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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

Inactive Publication Date: 2010-09-22
NAVIGENICS INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

But the relatively small number of DNA variations that exist between individuals can lead to differences in phenotypic traits and are associated with many human diseases, susceptibility to a variety of different diseases, and response to disease treatments

Method used

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  • Methods and systems for genomic analysis using ancestral data
  • Methods and systems for genomic analysis using ancestral data
  • Methods and systems for genomic analysis using ancestral data

Examples

Experimental program
Comparison scheme
Effect test

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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Abstract

The present disclosure provides methods and systems for assessing an individual's genotype correlations to a phenotype by analyzing the individual's genomic profile and using ancestral data to determine the correlations between genotypes and phenotypes.

Description

[0001] cross reference [0002] This application claims priority to US Provisional Application 60 / 975,495, filed September 26, 2007, which is hereby incorporated by reference in its entirety. Background technique [0003] Sequencing of the human genome and other recent developments in human genomics have shown that the genome composition between any two individuals can be more than 99.9% similar. But the relatively small number of DNA variations that exist between individuals can lead to differences in phenotypic traits and are associated with many human diseases, susceptibility to a variety of different diseases, and response to disease treatments. Inter-individual DNA differences occur in coding and non-coding regions and include base changes and insertions and deletions of DNA at specific sites in the genomic DNA sequence. Changes that occur at a single base position in the genome are called single nucleotide polymorphisms or "SNPs". [0004] Although SNPs are relatively ...

Claims

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Application Information

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IPC IPC(8): C12Q1/68G16B20/00G16B20/20G16B20/40
CPCG06F19/18G06F19/14G16B99/00C12Q1/6888C12Q2600/156G16B20/00G16B20/20G16B20/40G16B10/00
Inventor D·A·斯特普汉J·韦塞尔M·卡尔吉尔E·哈尔珀林
Owner NAVIGENICS INC
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