Pedigree Analysis Virtual Lab

A pedigree is a family tree drawn with standard symbols that records who has a particular trait and who does not. Geneticists and genetic counsellors read pedigrees to work out how a trait is inherited, to find which relatives may carry a hidden allele, and to estimate the chance that a future child will be affected. Reading a pedigree is detective work: the chart shows the evidence, and the rules of inheritance tell you which explanations are possible.

Every trait in this laboratory is fictional. The "silver-streak trait" is an invented, harmless trait, used so that nobody is reminded of a real family or a real condition. The probabilities, the rules and the reasoning are the real ones. The notes are written in three layers. Foundation material needs fractions and the idea that children inherit one copy of each gene from each parent. Core material matches typical A-level, IB Diploma, AP Biology, WASSCE and Cambridge AS/A Level genetics, including conditional probability. Extension material goes towards IB HL and first-year university: likelihood, Bayes' theorem with several pieces of evidence, Hardy-Weinberg and consanguinity.

Use the simulator alongside these notes. It builds a random family for one of four modes of inheritance, draws it on a canvas, lets you select individuals and test hypotheses, and then calculates how likely the pedigree is under each mode. Always predict first, then test.

Learning outcomes

Foundation

• Name the pedigree symbols for male, female, affected, unaffected, mating, children and the proband.
• Explain that a person inherits one allele of each autosomal gene from each parent.
• Distinguish dominant from recessive inheritance in a simple family.
• State that a carrier of a recessive allele does not show the trait but can pass the allele on.
• Give the chance (1/2 or 1/4) that a child is affected in the simplest crosses.

Core (A-level, IB, AP, WAEC)

• Recognise the typical pedigree patterns of autosomal dominant, autosomal recessive, X-linked recessive and X-linked dominant inheritance.
• Use exclusion rules to rule a mode of inheritance out, and explain why passing the rules does not prove a mode.
• Work out the genotype of each individual that can be deduced from the pedigree, including obligate carriers.
• Calculate the probability that a child is affected, and the probability of several affected children, with the binomial formula.
• Use Bayes' theorem to update a carrier probability when an unaffected relative or child is observed.
• Explain why an unaffected person with an affected parent in a dominant pedigree needs careful interpretation (reduced penetrance).

Extension (HL, AP, university)

• Compute the likelihood of a pedigree under each mode and a likelihood ratio between two modes.
• Combine prior probability, conditional probability and a population carrier frequency from Hardy-Weinberg into a recurrence risk.
• Explain how consanguinity raises the risk of recessive disorders.
• Discuss the ethics and privacy of genetic information, and the aims of non-directive counselling.

Genes, alleles and genotypes

Foundation

A gene is a stretch of DNA that influences a trait. Different versions of a gene are alleles. In this laboratory the normal allele is written N and the trait allele is written S. Your genotype is the pair of alleles you carry at a gene on an autosome (a non-sex chromosome), such as NN, NS or SS. Your phenotype is what can be observed, here whether you show the silver-streak trait. One allele of each pair comes from each parent, and which one is passed on is a matter of chance, each with probability 1/2.

Dominant and recessive

An allele is dominant if one copy is enough to show the trait: both NS and SS people are affected. An allele is recessive if two copies are needed: only SS people are affected, and NS people are carriers who look unaffected. These words describe the effect of an allele on the phenotype. They do not mean that an allele is common, or stronger, or more harmful.

Sex linkage

Females have two X chromosomes. Males have one X and one Y. A gene on the X chromosome is X-linked. A male has only one copy, so a single trait allele decides his phenotype whether it is dominant or recessive. A male cannot be a carrier in the usual sense, and he passes his X to every daughter and his Y to every son. A female has two copies and behaves like an autosomal case, but she receives one X from each parent and passes one of them, at random, to each child.

Pedigree symbols

The standard symbols are shown below. Squares are males, circles are females, filled shapes are affected, a horizontal line joins a couple, a vertical line descends to the children, and a bar joins siblings. Generations are labelled with Roman numerals, and individuals within a generation are numbered from the left, so III-4 is the fourth person from the left in the third generation. The proband (also called the propositus or index case) is the first affected person who brought the family to attention, marked with an arrow. A dot inside a shape marks a carrier who is known or presumed to carry the allele without showing the trait.

Why probability appears

Core

Each child receives alleles by chance, so the same parents can have an affected child and an unaffected child. Probabilities attach to individual children, and the children are independent: the result for one child does not change the chance for the next. This is the same idea as tossing a fair coin several times, and it is the reason the binomial formula appears in genetic counselling.

The basic cross probabilities

Foundation

Let each parent pass the allele S with probability a (father) and b (mother). For an autosomal gene a = 1/2 for an NS parent, 0 for NN and 1 for SS. The child's genotype probabilities are:

For a cross of two carriers (NS × NS) a = b = 1/2, giving 1/4 NN, 1/2 NS and 1/4 SS. For an autosomal recessive trait the chance of an affected child is 1/4. For an autosomal dominant trait with one heterozygous affected parent and one NN parent (NS × NN), a = 1/2 and b = 0, so the chance of an affected child is 1/2.

X-linked crosses

Core

A son receives the mother's X only. A daughter receives the father's X and one of the mother's two X chromosomes. If the mother passes the trait allele with probability b = 0, 1/2 or 1, then:

• Son is affected with probability b.
• Daughter has a trait allele from the mother with probability b, and from the father with probability 0 or 1 (1 if he has the allele).

For X-linked recessive inheritance with a carrier mother and an unaffected father: sons are affected with probability 1/2, daughters are never affected, and half of the daughters are carriers. With an affected father and a non-carrier mother: no son is affected, and every daughter is a carrier. For X-linked dominant inheritance with an affected father and an unaffected mother: every daughter is affected and no son is.

Several children: the binomial formula

If each child is affected with probability p, independently, then the probability that exactly r of n children are affected is:

The probability that none is affected is (1 − p)ⁿ, so at least one is affected with probability 1 − (1 − p)ⁿ.

Bayes' theorem for carrier probability

Core

Suppose a woman may be a carrier (hypothesis C) or not (hypothesis not-C). Before looking at her own children, her prior probabilities are P(C) and P(not-C). Then she has an observation E, for example three unaffected sons. For each hypothesis there is a conditional probability P(E | C) and P(E | not-C). Bayes' theorem gives the posterior:

A table is the clearest way to do it: list the hypotheses, write the prior and the conditional probability beside each, multiply to get the joint probability, add the joints, then divide each joint by the total. The Bayesian table in the Analyse section prints exactly this.

Hardy-Weinberg and the population carrier frequency

Extension

If the trait allele has frequency q in a large population with random mating, the genotype frequencies are NN: (1 − q)², NS: 2q(1 − q), SS: q². For a recessive trait the incidence is q², so q = √incidence and the carrier frequency is 2q(1 − q). For a male X-linked trait the frequency of affected males is q itself. A partner who is known to be unaffected is a carrier with probability 2q(1 − q) / (1 − q²) for a recessive trait, because the unaffected people are those who are not SS.

Likelihood of a pedigree

Extension

The likelihood of a mode of inheritance is the probability of the observed phenotypes if that mode is true. Founders (people with no parents in the chart) are given genotypes from the Hardy-Weinberg frequencies. Each child's genotype then follows from the parents by the cross probabilities above. Hidden genotypes are summed over. If any observed pattern is impossible under the mode (for instance an affected child of two unaffected parents under a dominant mode), the likelihood is exactly 0. A likelihood ratio L₁ / L₂ compares two modes: values near 1 mean the data do not separate them.

All trait names are fictional. N is the normal allele and S the trait allele.

Reading a pedigree like a graph

Foundation

A pedigree is a diagram, not a graph with axes, but it should be read systematically in the same way. Start with the generations (rows), then look for the pattern of affected individuals. Ask four questions in order: is the trait present in every generation? Is it more common in one sex? Do affected children have unaffected parents? Do affected fathers have affected sons?

Graphs in the simulator

Core

• Likelihood by mode. Bars show the base-10 logarithm of the likelihood under each of the four modes. A bar at the floor is a mode with likelihood exactly 0. Because the scale is logarithmic, a difference of 1 means a ratio of 10.
• Affected by generation. The fraction affected in each generation. A dominant trait tends to show a high fraction in every generation; a recessive trait often has a low fraction until carriers marry.
• Observed against expected. For every recorded pedigree, the expected number of affected children (from the hidden parental genotypes) is plotted against the observed number. Mendel's rules predict a line through the origin with gradient 1.
• Accuracy over runs. The share of mystery pedigrees you identified correctly, plotted as a running proportion.

Line of best fit through the origin

Extension

When a relationship must pass through (0, 0), as here (zero expected affected children means zero observed on average), the least-squares gradient is m = Σxy / Σx². The standard error of m is s / √(Σx²), where s² = Σ(y − mx)² / (n − 1). If m is within about two standard errors of 1, the data are consistent with the Mendelian rules.

What the simulation leaves out

Core

The simulation uses clean, idealised rules so that you can learn the reasoning. Real families are messier.

• Reduced penetrance. Some people with a dominant genotype never show the trait. Their phenotype looks unaffected, so an apparent "skipped generation" in a dominant trait does not always rule it out. The likelihood tool has a penetrance setting to explore this.
• Variable expressivity. The same allele can have mild effects in one person and strong effects in another, so affected status can be hard to assign.
• New mutations. A child may be the first affected person in a family. This is why "affected child of two unaffected parents" does not completely rule out a dominant mode in real life, even though the simulator treats it as impossible.
• Genetic heterogeneity. Different genes can produce the same phenotype, and a single family may mix causes.
• Other modes. Y-linked, mitochondrial (maternal), polygenic and multifactorial inheritance do not follow the four patterns here. Mitochondrial inheritance passes from mothers to all children.
• Small pedigrees. A small family often fits more than one mode. Real counsellors extend the chart, confirm diagnoses and use laboratory tests.
• Incomplete information. Real people die young, are adopted, or are not known to be unaffected. A person's status may change with age if a trait appears late.
• Consanguinity and population structure. The founders in the simulator are unrelated people drawn at random. In real populations, relatives marry more often than chance would predict.

Research question

A good question names what you will compare and what you expect. For example: "Can the pattern of affected individuals in a three-generation pedigree identify the mode of inheritance, and how often does a small pedigree leave more than one mode possible?" This is testable, uses the simulator's hidden answer as a check, and lets you measure your own accuracy.

Variables

Method for the virtual lab

1. Choose Mystery. Press New pedigree. Look at the chart and write down which modes you think are possible, with a reason.
2. Select individuals and read their relatives. Ask the four questions in section E.
3. Choose a hypothesis and press Test hypothesis. Broken rules are outlined in red. Test all four modes.
4. Record the pedigree. The simulator reveals the true mode and the hidden carriers, which you should compare with your reasoning.
5. Repeat for at least ten pedigrees, balancing the four modes by choosing them directly for some runs.
6. Open the Analyse section and run the likelihood check, the recurrence-risk calculation and the Mendelian fit on your recorded data.

Method for a real investigation of a family

A real family history is collected by a trained professional. It starts with the affected person, then asks about parents, siblings, children, grandparents, aunts, uncles and cousins on both sides, noting the age, sex, health and, where relevant, cause of death. Whether each person is truly affected should be confirmed from medical records, not memory alone. Consent is needed from the family member being asked, and relatives are not contacted without permission.

Sample size

Core

One pedigree is one data point about a mode, and chance affects small families a great deal. To judge your accuracy, record many pedigrees. If you identified the mode correctly in 6 of 10 mystery pedigrees, the standard error of that proportion is about √(0.6 × 0.4 / 10) = 0.15, so the true accuracy could be 0.3 to 0.9. Twenty or more pedigrees narrow that range.

Where uncertainty comes from

The simulator has no measurement error, because phenotypes are recorded exactly. The uncertainty is of three kinds.

• Chance in inheritance. Each child's genotype is random, so counts of affected children vary even when the model is exactly right. For n children with probability p, the number affected has mean np and standard deviation √(np(1 − p)).
• Ambiguity in the pedigree. Several modes may fit. The likelihood ratio quantifies how strongly the data favour one over another.
• Uncertain assumptions. The population allele frequency q and the penetrance are assumed. The recurrence-risk tool shows the range of the answer for q of 2%, 5% and 10%.

Binomial uncertainty and the standard error

Core

If you observe a proportion p̂ in N independent trials, its standard error is √(p(1 − p) / N). In the prediction calculator, simulating 2000 children with p = 0.25 gives a standard error of √(0.25 × 0.75 / 2000) = 0.0097. An observed proportion between 0.231 and 0.269 is within two standard errors and is therefore not surprising.

The Mendelian fit

The Analyse section plots observed against expected affected children for each recorded pedigree and fits a line through the origin. The gradient m = Σxy / Σx² should be near 1, with the standard error computed from the residuals. It is also useful to compute a z-score for the total: z = (O − E) / √V, where O is the observed total, E the expected total and V the sum of p(1 − p) over all children. Values of |z| less than 2 are within chance variation.

Likelihood and support

Extension

Given equal prior belief in the four modes, the support for a mode is its likelihood divided by the sum of the four likelihoods. This is a posterior probability under the stated assumptions. A mode with likelihood 0 has support 0. When one mode has support above 0.95 you can be fairly confident; when two modes share the support, you need more evidence. A likelihood ratio between 1 and 3 is usually called weak, 3 to 20 moderate and above 20 strong, though these labels are only conventions.

Recording and presenting data

• Record the seed, true mode, your hypothesis and the number of modes still possible, so that others can repeat your work.
• Show probabilities as fractions, decimals or percentages consistently, to a sensible number of significant figures (usually 2 to 3).
• State the assumptions behind every risk: mode of inheritance, allele frequency, penetrance and the partner's status.
• Download the CSV file to analyse your results further in a spreadsheet.

The virtual apparatus

Foundation

• Pedigree generator. Builds a random family from a founder couple. Each child receives alleles by chance according to the chosen mode. People who marry in are drawn from the population allele frequency.
• Canvas chart. Draws squares and circles, couples and sibships with Roman-numeral generations. You can select an individual by clicking or by the arrow keys.
• Hypothesis test. Marks individuals who break the inheritance rules of the mode you chose.
• Likelihood tool. Calculates the probability of the pedigree for each mode by summing over all hidden genotypes.
• Risk calculator. Gives the recurrence risk for a chosen individual, with a Bayesian table shown step by step.

How real family histories are gathered

Core

The first step in a real study is a structured conversation and review of records. The three-generation chart is the usual standard, because it shows inheritance patterns without being overwhelming. The most useful information comes from confirming diagnoses, as people may be unsure what condition a relative had or may use different names for it.

How real laboratories identify carriers

Extension

When a gene is known, a sample of blood or saliva can be tested for the specific allele. A positive result in a relative converts a probability into near certainty. This is called carrier testing, and results can then replace the Bayesian estimates in a pedigree, which usually changes the risk a great deal. Other kinds of testing include looking at chromosome structure under a microscope, and sequencing a gene. The details depend on the condition and are outside this laboratory, which uses a fictional trait with no real test.

Genetic counselling (introductory)

Core

A genetic counsellor helps individuals and families understand a condition, how it is inherited, the chances of it occurring again and what options exist. Typical stages are: gather the family history; confirm the diagnosis; assess the mode of inheritance; calculate risks and explain what they mean; describe testing and choices; and support the family emotionally. Professional guidelines describe counselling as non-directive: the counsellor gives balanced information and respects the person's decisions, rather than telling people what to do.

Explaining a risk

A risk of 1 in 300 is easier to understand than 0.33%, and a count such as "about 3 in 1000 families like this one" is more concrete still. Counsellors also say what the risk is a risk of, over what time, and how it compares with the background risk that every pregnancy carries. A good explanation names the uncertainty: the risk is an estimate under assumptions, and new information can change it.

Safety

This is a computer simulation with no physical hazards. The main safety issues are about people: family history can be personal and sometimes sad, and genetic information about one person can affect the whole family.

Ethics and privacy of genetic information

Core

Genetic information is unlike most personal data, because a result about one person says something about their relatives, who did not choose to take part. Think about the following ideas whenever you work with pedigrees.

• Informed consent. A person decides whether to share family information or to take a test, after understanding what the result might mean. Consent can be withdrawn.
• Confidentiality. Results are shared only with the people the person agrees to, and are stored securely. Sharing a pedigree can reveal who is a carrier.
• The right not to know. Some people choose not to learn their carrier status or the risk of a late-onset condition. Counselling respects that choice.
• Duty to relatives. A result may matter to a relative's health. Counsellors usually encourage a person to tell relatives themselves, and professional rules limit when anyone else may do it.
• Discrimination. Information about genes could be used to treat people unfairly, for instance in employment or insurance. Many countries have laws that limit this, and the details differ, so people should check the rules where they live.
• Autonomy and non-directive support. Decisions about testing, having children and treatment belong to the individual and family.
• Fairness and stigma. A trait should never be used to judge a person's worth, and a carrier is not "damaged". Everyone carries some alleles that could cause problems in particular combinations.

Limits of the simulation

• The trait is fictional and the families are random. Real conditions have details, variation and treatments that a model cannot capture.
• The generator builds families that fit one clean mode. It does not include new mutations, mosaicism, incomplete penetrance in the generated data, adoption or non-paternity.
• Founders are unrelated and the generator has no consanguinity. Real risks for related partners are higher (see example 7).
• The likelihood tool needs a pedigree without loops and complete information on phenotypes. Real charts can have loops and missing data.
• The numbers are for learning. They are not a medical or legal basis for any decision.

Command words

A reliable method for pedigree questions

1. Read the key and note which symbols are used for carriers, if any.
2. Label individuals by generation and number so you can refer to them (II-3, III-5).
3. Test each mode in turn. Quote the individuals that exclude a mode: for instance "II-4 and II-5 are unaffected but have an affected child III-3, so the trait cannot be dominant".
4. When you deduce a genotype, write it down on the chart in pencil, using N and S or the letters the question gives.
5. Mark obligate carriers (for example unaffected parents of an affected child in a recessive trait).
6. For a probability, state the assumptions, set out the table or the tree, and finish with a sentence.

Calculations

• Write the formula, substitute numbers, and give the answer with units or as a probability between 0 and 1.
• Give fractions as well as decimals when they are simple (1/9 and 0.111).
• Do not round early. Keep at least three significant figures until the last step.
• A probability must lie between 0 and 1. Check this on every answer.

Essay and discussion questions

Extension

For discussion on ethics, structure your answer by stakeholder (the individual, relatives, society), give a benefit and a concern for each, and finish with a reasoned view. Use specific terms such as consent, confidentiality, autonomy and discrimination, and say how a counsellor would put them into practice.

The table lists topic names only. It shows where pedigree analysis commonly appears in the four course families this laboratory supports. Courses change, so check your own current specification or syllabus, and your teacher's guidance, for the exact content, the notation your exams use and the equations you are given.

Levels used in these notes

• Foundation: symbols, simple crosses, dominant against recessive.
• Core: exclusion rules for four modes, probabilities, the binomial formula, Bayes' theorem with one piece of evidence, counselling principles.
• Extension: likelihoods, Hardy-Weinberg, consanguinity, combined risk calculations and ethics in depth.

Genetic counselling

Pedigree analysis is the central tool of genetic counselling. A counsellor draws the family tree, decides which mode of inheritance fits, identifies who could be a carrier and calculates risks. The calculation that you can do in the Analyse section, prior probability updated by a family observation, is the same kind of reasoning that counsellors apply, with real data, tests and care.

Medical research and gene discovery

Large pedigrees in which a trait is common have been used to locate genes. When many affected relatives share a stretch of DNA that unaffected relatives do not, the gene is likely to lie in that stretch. This is called linkage analysis. The first step is always to establish the mode of inheritance from the pedigree.

Newborn and carrier screening

When a recessive condition is common in a population, health services sometimes offer carrier screening to couples. The numbers in notes C and D, such as a carrier frequency of 2q(1 − q), explain why such a programme can be worthwhile in some populations and not in others.

Plant and animal breeding

Breeders use pedigrees to track traits and to avoid mating relatives who both carry a harmful recessive allele. Kennel clubs, horse registries and crop breeders keep detailed pedigrees for this reason.

Family history and public health

Even without gene tests, a family health history helps doctors to tailor screening. People with a close relative with certain conditions may be offered checks earlier. This is a use of pedigree reasoning in everyday medicine.

Genealogy and privacy

Family trees are also used in genealogy, and consumer genetic databases can link relatives who never meet. This raises the privacy issues of note J: a person's data can reveal facts about relatives who did not agree to share them.

Forensic and legal uses

Relationships in a pedigree can be checked with DNA to settle questions of parentage or identity. This must be done with proper legal and ethical safeguards, and the people tested must be treated respectfully.

Exact likelihood by peeling

Extension

The likelihood tool works by peeling. For each person it computes, for every possible genotype, the probability of their own phenotype and of everything below them in the chart. It then works upward, multiplying over children and summing over the genotypes of married-in partners. For a pedigree with no loops, this gives the exact likelihood without listing every combination of genotypes. The calculation is checked in the self-test against a brute-force enumeration of every genotype in small families, and the results agree to rounding error.

Conditioning on more evidence

The Bayesian table separates three parts. The prior uses the relatives above and beside a person. The conditional part uses the person's own phenotype and their descendants. The posterior multiplies the two and renormalises. This order shows why an unaffected child helps a little, and several unaffected children help more. Each unaffected child multiplies the conditional probability for a carrier mother of an X-linked trait by 1/2 for sons.

Consanguinity

Related parents are more likely to carry the same rare allele, because they share ancestors. The inbreeding coefficient F is the probability that the two alleles at a locus in a child are identical by descent. For first cousins F = 1/16. The risk of an affected child with a rare recessive allele of frequency q is approximately q² + Fq(1 − q) for related parents, compared with q² for unrelated parents. For a rare allele the second term dominates, which is why the risk rises sharply.

Reduced penetrance and age of onset

If a genotype shows the trait with probability less than 1, observing an unaffected person does not rule out the genotype. Likelihoods can include this with a penetrance parameter, as the simulator does. For late-onset traits the penetrance depends on age, so an unaffected young relative carries less information than an unaffected older relative.

Other modes of inheritance

• Y-linked: passes from father to all sons.
• Mitochondrial: passes from mothers to all of their children, and fathers do not transmit it.
• Polygenic and multifactorial: many genes and environment contribute, so no clean Mendelian ratios appear.
• Genomic imprinting: the effect of an allele depends on which parent it came from.

Questions to investigate

1. How does the number of children per couple change the number of modes that remain possible?
2. For which mode is the first pedigree most often ambiguous? Use your recorded table to find out.
3. How does the risk in the Bayesian calculator change as q rises from 2% to 10%, and why?
4. Why is a pedigree with four generations often more informative than one with three?

• A pedigree uses squares (male), circles (female) and filled shapes (affected). The proband is marked with an arrow.
• Autosomal dominant: every generation, affected people usually have an affected parent, males and females equal.
• Autosomal recessive: unaffected carrier parents can have affected children, trait can skip generations, males and females equal.
• X-linked recessive: more affected males, no father-to-son transmission, an affected daughter needs an affected father.
• X-linked dominant: all daughters of an affected father are affected, none of his sons.
• Exclusion rules can rule a mode out. Passing them does not prove a mode.
• For one child: carrier × carrier (autosomal recessive) gives 1/4 affected. Heterozygote × unaffected (autosomal dominant) gives 1/2.
• For several independent children: P(r of n) = C(n, r) p^r (1 − p)^{n − r}.
• Bayes' theorem updates a prior with a conditional probability: posterior = joint ÷ total.
• An unaffected sibling of an affected child in a recessive trait is a carrier with probability 2/3.
• Recurrence risk combines the individual's carrier probability, the partner's carrier probability and the cross probability.
• Hardy-Weinberg: carrier frequency 2q(1 − q) with q = √incidence.
• Likelihood is the probability of the observed pedigree under a mode. A likelihood of 0 means the mode is impossible.
• Genetic counselling is non-directive. Consent, confidentiality, the right not to know and fairness guide the use of genetic information.
• The silver-streak trait is fictional. The simulator is for learning, not for medical decisions.

Allele

One version of a gene.

Autosome

A chromosome that is not a sex chromosome.

Bayes' theorem

A rule for updating a probability in the light of new evidence.

Binomial probability

The probability of r successes in n independent trials with the same chance p each.

Carrier

A person with one copy of a recessive allele who does not show the trait.

Conditional probability

The probability of an event given that another event has occurred.

Consanguinity

A relationship in which two people share recent ancestors.

Dominant

An allele whose effect shows when one copy is present.

Exclusion rule

A rule that makes a mode of inheritance impossible if a pedigree breaks it.

Expressivity

The degree to which a genotype affects a person's phenotype.

Founder

A person in a pedigree with no parents shown.

Genetic counselling

Help for people to understand inherited conditions and make informed decisions.

Genotype

The alleles a person carries at a gene.

Hardy-Weinberg principle

The relationship between allele frequency and genotype frequency in a randomly mating population.

Hemizygous

Having only one copy of a gene, as in males for X-linked genes.

Heterozygote

A person with two different alleles at a gene.

Homozygote

A person with two identical alleles at a gene.

Incidence

How often a trait occurs in a population.

Informed consent

Agreement given freely after understanding the purpose, benefits and risks.

Likelihood

The probability of the observed data if a model is true.

Likelihood ratio

The ratio of the likelihoods of two models for the same data.

Mode of inheritance

The pattern in which a trait is passed from parents to children.

Non-directive counselling

Counselling that gives information and support without telling people what to decide.

Obligate carrier

A person who must carry an allele, deduced from the pedigree.

Pedigree

A family tree that records a trait with standard symbols.

Penetrance

The probability that a person with a genotype shows the trait.

Phenotype

The observable trait of a person.

Posterior probability

The probability after taking new evidence into account.

Prior probability

The probability before taking new evidence into account.

Proband

The affected person through whom a family is first identified.

Recessive

An allele whose effect shows only when two copies are present.

Recurrence risk

The probability that a condition occurs again in a family.

Sex linkage

Inheritance of a gene on the X or Y chromosome.

Sibship

A set of brothers and sisters with the same parents.

Standard error

A measure of how much a sample estimate would vary from sample to sample.

X-linked

Located on the X chromosome.

Only titles and publishers are given, together with stable home pages. Search each site for the title to reach the exact page.

• OpenStax, Biology 2e, chapters on Mendel's experiments and on modern understandings of inheritance. Free and open textbook. https://openstax.org/
• OpenStax, Concepts of Biology, chapter on heredity. Free textbook with an introduction to pedigrees. https://openstax.org/
• National Human Genome Research Institute (NHGRI), educational resources on genetics and genomics, including the Talking Glossary of Genomic and Genetic Terms. https://www.genome.gov/
• National Society of Genetic Counselors, resources on genetic counselling as a profession. https://www.nsgc.org/
• World Health Organization, publications on genomics, genetics and ethics in public health. https://www.who.int/
• Hartl, D. L. and Clark, A. G., Principles of Population Genetics, Sinauer Associates (extension reading on Hardy-Weinberg and inbreeding).
• Ott, J., Analysis of Human Genetic Linkage, Johns Hopkins University Press (extension reading on likelihood methods for pedigrees).

The silver-streak trait used in the simulator is invented. It does not describe any real condition.