The Carnegie Mellon Genetics Cognitive Tutor
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The Genetics Cognitive Tutor Curriculum - 11 modules, each consisting of multiple problems  

Objective: Students reason backward from pedigree evidence to the underlying mode of transmission of rare traits, reinforcing the student’s understanding of genetic transmission.
Each problem presents a family pedigree displaying a rare trait and asks the student:
    • to determine whether the trait is dominant or recessive.
    • to determine whether the trait is autosomal or x-linked.

The problems include traits that are (a) recessive autosomal, (b) recessive x-linked, (c) recessive indeterminate linkage, (d) dominant autosomal, (e) dominant indeterminate linkage, or (f) indeterminate dominance and linkage.

Objective: Students develop an understanding of transmission probabilities involving carriers of recessive traits.
Each problem presents a family pedigree displaying a rare recessive trait and asks the student:
    • to determine the dominance and linkage of the trait;
    • the probability that various unaffected family members is a carrier of the allele for the trait;
    • the probability that an unobserved family member will be affected by the trait.

The problems include traits that are recessive autosomal or recessive x-linked.

Objective: This lesson extends basic Mendelian transmission to two genes and gene interactions that result in epistasis.
Each problem describes three parents that are true breeding for a single phenotypic trait. Each trait is governed by two genes, which have two alleles. The student:
     • performs three crosses on the parent strains along with intercrosses on the resulting F1 progeny;
     • determines the genotypes of the three true breeding strains and the genotype and phenotype of
    the fourth possible true-breeding strain;
     • determines the genotypes of all the F1 and F2 progeny;
     • draws an inference about how the two genes interact to determine the phenotype.


Objective: Students reason about how crossovers in meiosis reveal the order and inter-gene distances on chromosomes.
In each problem, students analyze the offspring resulting from a test cross with an organism that is heterozygous for three genes. Students:
     • classify offspring phenotypes (parental, single-crossover, or double-crossover)
     • identify the middle gene in the parental genotype
     • calculate the recombination frequencies between each pair of genes along with the distances in
       centimorgans between the pairs of genes.


Objective: Students analyze populations and determine whether they are in Hardy-Weinberg equilibrium.
Each problem presents three phenotype numbers for a trait that is determined by a single gene with a dominant and recessive allele. The student:
     • calculates the underlying allele frequencies;
     • calculates the observed and expected genotype frequencies;
     • calculates a chi-square test comparing observed and expected numbers to determine if the population is         in equilibrium.


Objective: Students calculate the short-term impact of genotype fitness scenarios and reason about the long-term consequences for the population.
Each problem presents the homozygous recessive frequency in a population and describes selection pressure(s) on one or more genotype classes. The student:
     • calculates allele frequencies, remaining genotype frequencies, and surviving genotype numbers in the
        current generation;
     • calculates the allele frequencies, genotype frequencies, and surviving genotype numbers in the next         generation;
     • summarizes how the genotype frequencies are changing across these generations and why;
     • then views a graph displaying genotype frequencies across tens of generations;
     • describes the long term impact of the selection pressures on genotype frequencies.


Objective: Students model the interactions among the four components of various systems that regulate transcription.
Each problem describes a system that regulates transcription of a gene. The student:
     • completes a summary description of the system;
     • indicates how the presence or absence of the effector affects synthesis in the normally functioning         system;
     • indicates the impact of mutations to the three constituent genes, and whether extra-chromosomal wild-
        type copies of the gene restores normal function.

The problems cover positive and negative inducible regulation, and negative repressible regulation.
Gene Regulation Exp

Objective: Students design experiments to determine the functioning of a gene regulation system. Each problem presents three genes and two possible effectors in a regulatory system. The student designs experiments to :
     • examine the effect of the two possible effectors on gene expression to determine the actual effector in         the system and to determine whether the system is inducible or repressible;
     •examine the impact of selectively knocking out one gene at a time, and the impact of substituting a        plasmid functional copy of the gene, to determine whether this is a positive or negative regulatory system        and to identify the role of each gene.

Gene Interaction Pathway Modeling

Objective: Students reason about how two genes act together to create offspring phenotype categories for a single trait. This activity is intended to precede the Gene Interaction and Epistasis module. Some problems describe the genes’ function and the student:
     • summarizes how the genes interact in words;
     • indicates the phenotypes of the true-breeding genotypes;
     • indicates the offspring genotypes and phenotypes that result from crossing two true-breeding strains and         intercrossing the offspring;
     • describes in words how the genes interact to determine each phenoytpe.

In other problems, students are given the results of crossing true-breeding strains and intercrossing the offspring. The student:
     • summarizes how the genes appear to interact in words;
     • indicates the phenotypes of the true-breeding genotypes;
     • explains the F2 phenotypes, phenotype ratios, and genotypes in the cross and describes how the genes         interact to determine each phenotype.

Tetrad Analysis

Objective: Students are given the frequencies of unordered tetrad types resulting from a cross and determine whether two genes are linked to each other or to the centromere. If so, students calculate the corresponding map distance. The student:
     • classifies the tetrad types;
     • reasons about the quantitative relationships among the tetrad types;
     • draws qualitative linkage conclusions about the genes;
     • calculates map distance when possible

Transmission Probabilities

Objective: Students calculate the probability that a child will be affected by each of two rare traits. Each problem presents: (a) the mode of transmission of each trait (autosomal or X-linked, dominant or recessive); (b) the frequency in the population of dominant traits and the carrier frequency of recessive traits; and (c) the phenotypes of each parent. The student:
     • calculates the probability of inheriting an allele for each trait from each parent;
     • the probability the child is affected by each trait;
     • the probability the child is affected by both traits.

©2013 Genetics Cognitive Tutor Project, Carnegie Mellon University