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.
In conclusion, it is important for nurses to have proper training and information in the area of genetics and genomics so that it can be used in daily clinical practice (Thompson & Brooks, 2011). Using this information with clients and conducting a detailed genetic nursing assessment is a valuable component of being an effective health care provider and can help clients recognize, prevent, and/or treat diseases that are unique to their particular
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
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...
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.
In hereditary CJD, the infected person has inherited an abnormal gene due a family history of the disease or takes a test in which their results are positive for a genetic mutation that is associated with Creutzfeldt-Jakob disease. About 5 to 10 percent of cases of Creutzfeldt - Jakob disease in the United States are hereditary and the United Kingdom has a population in the region of 58 million and there are only a few instances of deaths due to genetic CJD in a year.
-Reilly Philip. Is It In Your Genes. Cold Spring Harbor Laboratory Press. 2004: 223-228. Print
Kellems, Richard O., and D. C. Church. Livestock Feeds and Feeding. 6th ed. Boston: Prentice Hall, 2010. Print.
Rantala, M. J., and Roff, D. A. 2006. Analysis of the importance of genotypic variation,
al. One of the first widely-available tests to hit the market is AmpliChip, introduced by Roche in 2004 (Kaplan, 2011). This genetic assay tests for 29 different polymorphisms of CYP2D6, as well as two polymorphisms of CYP2C19. An experiment comparing the results of the AmpliChip test with those of real-time polymerase chain reaction (PCR) techniques found that the AmpliChip “is rapid, reliable, accurate and very easy to perform” (Rebsamen et. al., 2008). Numerous other tests for CYPs have been developed since the introduction of AmpliChip, including laboratory services and reports offered by Seryx-Signature Genetics and Genelex Corporation, Third Wave Technology’s Invader UGT1A1 assay, and GE Healthcare’s Codelink to name a few (Gates & Davies,
Conclusion for class mono-hybrid cross: The p value 0.222 was in the non-significant range in the chi square table. The null hypothesis was therefore correct. The colors of the eyes are sex linked due to the equality in the amount of phenotypes given to both male and female.
...le promiscuity." Nature Genetics 36.12 (2004): 1326-1329. Academic Search Complete. EBSCO. Web. 24 July 2011.
" Society & Animals 18.2 (2010): 183-203. Academic Search Premier -. EBSCO. Web. The Web. The Web.
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.