human molecular genetics - MODULE 1 ( single gene disorders - mapping and identification of causative mutations)

what role does genetics play in our lives ?

1- Predisposition to possessing a trait/disorder- predisposition can be strong or weak- for single-gene disorders, predisposition = causation genetic variants result at some point from a mutation that can change the risk of ending up with a particular trait/disorder .. it can alter your risk which is the same as predisposition. the degree of that risk can vary, from it being very strong or very weak coming from one genetic variant .. the genetic bit of that contribution also can be strong or weak. Influencing severity (or clinical picture) of a disorder for single gene disorders, one variant at a locus in the genome contributes a lot of predisposition, a lot of increased risk and we can think of it as being causative .. it's almost entirely the cause of who has the disorder 2- Protection from trait/disorder- e.g. immune system genes and infection risk - similar predisp. vs protection seen in other disorders some variants however, don't change predisposition so much but they only do once they've acquired the disorder. they may be influencing the severity ( expressivity ) if one variant at a position increases your risk than another variant, the position must therefore protect you ( if one is a risk variant the other is a protective variant) example - Type 1 diabetes Type 1 diabetes (T1D) is one of the most widely studied complex genetic disorders, and the genes in HLA are reported to account for approximately 40% to 50% of the familial aggregation of T1D. The major genetic determinants of this disease are polymorphisms of class II HLA genes encoding DQ and DR. The major histocompatibility complex (MHC) is reported to account for approximately 40% to 50% of the familial aggregation of T1D thus, the human MHC is also referred to as the HLA complex. HLA molecules were originally studied for their ability to confer tolerance (histocompatibility) following tissue grafts [11]. Later studies revealed that their primary function is to provide protection against pathogens. HLA class I molecules present endogenous antigens, and class II molecules present exogenous antigens to T cells, creating the "tri-molecular complex" (HLA-peptide-TCR) that initiates the immune response. Although T1D susceptible HLA alleles are very common in the general population, the HLA genotype, which is the combination of HLA alleles inherited from both parents, is key for the development of T1D complex disorder but with a very strong genetic component, and one particular bit of the genome contributing. Most of the genetic component. The, the HLA complex on chromosome six https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233362/ You can kind of see how this predisposition versus protection works. If you read some of those 3- when its fully genetics the single gene disorder having the mutation is the whole explanation for whether you are effective or not those are Entire basis for certain differences between people- Mendelian (single gene) Those are single gene disorders Mendelian disorders, they, they are generally pretty much obey Mendel's inheritance laws. , varying traits with high heritability -( measure to what extent is genetics); It's just a measure of to what extent is genetics and explanation for who does. And who does not have the disorder. Some, some disorders have low heritability. They're a little bit genetic but not very genetic so eye colour - high heritability - complete genetics fingertip ridge count ( complex trait not single gene ) - completely genetics skin colour - environmental component to it personality dimensions - extrovert-introvert = partly genetics and environment cognitive function / intelligence = not all genetic but partly genetics More often, genetics partially explains degree of difference - each gene that varies contributes a certain amount to the 'genetic variance' in a trait between individuals- some genes have larger effects than others for each trait/disorder But there are lots of traits and disorders where the complex and where the genetic bit comes from a lots of genes. So genetics often partially explains where you are in the phenotype distribution or spectrum.And then each gene that contributes contributes a certain amount to that. some genes have larger effects than others genetic architecture - in every disorder; The list of genes that plays any role and the relative strength of each of those genes and that kind of goes into distribution for the single gene disorders. It's almost all coming from one gene every other gene plays almost no role at all.

genotype - baileys way

DD - disease allele mom must've carried a copy of the mutant allele ( Dd) same with father disease locus phenotype for those people deduced who else must have had a carrier of ( D) ? - OFFSPRING in generation 4 III first father genotype - homozygous wildtype so dd or heterozygous which is highly unlikely chance of passing it to the offspring ? IV ? if heterozygous segregation ratio 50/50 for every myotic transmission therefore each the chance of each offspring getting that particular Leo was exactly the same for each one. So the chance of seeing that set of phenotypes. is therefore 50/50 overall chance of seeing that pattern across all offspring ? 0.5x0.5x0.5x0.5

autosomal dominant

Name the pattern of genetic transmission characterized thus: both M and F are affected; M may transmit to M; each generation has at least one affected parent; and one mutant allele may produce the disease. In autosomal dominant disorders, the normal allele is recessive and the abnormal allele is dominant. It might seem paradoxical that a rare disorder can be dominant, but remember that dominance and recessiveness are simply reflections of how alleles act and are not defined in terms of predominance in the population. An example of a rare autosomal dominant phenotype is achondroplasia, a type of dwarfism (see Figure 4-21). In this case, people with normal stature are genotypically d/d, and the dwarf phenotype in principle could be D/d or D/D. However, it is believed that in D/D individuals the two "doses" of the D allele produce such a severe effect that this genotype is lethal. If true, all achondroplastics are heterozygotes. In pedigree analysis, the main clues for identifying an autosomal dominant disorder are that the phenotype tends to appear in every generation of the pedigree and that affected fathers and mothers transmit the phenotype to both sons and daughters. Again, the representation of both sexes among the affected offspring argues against X-linked inheritance. The phenotype appears in every generation because generally the abnormal allele carried by an individual must have come from a parent in the previous generation. (Abnormal alleles can arise de novo by mutation. This is relatively rare, but must be kept in mind as a possibility.) As with recessive disorders, individuals bearing one copy of the rare allele (D/d) are much more common than those bearing two copies (D/D), so most affected people are heterozygotes, and virtually all matings involving dominant disorders are D/d × d/d. Therefore, when the progeny of such matings are totaled, a 1:1 ratio is expected of unaffected (a/a) to affected individuals (A/a). rare if homozygous // mostly heterozygous what was the likelihood of the first offspring being affected and does their sex matter ? 50%, no. 50%,50% for each offspring. 2/4 r. Is that consistent with expectation for in terms of segregation ratio. yes It's kind of extreme but the extreme is not very far from what you'd expect if you had 15 siblings and all of them are affected. Then there's something weird going on because the chance of that happening is very, very low. more people affected than predicted what's happening ? epistasis / non-viable emboss so so if viability. If it's partly lethal if some offspring, do not survive to birth, then you will see fewer affected than you'd expect. In genetics, anticipation is a phenomenon whereby as a genetic disorder is passed on to the next generation, the symptoms of the genetic disorder become apparent at an earlier age with each generation. In most cases, an increase in the severity of symptoms is also noted. Anticipation is common in trinucleotide repeat disorders, such as Huntington's disease and myotonic dystrophy, where a dynamic mutation in DNA occurs. All of these diseases have neurological symptoms. Prior to the understanding of the genetic mechanism for anticipation, it was debated whether anticipation was a true biological phenomenon or whether the earlier age of diagnosis was related to heightened awareness of disease symptoms within a family. but this is not the case.. it won't be causing more than what you would expect MYOTIC DRIVE Meiotic drive is a type of intragenomic conflict, whereby one or more loci within a genome will effect a manipulation of the meioticprocess in such a way as to favor the transmission of one or more alleles over another, regardless of its phenotypic expression. More simply, meiotic drive is when one copy of a gene is passed on to offspring more than the expected 50% of the time. According to Buckler et al., "Meiotic drive is the subversion of meiosis so that particular genes are preferentially transmitted to the progeny. Meiotic drive generally causes the preferential segregation of small regions of the genome" skipped generation ? still don't rule out the possibility of it being an autosomal dominant ... they're patterns not rules ! does allele frequencies have any bearing on how likely we'd see this pedigree ? no

x linked recessive

What pattern of genetic transmission affects only M and has no M-to-M transmission, and mother is usually an unaffected carrier? Few phenotypes determined by alleles on the differential region of the X chromosome are related to sex determination. Phenotypes with X-linked recessive inheritance typically show the following patterns in pedigrees: 1.Many more males than females show the phenotype under study. This is because a female showing the phenotype can result only from a mating in which both the mother and the father bear the allele (for example, X A /Xa × X a /Y), whereas a male with the phenotype can be produced when only the mother carries the allele. If the recessive allele is very rare, almost all individuals showing the phenotype are males. 2.None of the offspring of an affected male are affected, but all his daughters must be heterozygous "carriers" because females must receive one of their X chromosomes from their fathers. Half the sons born to these carrier daughters are affected (Figure 4-24). Perhaps the best-known example is hemophilia, a malady in which a person's blood fails to clot. Many proteins must interact in sequence to make blood clot. The most common type of hemophilia is caused by the absence or malfunction of one of these proteins, called factor VIII. The most famous cases of hemophilia are found in the pedigree of the interrelated royal families of Europe (Figure 4-25). The original hemophilia allele in the pedigree arose spontaneously (as a mutation) in the reproductive cells of Queen Victoria's parents or of Queen Victoria herself. Alexis, the son of the last czar of Russia, inherited the allele ultimately from Queen Victoria, who was the grandmother of his mother Alexandra. Nowadays, hemophilia can be treated, but it was formerly a potentially fatal condition. It is interesting to note that in the Jewish Talmud there are rules about exemptions to male circumcision which show clearly that the mode of transmission of the disease through unaffected carrier females was well understood in ancient times. For example, one exemption was for the sons of women whose sisters' sons had bled profusely when they were circumcised. Duchenne muscular dystrophy is a fatal X-linked recessive disease. The phenotype is a wasting and atrophy of muscles. Generally the onset is before the age of 6, with confinement to a wheelchair by 12 and death by 20. The gene for Duchenne muscular dystrophy has now been isolated and shown to encode a muscle protein, dystrophin. Such insight holds out hope for a better understanding of the physiology of this condition and, ultimately, a therapy. A rare X-linked recessive phenotype that is interesting from the point of view of sexual differentiation is a condition called testicular feminization syndrome, which has a frequency of about 1 in 65,000 male births. People afflicted with this syndrome are chromosomally males, 44A + XY, but they develop as females (Figure 4-26). They have female external genitalia, a blind vagina, and no uterus. Testes may be present either in the labia or in the abdomen. Although many such people are happily married, they are, of course, sterile. The condition is not reversed by treatment with male hormone (androgen), so it is sometimes called androgen insensitivity syndrome. The reason for the insensitivity is that the causative allele codes for a malfunctioning androgen receptor protein, so male hormone can have no effect on the target organs that are involved in maleness. In humans, femaleness results when the male-determining system is not functional. males - XY females - XY genotype - D,- ( dpsent have the other allele) obligate carrier - An obligate carrier is an individual who may be clinically unaffected but who must carry a gene mutation based on analysis of the family history; usually applies to disorders inherited in an autosomal recessive and X-linked recessive manner. In X-linked recessive disorders, only females can be the carriers of the recessive mutation, making them obligate carriers of this type of disease. Females acquire one X-chromosome from their father and one from their mother, and this means they can either be heterozygous for the mutated allele or homozygous. But these two females here have a dot, but they have no children. So we can't tell if they've heterozygous or not just from their offspring so how do we know that they are unaffected heterozygous carriers. How do we know that ? cant tell by evidence from pedigree// additional evidence in the form of actual experimental data So that's basically based on the linkage. If we have markers that are very close to the disease locus, we can say carrying this allele at this marker means that you will be carrying a big D at the disease locus as well. if we know markers are closely linked to the disease locus, we can genotype those markers and tell the likelihood of being a carrier. Carriers only shown once known or deduced nowadays we know what mutations in each disorder is on the chromosome and we can go sequence that to see whether they're carrying a mutation or not but years ago that wasn't possible and we would deduct by linkage data And the disorder is x linked recessive. What proportion of male offspring, on average, would you expect to be affected ? 50 % Okay, so for each male, the chance was 5050 so some over all the males, it's going to be about 50% affected. Okay. Is that consistent with what we're seeing here.? 2/3 affected out of 3 male children , that's what you'd expect

Genetics, haplotypes and recombination - mapping disease/trait genes

autosomal dominant disease pedigree part of the genome is in common to these 3 people is where the disease gene is .. haplotypes recombine in every generation to narrow down which bit of the genome has to be the location of the disease genotype. To find disease/trait genes, we need to detect where these recombinations have taken place; - problem - we can't see them And now you can see it's mixing up with a chromosome holotype that came from the other grandparents have here. So you've now got different chunks of this chromosome having have representing different bits of the ancestral grandparents chromosomes. And the pattern of recombinant is going to be unique in everybody. And therefore, everybody mixes up has mixed up haplotypes in a unique pattern. Okay. We can follow if we had a way of seeing what's present on each of these little chunks of what we're actually big chunks of haplotype. We would instantly be able to see, well, which bit of haplotype is in common. And there's come down from this ancestor.

modifier genes

genes that enhance or dilute the effects of other genes

x linked dominant

male to male transmission impossible ( can only get Y chromosome from dad) x linked dominant can affect both males and females but can only be transmitted to males from an affected or carrier mom Pedigrees of rare X-linked dominant phenotypes show the following characteristics: 1. Affected males pass the condition on to all their daughters but to none of their sons 2. Females married to unaffected males pass the condition on to half their sons and daughters. There are few examples of X-linked dominant phenotypes in humans. One is hypophosphatemia, a type of vitamin D-resistant rickets. The mechanisms of X-linked dominance and recessiveness in humans are somewhat complicated by the phenomenon of X chromosome inactivationfound in mammals. affected male = genotype is D/- no wild type allele carried at locus so they cant pass it to their sons as they pass Y if dominant must pass to all daughters but none sons if mutation is severe enough to give affected female how severe will it be in male ? same mutation ? female D/d = affected male D/- = very severe , no compensating WT allele / protective allele and therefore they will not survive

The Lactase gene

- encodes the enzyme lactase breaks down lactose to constituent sugars - Human/mammal infants need lactase to digest maternal milk • thus, lactase, in all mammals known, is only expressed in infancy lactase must be present in gut So basically this gene has evolved and it is present in all placental mammals, it is turned on, only an infancy and it provides the enzyme in the gut that enables the offspring to derive energy from milk.

full penetrance

100% of the individuals with the allele show phenotype penetrance relates to heritability complex disorders. The predisposing alleles, The risk alleles have very low penetration. So you can be carrying those alleles and not have the disorder.That's the typical situation in complex disorders. So that's actually the biggest distinction in genetics between high penetration alleles, which caused single gene disorders. and low penetrance alleles which are to do with risk penetrance or full penetrance What we're looking to see is, is there an individual that we can say must be an obligate carrier, but his own affected if we can see such an individual, we say that that That person is non penetrate and the the disease causing allele has reduced penetrance okay this is a big factor. It really matters for autosomal dominant rarely you see an autosomal dominant will full penetrance

Pleiotropy

A single gene having multiple effects on an individuals phenotype Pleiotropy (from Greek πλείων pleion, "more", and τρόπος tropos, "way") occurs when one gene influences two or more seemingly unrelated phenotypic traits. Such a gene that exhibits multiple phenotypic expression is called a pleiotropic gene. Mutation in a pleiotropic gene may have an effect on several traits simultaneously, due to the gene coding for a product used by a myriad of cells or different targets that have the same signaling function. Pleiotropy can arise from several distinct but potentially overlapping mechanisms, such as gene pleiotropy, developmental pleiotropy, and selectional pleiotropy. Gene pleiotropy occurs when a gene product interacts with multiple other proteins or catalyzes multiple reactions. Developmental pleiotropy occurs when mutations have multiple effects on the resulting phenotype. Selectional pleiotropy occurs when the resulting phenotype has many effects on fitness (depending on factors such as age and gender)

Epistasis example of modifier gene

A type of gene interaction in which one gene alters the phenotypic effects of another gene that is independently inherited.

Structure of a 'typical' eukaryotic gene

Essential to have this picture in mind when considering where variation is located, and its possible functional effects 10% one exon no introns , 90% one intron exon - bits of genomic sequence that end up in mRNS , if spliced out is intron CODING HAS NOTHING TO DO WITH EXONS first exon begins at TSS, then comes start codon and stop codon , the exonic is part of the ORF in the gene but interrupted by introns ( consiguos regions) in mRNA, it's fully exons, introns are spliced out stop codon has to be in the last exon = NMD, non-sense mediated decay ; if there's a stop codon in exon 3 then NMD will kick in in the mRNA and the ribosomal sense will sense there's a stop codon and see there's proteins after that after splicing ( exon boundaries after), it is not naked RNA its a ribonucleic protein complex, there's proteins bound to points where exons bound together Nonsense mutation !! if NMD is in last exon; cant do that there's no exon boundary .. will you see mutant allele ? yes ! if the nonsense mutation is in an upstream exon; no protein made at all its own protein null. No, but if they nonsense mutation is in the final Exon, truncated protein product • affects type of expressed protein product - protein coding (non-synonymous/synonymous), splice site? Missense/ Nonsense (beware nonsense-mediated decay...) • or affects level of expressed protein product - splice site, UTR, promoter/regulatory region, intronic, intergenic - works via effects on transcription or stability of mRNA/translation rate some mutations affect nature of proteins being made Remember that some mutations will affect the nature of the protein that gets made ,missense mutations. last exon nonsense mutations and certain splice site mutations that could lead to have kind of forced alternative splicing. Those will change the protein. all other mutations don't change sequence of protein, but affect phenotype so the level of product by affecting whether mRNA lives long enough to get translated if degraded really quickly ? no protein ! where would you expect to see mutation that acted through that mechanism ? in the 3' UTR affect on translation rate ? more protein or fewer protein per molecule of mRNA ? where would you expect to see those mutations ? regulatory sites in 3' UTR, most of them 5' UTR ( if affects translations) coding mutations ! don't change sequence or aa but affect translation rate ( 5'UTR) less protein because there's less mRNA to be made ? where are those mutations. ? in regulatory regions that regulate transcription // promoter more are upstream of promoter ( enhancers and repressers ) enhancers and repressors can be found in intron 1 ! and also miles away from the gene Okay, regulate three regions that affect transcription can be in the gene or near the gene or miles away from the gene in both directions. So it could be miles upstream or it could be miles downstream. Okay, there are examples of where human disease is caused by a mutation in a regulatory element a million bp away from the beginning of the gene and often those mutations affect chromatin structure not just transcriptional regulation ( epigenetic aspect )

Mendelian disorders and modes of inheritance

For all problems with human pedigrees where you are NOT told the M.O.I., the trick is... 1- Look at the pedigrees. You are given, look at the pattern and immediately you can say, does that pattern. Look, typical of any of the modes of inheritance that I know about 2- Deduce the genotypes ( homozygous for WT allele, Heterozygous but carry one copy of the mutant allele or homo for the mutation ) at the disease locus under each MOI - Reject any M.O.I. whose rules are broken by the pedigree you are faced with 3- Accept all the POSSIBLE M.O.I.s (even if the pattern is atypical) eg . who would have bought the disease allele into the family ? - data you've been told ( allele frequency) - typical assumptions ( inbreeding?) - Calculate (roughly )likelihoods of seeing each sibship under eachM.O.I. given the data (use Mendel's 1st law....) Remember to take reduced penetrance into account

autosomal recessive

In a pedigree this phenotype will appear with equal frequency in both sexes but it will not skip generations. The unusual phenotype of a recessive disorder is determined by homozygosity for a recessive allele, and the unaffected phenotype is determined by the corresponding dominant allele Two key points are that generally the disease appears in the progeny of unaffected parents and that the affected progeny include both males and females equally. When we know that both male and female phenotypic proportions are equal, we can assume that we are dealing with autosomal inheritance, not X-linked inheritance Notice another interesting feature of pedigree analysis: even though Mendelian rules are at work, Mendelian ratios are rarely observed in single families because the sample sizes are too small. In the above example, we see a 1:1 phenotypic ratio in the progeny of what is clearly a monohybrid cross, in which we might expect a 3:1 ratio. If the couple were to have, say, 20 children, the ratio would undoubtedly be something like 15 unaffected children and 5 with PKU (the expected monohybrid 3:1 ratio), but in a sample of four any ratio is possible and all ratios are commonly found. In the case of a rare recessive allele, in the population most of these alleles will be found in heterozygotes, not in homozygotes. The reason is a matter of probability: to conceive a recessive homozygote, both parents must have had the p allele, but to conceive a heterozygote all that is necessary is one parent with the allele. The formation of an affected individual usually depends on the chance union of unrelated heterozygotes, and for this reason the pedigrees of autosomal recessives look rather bare, generally with only siblings of one cross affected. Inbreeding (mating between relatives) increases the chance that a mating will be between two heterozygotes. An example of a cousin marriage is shown in Figure 4-18. Individuals III-5 and III-6 are first cousins and produce two children. You can see from the figure that an ancestor who is a heterozygotemay produce many descendants who are also heterozygotes. Matings between relatives thus run a higher risk of producing abnormal homozygous recessives than do matings between nonrelatives. It is for this reason that first cousin marriages are responsible for a large portion of recessive diseases in human populations. segregation ratio ? = In the mid 1800's, Gregor Mendel demonstrated the existence of genes based on the regular occurrence of certain characteristic ratios of dichotomous characters (or traits) among the offspring of crosses between parents of various characteristics and lineages. These ratios are known as segregation ratios The analysis of segregation ratios remains an important research tool in human genetics. The demonstration of such ratios for a discrete trait among the offspring of certain types of families constitutes strong evidence that the trait has a simple genetic basis. How can you do segregation analysis to test if a disease that is fully penetrant autosomal recessive? For this model we know that affected individuals are DD, but unaffected individuals could be Dd or dd. One proposal is to look at the segregation ratios in families with at least one affected individual. What are some problems with this proposal? Simple segregation analysis tests the segregation parameter θ under a specified sampling scheme and mating type. Pedigrees used for segregation analysis may be from specifically planned matings or randomly sampled pedigrees with arbitrary structure or sampled through ascertained cases in clinics or veterinary practice. Arranged matings among animals can be more easily tested for specific modes of inheritance than pedigrees with arbitrary structure, missing data and many inbred animals. In the case of a rare disease and an autosomal dominant hypothesis, the segregation ratio θ is assumed to be 0.5 as families segregating for the trait are most likely composed by matings of heterozygous affecteds and homozygous non-carriers. As far as the segregation ratio is not significantly different from θ = 0.5, this mode of inheritance is accepted. Different methods for estimating θ have been developed and are easily applied (Singles Method, Weinberg's General Proband Method). These simple approaches to segregation analyses often encounter problems when different mating types have to be considered and several hypotheses are more or less likely. Complex segregation analyses have been developed to allow for more factors to vary and to reduce the restrictions on assumptions to be made for the model tested. Methods used to solve the likelihood functions are based on maximum likelihood or Markov chain Monte Carlo approaches (Gibbs sampling). In other words, there will be a certain expected proportion of each sibship affected. So for autosomal recessive, heterozygote parents - what proportion of offspring of that mating , would you expect to be affected.? ( segregation ratio ) 25%, each offspring.. 50% chance of getting 'D' from dad and 50% chance of getting 'D' from mom. multiply those together and you get 0.25, 25% each offspring had a 25% chance ( 6) over lots, you'd expect to see quarter to be affected but in this example we see 2/6 ( 0.33) affected what's the experimental or observed segregation ratio for that sibship ? that ratio consistent with the predicted theoretical ratio of 0.25 ? no . How many of these meiotic events would have had to gone a different way to give you exactly a quarter. So how many children is a quarter here ? 1 1/2 5/6 affected would be less likely to happen by chance if wed seen it, should we be considering any other genetic evidence ? So use the segregation ratio as part of your evidence, but it's not absolute. It's an argument in favor of something and you have to consider how likely it is to see this pattern under the particular expectation

Alleles and polymorphisms

Only sites in the genome that vary have alleles.... - genetic polymorphism variation type - SNP/SNV SNPS ; freq. = ~1 per 400 nucleotides SNP is concept that there's more than one allele at that position This polymorphic site thus has 2 alleles, each with its own freq. in the popn. locus not at equilibrium - skew genotype frequencies : 1- inbreeding 2- small populations 3- recurring mutations 4- Migration 5- selection for any variant ( old or new ) alleles will have a frequency ! new mutation will have a smaller frequency ! disease causing allele low freq in population

"

Set of mutation lifetime trajectories - mutation creates derived allele new allele goes straight to extinction - strong deleterious effect new allele goes to extinction after a few generations - weaker deleterious effect new allele hangs about and becomes part of the 'genetic background' in the population - new allele drifts (freq. changes at random) and then eventually goes extinct - new allele drifts to high freq. - new allele is selected ('positive selection') and goes to high freq. » new allele goes to fixation - sequence has changed for ever - new allele and old allele co-exist for a long time » balancing selection or neutrality - for a neutral allele in humans, once past initial extinction-risk phase, average time to eventual extinction/fixation is c.1Myr

For some problems with human pedigrees you ARE TOLD what the M.O.I. is (or told that you MUST assume it's what you are told it is for the context of the problem)

In this case, DO NOT consider other M.O.I.s, but you'll probably need to explain the data you see in the pedigree given the assumption that the given M.O.I. holds - i.e. who's affected, who's an unaffected carrier, likelihood of being a carrier or future affected for each offspring in sibship etc. Apply the same rules, look at the patterns and explain them Work out what other assumptions MUST hold - e.g.allele frequency ,penetrance ,inbreeding etc.

Mendel's Laws

Law of Segregation (The "First Law"): The alleles at a gene segregate (separate from each other) into different gametes during meiosis. An individual receives with equal probability one of the two alleles at gene from the mother and one of two alleles at a gene from the father. Law of Independent Assortment (The "Second Law"): The segregation of the genes for one trait is independent of the segregation of genes for another trait, i.e., when genes segregate, they do so independently

Haplotypes and recombination

• 'Haplotype' - haplotype combinations of alleles change in every generation (in a diploid organism) due to..... » RECOMBINATION • EVERYTHING IN HUMAN GENETICS COMES DOWNTO COMBINATIONS OF VARIANT ALLELES IN HAPLOTYPES how many recombination events ? and where ? 1 recombination event and between two loci can you tell which side of locus this recombination happened ? you cant tell ! not exact ! they don't happen at a locus they occur between loci between 5th locus and 7th locus here on haplotype one

Haplotypes and their importance

'Haplotype' - the half of the genome that is transmitted from parent to each offspring, consisting of one of each homologous chromosome pair - by implication, • in a parent, at every locus along each chromosome - one allele is carried on one chromosome homologue - the other allele on the other homologue - these combinations of alleles on each homologue are also known as the parental 'haplotypes' Each other type is the half of the genome that came from each parent, but it got mixed up in that parent because of recombination 'Diplotype' - the combination of two haplos possessed by one indiv. Your diplotype is the combination of the two haplotypes. You got one from father and one from mother. So that's your deploy type At any two loci you can express genotype at one locus or joint genotype haplotype to loci. In other words, diplotype.

types of genetics ( single gene disorders)

- mode of inheritance Mode of inheritances is an idea that comes into this strongly, we've got this idea of heterogeneity; different patients might have different causative mutations, and that might be at the allele level or the locus level. In some cases, there are special types of inheritance for single gene disorders such as disorders of imprinting - heterogeneity ( covered up ) - polygenic disorders and traits • Multifactorial • environment also plays a role Is combined with an environmental contribution and the genetic bit almost never comes from one gene. It comes from lots of genes at the same time in each Person. And then the third category really are the mitochondrial disorders - mtDNA mutations ( not assessed )

continuation

-13910 C / T varying site - both alleles are segregating in the popn. - it's now classed as a (single nucleotide) polymorphism (SNP) What is the phenotype associated with the T allele? - Lactase persistence = lactose tolerance - Ability to digest milk in adulthood => ability to use milk/dairy as part of diet throughout life - Indivs with (the ancestral) CC genotype are lactose intolerant The derived 'T' allele is currently common in many European populations, with allele freq. of ~0.6 or more - why? - Has it been subject to natural selection?

genome is functioning and is dynamic/

How the genome actually exists inside cell nuclei Basic 1D structure - DNA sequence Most DNA is bound to protein • Chromatin= DNA+ proteins Assembly of chromatin into higher order structures nucleosomes - histones 30nm fibre - solenoid chromatin 'loops' fully condensed metaphase chromo. Other protein/DNA interactions • transcription factors • scaffolds Regulation of gene expression governed by 'rules' of chromatin • DNA modification • methylation of CpG • Histone protein modifications • acetylation, methylation etc. • 'epigenetic' control of expression

what's in a genome ?

In genetics, focus is on genes as 'abstract entities governing traits' • e.g. gene 'for' blue eyes So there isn't there isn't a gene for blue eyes and a gene for brown eyes, there is one gene. And there's a certain that gene that Is that the various there's a polymorphism in that gene. And if you have genotype, where one a little is present, the outcome is a blue eye. And if you have the other genotype, where the brand is present the phenotype outcome is a brown ik same gene does both things, etc, etc. In molecular genetics, focus is on genes as real physical entities • original (molecular) definition - one gene - one polypeptide • newer concept - a functional segment of DNA sequence occupying a fixed location on a chromosome..... blah, blah, blah...... Somewhere on a chromosome, there is a base that represents the beginning of a gene further along that chromosome is the base that represents the end of that gene.everything between those two points is the genes. ( sequence between two points on a chromosome ) • think in terms of information content arrow ? transcribed from left to right ( coding strand); transcribed from coding strand ; template strand non coding strand ( left to right top strand ) If I put the arrow. The other way, it means it's read right to left on the bottom strand still five prime, three prime, and that is the coding strand is now the bottom strand • DNA carries out storage, copying and coding of information - a gene is like one line in a recipe • this enables us to define the 'structure' of a gene (see below) • other meanings/uses of the word 'gene'....- unit of selection (Dawkins 'selfish gene' point of view)

mutation occurs ( gonads mutation )

It was probably more likely to be a simple chemical change changing the base at a certain position in the DNA from one place to another base. A (de novo) mutation occurred in one copy of the Lactase gene in one of his germline cells (spermatogonia/spermatocytes) The result would be.... - a change in the function of the lactase gene - Genotype = C -> T change at position -13910 ; single nucleotide change - Phenotype = lactase persistence (i.e. a functional change) • lactase gene remains turned 'on' after weaning - lactase expression continues into adulthood What happened next? - Man had children, one or more of whom received T mutant lactase - His children also had children, some of whom received T mutant lactase - Soon (several generations later...) quite a few people in the local population carried one, maybe even two copies of this mutation

locus and alleles

Locus - An arbitrary point in the genome- A particular position on a chromosome (e.g. 'D4S316')- The known or unknown 'place' in the genome that harbours a disease-causing mutation e.g. 'the CF locus' - location of the cystic fibrosis gene - Location of any gene can be expressed in terms of its position relative to a set of loci at a locus sequence can vary Alleles- any locus with >1 allele is polymorphic - variants at a polymorphic locus are alleles - each person (diploid) carries two alleles - this is their 'genotype' At a particular polymorphic locus:- Homozygotes -carry two identical alleles Heterozygotes - carry two different alleles chromosome homolog at a locus, genotype is 1,2 ( put comma), heterozygotes at B locus 2,2 homo for 2 allele

Gonadal mosaicism

Mutation only in egg or sperm cells. If parents and relatives do not have the disease, suspect gonadal (or germline) mosaicism Germline mosaicism, also called gonadal mosaicism, is a type of genetic mosaicism where more than one set of genetic information is found specifically within the gamete cells; conversely, somatic mosaicism is a type of genetic mosaicism found in somatic cells. Germline mosaicism can be present at the same time as somatic mosaicism or individually, depending on when the conditions occur. Pure germline mosaicism refers to mosaicism found exclusively in the gametes and not in any somatic cells. Germline mosaicism can be caused either by a mutation that occurs after conception,[1][2] or by epigenetic regulation,[3] alterations to DNA such as methylation that do not involve changes in the DNA coding sequence. A mutation in an allele acquired by a somatic cell early in its development can be passed on to its daughter cells, including those that later specialize to gametes. With such mutation within the gamete cells, a pair of medically typical individuals may have repeated succession of children who suffer from certain genetic disorders such as Duchenne muscular dystrophy and osteogenesis imperfecta because of germline mosaicism. It is possible for parents unaffected by germline mutations to produce an offspring with an autosomal dominant (AD) disorder due to a random new mutation within one's gamete cells known as sporadic mutation; however, if these parents produce more than one child with an AD disorder, germline mosaicism is more likely the cause than a sporadic mutation.[4][unreliable source?] In the first documented case of its kind, two offspring of a French woman who had no phenotypic expression of the AD disorder hypertrophic cardiomyopathy, inherited the disease.

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Origin of the lactase -13910 T allele dated to around 6-9,000 ybp - roughly the same time that cows were being domesticated and milk production started Some genetic evidence exists that is consistent with selection having acted on this gene recentlyin certain populations Gradient of T allele freq. in Europe and coincidence with centre of dairy farming development High freq. of other lactase persistence alleles in other populns. using milk from cows Hypothesis - lactase persistence selected on the basis that those able to drink milk as adults might survive drought or e.g. cholera better...? - if milk available from domesticated cows, those able to drink it would receive fluid and nourishment for a few extra days - in a milk-drinking culture, those drinking milk but not able to digest lactose would suffer from diarrhoea, which exacerbates dehydration What will happen next (in the evolution of this system)...? lactase -13910 T allele currently at a freq. of >60% in Northern Europe Three things can happen: - Freq.willgodown-relaxedselectionduetomodernmedicine • polymorphism maintained for a while • starts to undergo random fluctuations - genetic drift • eventually its freq. would be so low that it could be lost entirely in 1 generation - extinction - Freq.willstaythesame-selection for both alleles prevents freq. from going up or down in the long run • balancing selection - Freq.willincrease(bypositiveselectionorbottleneck)to100%-fixation • all descendants of popns. with fixed new allele will have a lactase gene sequence that is different to all other humans • fixation is an important part of population divergence and speciation process - will lactase diffs. contribute to human speciation....??

Autosomal dominant with reduced penetrance

Penetrance refers to the proportion of people with a particular genetic change (such as a mutation in a specific gene) who exhibit signs and symptoms of a genetic disorder. If some people with the mutation do not develop features of the disorder, the condition is said to have reduced (or incomplete) penetrance. Reduced penetrance often occurs with familial cancer syndromes. For example, many people with a mutation in the BRCA1 or BRCA2 gene will develop cancer during their lifetime, but some people will not. Doctors cannot predict which people with these mutations will develop cancer or when the tumors will develop Reduced penetrance and variable expressivity are factors that influence the effects of particular genetic changes. These factors usually affect disorders that have an autosomal dominant pattern of inheritance, although they are occasionally seen in disorders with an autosomal recessive inheritance pattern. For many inherited diseases, the same mutation is not always expressed in all persons who carry it, moreover, when the mutation is expressed, it is not always expressed in the same way Until recently reduced penetrance is a term used exclusively for autosomal dominant disorders. However the existence of healthy homozygotes of autosomal recessive disorders has been demonstrated by molecular analysis Reduced penetrance being a widespread phenomenon in human genetics as evidenced from next generation sequencing of entire exomes or genomes of apparently healthy individuals represents a major challenge to genetic counsellors in quantifying the disease risk to the patient's offspring carrying 'D' , but not affected ? carry disease allele but not penetrant 0 penetrance = not a disease causing gene; no affect on phenotype 100 penetrance = all heterozygotes are affected de novo mutations in meiotic events, unaffected dad might be homozygous WT and in gonad there's been a de novo mutation that created an affected son .. would we see others affected ? depends on when mutation happened in reproductive pathway if it happened in the germline very late on so that only a few gametes were produced with the mutation, the chance that two of those gametes gets into the next generation is vanishingly small. But what if the mutation happened earlier in the development of either the testis or the ovary? What happens if it was shortly after the germline got separated from the soma, there was an early mutation that affects what turns out to be lots of spermatozytes or oocytes ? might affect significantt proportion of cells in the gonad and gametes and therefore can get multiple times in the next generation pic shows early acting de novo mutation 2 de novo mutations creating an affected offspring is incredibly unlikely gonadal mosaism - early de novo mutations

Genetic Markers and genetic variation

Three major classes of variation - ...and four means of genotyping them (see 'slidesonmapping' file...) • this variation can be - causal (only rarely) - neutral (no effect on pheno - most polymorphic loci) • SNPs- RFLPs are a subset of SNPs Microsatellites - simple tandem repeats - copy no. varies... Other types of CNV- large(upto>1Mbp)and small(downto1bp) ( size of sequence variant) could include Alu repeat(or other retro element) insertions- copy no. per diploid genotype could be 0,1,2,3or4(or may be even more...) • deletions-0,1,2copies duplications-2,3,4copies etc. diff genotypes with diff no of copies deletion polymorphic sites neutral polymorphic sites

disorder of imprinting / parent of origin specific penetrance

What matters is who you inherited your mutant allele from, not what sex you are // non Mendelian patterns of inheritance Pattern of transmission of trait/disorder Penetrance An all-or-nothing state defined as the probability that: • a particular genotype will exhibit a particular phenotype • an individual with a disease-causing allele will show the associated signs/symptoms • if they do not, they are said to be non-penetrant• if a disorder exhibits reduced penetrance - some indivs. carrying mutant gene don't exhibit affected phenotype Variable expressivity the propensity of a genotype to be associated with differentphenotypes (e.g. signs/symptoms) in different indivs. • 'pleiotropy'• also used if severity is very variable - both are influenced by modifier genes, epistasis, genetic background, environment

calculating risks in pedigree analysis

When a disease allele is known to be present in a family, knowledge of simple gene transmission patterns can be used to calculate the probability of prospective parents' having a child with the disorder. For example, a married couple finds out that each had an uncle with Tay-Sachs disease (a severe autosomal recessive disease). The pedigree is as follows: The probability of their having a child with Tay-Sachs can be calculated in the following way. The question is whether or not the man and woman are heterozygotes (it is clear that they do not have the disease) because if they are both heterozygotes then they stand a chance of having an affected child. 1. The man's grandparents must have both been heterozygotes T/t because they produced a t/t child (the uncle). Therefore, they effectively constituted a monohybrid cross. The man's father could be T/T or T/t, but we know that the relative probabilities of these genotypes must be 1/4 and 1/2, respectively (the expected progeny ratio in a monohybrid cross is 1/4 T/T, 1/2 T/t, and 1/4 t/t). Therefore, there is a 2/3 probability that the father is a heterozygote [calculated as 1/2 divided by ( + 1/4+1/2)]. 2. The man's mother must be assumed to be T/T, since she married into the family and disease alleles generally are rare. Thus if the father is T/t, then the mating to the mother was a cross T/t × T/T and the expected progeny proportions are 1/2 T/T and 1/2 T/t. 3. The overall probability of the man's being a heterozygote must be calculated using a statistical rule called the product rule, which states that the probability of two independent events both occurring is the product of their individual probabilities. Hence the probability of the man's being a heterozygote is the probability of his father's being a heterozygote timesthe probability of the father having a heterozygous son, which is 2/3 × 1/2 = 1/3. 4. Likewise the probability of the man's wife being heterozygous is also 1/3. 5. If they are both heterozygous (T/t), then the probability of their having a t/t child is 1/4, so overall the probability of the couple having an affected child is 1/3 × 1/3 × 1/4 = 1/36; in other words, a 1 in 36 chance.

Real vs apparent allele-sharing between relatives

When tracing inheritance of chunks of chromosome through a family or in a population, we need to know whether alleles shared by two indivs. have come from a single, recent, common ancestor or not ( by chance) Q - how many parental alleles do 2 sibs share - 0, 1, or 2 ? identical by state dosent tell us linkage go through the picture ( pretty straightforward)

Haplotype

area of linked genetic variations in the human genome Understanding patterns of variation and functional effects on phenotype Parental chromosome sets are the 'haplotypes' of your indiv. genome Imagine a cell in the germline of a man hoping to become a father. A haplotype is a group of genes within an organism that was inherited together from a single parent. The word "haplotype" is derived from the word "haploid," which describes cells with only one set of chromosomes, and from the word "genotype," which refers to the genetic makeup of an organism. A haplotype can describe a pair of genes inherited together from one parent on one chromosome, or it can describe all of the genes on a chromosome that were inherited together from a single parent. This group of genes was inherited together because of genetic linkage, or the phenomenon by which genes that are close to each other on the same chromosome are often inherited together. In addition, the term "haplotype" can also refer to the inheritance of a cluster of single nucleotide polymorphisms (SNPs), which are variations at single positions in the DNA sequence among individuals. By examining haplotypes, scientists can identify patterns of genetic variation that are associated with health and disease states. For instance, if a haplotype is associated with a certain disease, then scientists can examine stretches of DNA near the SNP cluster to try to identify the gene or genes responsible for causing the disease. 2 haplotypes in each organism genetic recombination - cross over between chromosomes

familial x linked dominant - lethality in males

females = D/d they can pass it on to their daughters and 50% chance to their sons as well but if they do receive it they're incompatible with life, people conceived ( miscarriage) ( represented by little dot ) So the point here is, you will see only female people affected but there will be a dearth of males in each sib ship, there will be fewer males than you expect. Because the ones who received Big D from their mom didn't get born Okay, so that so you see a slightly different segregation pattern sex ratio segregation ratio and a very big sex skewing here. If you do not get the typical pattern for dominant, which is half male, female, remember that most cases result from de novo mutations and XLD disorders are therefore usually NOT strongly familial rett syndrome - we only see singleton affected females not males / We don't see the males because it's lethal or they have something that's so severe. We don't call it Rett syndrome. If they get the same mutation. And we don't tend to see it in familial form because if you're female and you have the disease, allele you're not going to have babies. It's so severe that you don't reproduce So you generally only see singleton's and therefore the explanation for them has to be de novo mutation. So there are hundreds of different excellent dominant disorders that arise from de novo mutations and they're only seen in females.