This paper addresses a currently relevant topic of detection of associations of copy number polymorphism with traits and will be of interest to readers of Genetics Research.
The simulation study showed that the additional information of CNP could increase the accuracy of predicted genotypic value, compared to using SNP information alone in an association study. The accuracy was heavily dependent on the heritability of CNP phenotypes (correlation of CNP genotype and phenotype) (Table 3). The higher accuracy of the prediction with CNP information might also result in smaller mean squared errors of prediction (Table 4)’.
On the other hand, the authors found that linkage disequilibrium (LD) between SNP and CNP was not much different from that between two SNPs. The authors demonstrated that an increased mutation rate and larger number of segregating alleles hardly affects LD with a nearby SNP.
I have the following major comments.
1) A possible reason for a high accuracy with using CNP information was that the CNP was the causal gene itself in the simulation. If the CNP had negligible effects, and was just linked with a causal gene, the performance might not be much different from SNPs, because as stated above that LD structure was not much different between SNP and CNP. In this situation, the success of using CNP information to predict genotypic values would be conditional on 1) the effects due to the causal CNP should explain significant proportion of genetic variation, 2) those causal CNP should be genotyped, and 3) the genotyping accuracy for CNP should be reasonably high. In general, how easily and accurately are the causal CNPs identified? What is underlying distribution of the effects due to CNPs? Can we expect that the corr...
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... the same effect of the same direction and magnitude. Would this be realistic?
10) Line 158, In case of the copy number is the same (c=b), the equation would give zero. Is this right?
11) Line 171, SNP phenotypes -> CNP phenotypes?
12) Line 242, 2 or 3 alleles > 2 or 3 copies?
13) Table 2. It may be useful to have likelihood ratio for each model.
14) Line 267, fenotype -> phenotype?
15) The introduction is human/livestock orientated, but the remainder of the paper is presented in livestock terminology. Some discussion about the relevance of the results to human populations would be useful.
16) Line 343 “Under the assumption that x copies at a CNP locus lead to the effect of x times the effect of 1 copy,” Is this a realistic assumption? Is CNP genotype of 4 copies likely to have the same functional impact for individuals with alleles 2/2 vs 4/0.
Rantala, M. J., and Roff, D. A. 2006. Analysis of the importance of genotypic variation,
Test 4: All three phenotypic frequencies saw a reduction in their number as the homozygote fishes saw a reduction in their number and were not able to pass on their alleles to create either their colored fish or a heterozygote. Both yellow and blue allele frequencies decreased by the same
revealed that three of the fourteen samples were were homozygous while the other eleven were
The major topic of this experiment was to examine two different crosses between Drosophila fruit flies and to determine how many flies of each phenotype were produced. Phenotype refers to an individual’s appearance, where as genotype refers to an individual’s genes. The basic law of genetics that was examined in this lab was formulated by a man often times called the “father of genetics,” Gregor Mendel. He determined that individuals have two alternate forms of a gene, referred to as two alleles. An individual can me homozygous dominant (two dominant alleles, AA), homozygous recessive, (two recessive alleles, aa), or heterozygous (one dominant and one recessive allele, Aa). There were tow particular crosses that took place in this experiment. The first cross-performed was Ebony Bodies versus Vestigle Wings, where Long wings are dominant over short wings and normal bodies are dominant over black bodies. The other cross that was performed was White versus Wild where red eyes in fruit flies are dominant over white eyes.
-Reilly Philip. Is It In Your Genes. Cold Spring Harbor Laboratory Press. 2004: 223-228. Print
A permanent change in the DNA sequence which makes up a gene is what is referred to as gene mutation (Mahoney & Springer 2009). It is believed that gene mutation occurs in two ways: that is, it can be acquired in personal lifetime or inherited from a parent. Those that are passed from parents to the child are referred to as hereditary mutation. They acquire the name since they are present in the eggs and sperms or the germ cell. In this case, such kind of mutation is present all through one’s life in almost every cell in the body. A similarity in mutation and gene diversity is the change in the DNA sequence which makes both mutation and genetic diversity have related issues.
The main purpose of this lab was to determine if the mutant genes were dominant or recessive, autosomal or x-linked, and if either gene combination was linked. Also, if they were linked, one was to determine how far apart. In this experiment, fruit flies were used to obtain a better understanding of Gregor Mendel’s genetic principles. Using the law of segregation and the law of independent assortment, one of the main objectives was to learn how certain traits were inherited while others were not and to determine if two different fruit fly crosses fit the 9:3:3:1 ratio. In the beginning of the experiment, a two vials were obtained and prepared, and following this the phenotypes and sexes were observed. In each vial, there was a cross with first
Lewis, Ricki, (2014), Human Genetics, 11th Edition, Chapter 12. Gene Mutation. [VitalSource Bookshelf Online]. Retrieved from
Linkage analysis is the analysis of the linkage in the inheritance between genes at different loci based on the observational phenotypes and the known pedigree structure (Palmer, 2011). Linkage between loci is the tendency for alleles of two or more loci close on the chromosome to be transmitted to the next generation together. So generally the closer two genes lie on a chromosome, the more likely they will show linkage. Genes located on different chromosomes, for example, do not show linkage. Genetic linkage studies aim to estimate the distance between a set of markers (polymorphic DNA sequences with known location) and a putative trait gene by estimating the recombination fractions. If a disease tends to be passed to offspring along with specific markers, then it can be concluded that the gene(s) which are responsible for the disease are located close on the chromosome to these markers. The disease could be a Mendelian disease (caused by one gene) or a complex disease, which is caused by the action of many
National Genome Research Institute. "Genetic Information and the Workplace Report." Genetic Information and the Workplace Report. National Genome Research Institute, 20 Jan. 1998. Web. 28 Apr. 2014.
In our genes, multiple different alleles determine whether one person will have a certain trait or not. Alleles are what make-up our genotypes and in this lab, we wanted to determine the genotypes of our class in the two loci: TAS2R38 and PV92. The TAS2R38 locus codes for a protein that involves the bitter taste of PTC; the gene determines whether or not a person will taste the PTC paper as very bitter or no taste at all. People with the “T” allele are tasters while those that are homozygous recessive (tt) are non-tasters. The taster locus can be found chromosome 7.3 The two different alleles present in the could be due to the effect of evolution and natural selection because the same can be found in chimps.4 The PV92 locus does not code for any protein but rather involves an Alu element that is 300-bp long. A person with the “+” allele would have the Alu element making that sequence longer while those with the “-“ allele don’t have the element and would have a shorter sequence. This locus can be found on chromosome 16.3 There are multiple Alu sequences found among primate genomes but there are human specific sequences such as the one found on the PV92 locus.1 In the experiment, student DNA was collected from cheek cells and PCR was used to target the loci and amplify the region of DNA. In the taster gene, after amplification, a restriction digest was performed to differentiate between the two alleles. The digest was able to show differentiation because those with the “T” allele would have two bands from gel electrophoresis and those with “t” will have one band because the restriction enzyme doesn’t cut it. For the PV92, we were able to distinguish between the alleles due to the added length of the Alu element. Those...
Taylor, J., Loney, B. R., Bobadilla, L., Loacono, W.G., & McGue, M. (2003). Genetic and
U.S. Dept. of Energy. Understanding our Genetic Inheritance the U.S. Human Genome Project. "The first Five Years: Fiscal Years 1991-1995", Obtained from WWW 10/19/99:1/13/99: http://www.ornl.gov/hgmis/project/5yrplan/intro.html.
more than half the variation was found to be due to heredity. Among these traits were
...ary part in genotypes of potential interest that human geneticists breeders, as well as evolutionary geneticists are investigating. However, although we have the capability to unravel experiments that the founders of quantitative genetics would have never imagined, but their basic, un-computational machinery that they developed is most easily adaptable to the latest analyses that will be needed. We are far from ‘letting-go’ molecular biologists from the mathematical techniques/systems, because this age in respect to genomics has been forced into accepting gratitude due to the major importance of quantitative methods as opposed to the new molecular genetics. As geneticists tend to map molecular variation as well as genomic data, quantitative genetics will be moving to the front position because of its relevance in this age of rapid advancement in molecular genetics.