Methods and systems for genomic analysis using ancestral data
A genome and genotype technology, applied in genomics, electrical digital data processing, special data processing applications, etc., can solve problems such as differences in phenotypic traits
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Embodiment 1
[0253] Example 1: Generation and Analysis of SNP Profiles
[0254] The individual is provided with a sample tube from a kit (eg, available from DNA Genotek) into which the individual places a saliva sample (approximately 4 ml) from which genomic DNA will be extracted. Saliva samples were sent to a CLIA-licensed laboratory for processing and analysis. Samples are usually sent to the facility by overnight mail in a collection kit shipping container readily available to the individual.
[0255] In a preferred embodiment, genomic DNA is isolated from saliva. For example, using the DNA Self-Collection Kit technology from DNA Genotek, individuals collect samples of approximately 4 ml of saliva for clinical processing. After sending the sample to an appropriate laboratory for processing, DNA is isolated by heat denaturation and protease digestion of the sample, usually using reagents provided by the collection kit manufacturer, at 50°C for at least one hour. The samples were the...
Embodiment 2
[0259] Example 2: Updating of Genotype Correlations
[0260] In response to a request to initially determine an individual's genotype correlation, a genomic profile is generated, the genotype correlation is established, and the results are provided to the individual, as shown in Example I. After an initial determination of genotype correlations for individuals, subsequent updated correlations are or can be determined when additional genotype correlations are known. Registered users enjoy a premium level of registration and their genotype profiles are maintained in an encrypted database. The updated correlations are performed on the stored genotype profiles.
[0261] For example, an initial genotypic correlation (such as described above in Example 1) may have been determined: a particular individual does not have ApoE4 and is therefore not predisposed to early-onset Alzheimer's disease, and the individual does not have Factor V Leiden. After this initial determination, new...
Embodiment 3
[0262] Example 3: Correlation of the ApoE4 locus and Alzheimer's disease
[0263] Alzheimer's disease (AD) risk has been shown to be associated with polymorphisms in the apolipoprotein E (APOE) gene that give rise to three isoforms of APOE, known as ApoE2, ApoE3 and ApoE4. The isoforms differ by 1 or 2 amino acids at positions of residues 112 and 158 in the APOE protein. ApoE2 contains 112 / 158cys / cys; ApoE3 contains 112 / 158cys / arg; and ApoE4 contains 112 / 158arg / arg. As shown in Table 2, the risk of Alzheimer's disease onset at an earlier age increased with the copy number of the APOE ε4 gene. Also, as shown in Table 3, the relative risk of AD increased with the APOEε4 gene copy number.
[0264] Table 2: Prevalence of AD risk alleles (Corder et al., Science: 261:921-3, 1993)
[0265] APOE ε4 copy
Popularity
Alzheimer's disease risk
age of onset
0
73%
20%
84
1
24%
47%
75
2
3%
91%
68
...
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