what is chimerism?
the presence of cells derived from 2 different individuals (2 separated fertilised eggs) in the same body
what is a tetragametic chimera?
when fraternal twin embryos fuse in utero forming a single embryo
what are blood chimeras?
a pair of fraternal twins who exchange blood cells in utero
what % of fraternal twins have blood chimerism?
10%
which sex chromosome is smaller?
Y
what are the regions at the tips of the Y chromosome that are homologous with the X chromosomes?
the pseudoautosomal regions (PAR)
what allow the X and Y chromosomes to pair and recombine during meiosis in the male?
the PARs on the tips of the Y
what are many of the genes on the Y chromosome involved in?
spermatogenesis
what is the distal half of the long arm on the Y chromosome like?
made up of highly repetitive DNA and is heterochromatic
what is the region of the Y chromosome involved in sex determination?
the SRY gene
what does the SRY gene encode?
a transcription factor that activates a testis-forming pathway early in development
what is the embryonic gonad described as before the SRY pathway is triggered?
indifferent- meaning it is capable of developing into either a testis or ovary
what is dosage compensation between the mammalian sexes achieved by?
inactivating one of the 2 X chromosomes in females
how many X linked recessive traits are known in humans to date?
515
what % of daughters of females affected with an X-linked dominant disorder will be affected?
50%
what is the important difference between the pedigree of an X-linked dominant trait and an autosomal dominant condition?
lack of father to son transmission for X linked dominant trait
is X inactivation always the maternal chromosome?
no, random which is inactivated
which specific genes are included in the genes that escape X inactivation?
the PAR genes
what gene does X inactivation require the expression of?
the non-coding RNA gene Xist
what does Xist expression initiate?
a hierarchy of epigenetic events that lead to progressively stronger silencing of the inactive X
what are the repressive histone modifications found along the length of the inactive X?
H3K27me3 and H3K9me3
what are epigenetic modifications?
chemical marks on DNA and post-translational modifications to chromatin-associated histone proteins
what dinucleotides does DNA methylation occur on in mammalian cells
CG dinucleotides
why is DNA methylation symmetrical on the 2 DNA strands in mammals?
it occurs on CG dinucleotides
what maintains DNA methylation during DNA replication?
the maintenance methyltransferase Dnmt I
how is DNA methylation acquired anew?
by de novo DNA methyltransferases
what does deamination of unmethylated cytosine convert it to?
uracil
what does the cytosine->urine conversion cause cell to do?
recognition as alien in DNA, repair back to cytosine by cell
what is produced when 5’-methylcytosine is deaminated?
thymine
what happens if the methylcytosine -> thymine shift is not corrected?
the change becomes a permanent mutation of C to T, CPG dinucleotide lost
what % of CpG dints are methylated in somatic cells of mammalian genomes?
75%
what % of their expected frequency do CpG dints occur at?
21%
what is the exception to CpG depletion in mammals?
CpG islands which are generally hypomethylated so have retained CpG content
what does loss of the heterochromatic marks H3K9me3 and H3K9me2 result in?
inability of chromosomes to segregate properly
what are the 3 essential processes in cells that epigenetic modifications regulate?
chromosome architecture, silencing of repetitive transposable elements, somatically heritable changes in gene expression
what is an example of 2 epigenetic modifications that are incompatible with the presence of each other?
H3K27me3 and H3K27Ac
what is an example of 2 epigenetic modifications that go hand in hand?
DNA methylation and H3K9me3
what suggests that DNA methylation can sometimes be a consequence of gene repression not a cause?
sometimes acquired at repressed promotors long after gene has been repressed
is epigenetic information generally inherited from 1 generation to the next?
no
when is DNA methylation erased from the germline?
epigenetic marks are erased early in PGC development
what does PGC stand for?
primordial germ cell
when does establishment of new epigenetic marks occur in the male germline?
on prospermatogonia during foetal development
when does establishment of new epigenetic marks occur in the female germline?
after birth during the growing oocyte phase
when does the second phase of genome-wide epigenetic erasure and re-establishment occur?
immediately after fertilisation
what mechanisms remove epigenetic marks immediately after fertilisation?
active (enzymatic) and passive (dilution during DNA replication)
what are genomic imprints?
DNA methylation marks that are established in different places in the male and female germlines and are resistant to the 2nd wave of epigenetic reprogramming immediately after fertilisation
how many genes have been identified that are expressed solely from 1 of the 2 parental chromosome homologues?
around 200
which allele expresses and represses the IGF2 gene in developing embryos?
the paternally inherited chromosome homologue expresses, the maternally inherited one represses
what regulates the monoallelic expression of an imprinted gene?
DNA methylation that differs on the 2 parental chromosomes
what is the imprinting control region?
a differentially methylated region (DMR) located at the promoter of an imprinted transcript or in the vicinity of an imprinted locus
when are ICRs established?
in the germline
how are imprinted genes often arranged?
in clusters, with a single ICR regulating the monoallelic expression of all imprinted genes in the cluster
what do imprinting disorders in humans arise from?
mis-expression of imprinted genes
what can cause imprinting disorders in humans?
uniparental disomy, or epimutation
what does epimutation cause in the ICR?
it to lose its appropriate differential methylation status and hence normal imprinting perturbed
why is evidence as to whether the environment talks to the genome (via epigenome) hard to ascertain?
- it’s hard to rule out genetic effects 2. it’s hard to determine whether an observed epigenetic change associated with an environmental influence is causal or a secondary consequence of the phenotype
what does undernourishment of the embryo in utero lead to in mice?
developmental delay, smaller pups and adult onset diseases, effects also seen in F2 generation
what is the Dutch Hunger winter an example of?
how in utero nutritional compromise during a defined developmental window can lead to adult onset disease in offspring
how long is the mitochondrial genome?
16.5kb
characteristics of the mitochondrial genome?
16.5kb long, circular, each mitochondrion has several copies (2-10), 27 genes, no introns
how many genes does the mitochondrial genome contain?
27
how much of the mitochondrial genome makes a functional gene product?
all but 1kb of it
what does the mtDNA encode?
some of the components needed for mitochondrial protein synthesis on mitochondrial ribosomes
what does the endosymbiont theory propose?
the 2 genomes (mitochondrial and nuclear) originated when a type of aerobic prokaryotic cell was endocytosed by an anaerobic eukaryotic precursor
how are mitochondria inherited?
matrilineally
why do sperm mitochondria not contribute any mtDNA to the embryo?
they are degraded upon fertilisation
what is homoplasmy (mtDNA)?
every mtDNA is the same
what is heteroplasmy (mtDNA)?
can be a mixed population of normal and mutant mtDNAs
what is the threshold level for most pathogenic mtDNA mutations?
60-80%
why can level of heteroplasmy change over time?
due to the random way mtDNAs are replicated and segregated
characteristics of mtDNA replication?
stochastic (random), not directly linked to cell cycle
how many mitochondria do egg cells contain?
more than 100000
where do mitochondrial disorders show the greatest impact?
in tissues of high energy requirements- muscle and brain
when did the UK government make mitochondrial therapy legal?
Feb 2015
what is MRT?
mitochondrial replacement therapy
when is the nuclear genome transferred in metaphase II spindle transfer MRT?
before fertilisation of the egg
when is the nuclear genome transferred in pronuclear transfer MRT?
after fertilisation of the egg
what does MRT require?
preimplantation genetic diagnosis and in vitro fertilisation
what is a polymorphism?
an allele with a frequency <1%
what is a haplotype?
a group of alleles inherited from a single parent on the same chromosome homologue
what does the Hardy-Weinberg law provide?
a mathematical relationship between allele and genotype frequencies
what is the hardy weinberg law?
p + q = 1, p2 + 2pq + q2= 1
what are the requirements for the hardy-weinberg law to be applicable
no mutation, random mating, no gene flow, infinite population size, no selection
example of an allele that doesn’t obey Hardy-Weinberg predictions?
sickle cell anaemia allele HbS provides comparative resisitance to malaria
which genome variants are more likely to be neutral, those in introns or exons?
introns
what do genetic linkage studies do?
follow the inheritance of a trait in an affected family (pedigree) and look for co-segregation of the phenotype with alleles of polymorphic genetic loci from across the genome
what are identical twins?
monozygotic
what are non-identical twins?
dizygotic
what are concordant twins?
twins that both show a trait
when are twins discordant?
if only 1 shows a trait
for which is the concordance rate higher, monozygotic or dizygotic twins?
monozygotic twins
what does the concordance rate in monozygotic twins range from?
6-100%
how can twin studies be used to obtain an idea of the contribution of genetics to a disease?
comparing ratio of concordance between monozygotic and dizygotic twins
what is a GWAS?
a genome wide association study
what is a genome wide association study?
the approach of scanning the genome for regions contributing to complex phenotypes
what happens in a GWAS screen?
a large number of individuals with the trait/disorder of interest are genotyped alongside a large set of neutral control individuals from the same population
how is GWAS data presented?
in the form of Manhattan plots where the x axis shows the chromosomal location of each SNP, each dot represents an SNP, y axis shows statistical significance of association of each SNP with the particular trait
what is the OMIM database?
online mendelian inheritance in man database, has info on all known monogenic disorders on over 15000 genes
