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Single-Nucleotide Polymorphisms (SNPs) (view source)
Revision as of 11:49, 26 April 2024
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== Phasing == | == Phasing == | ||
Your raw data file lists your SNPS in the following order | Your raw data file lists your SNPS in the following order: <br> <br> | ||
1. The leftmost SNP on chromosome 1 is listed first. | 1. The leftmost SNP on chromosome 1 is listed first. <br> | ||
2. The next SNP listed is whatever SNP comes next moving from left to right | 2. The next SNP listed is whatever SNP comes next moving from left to right <br> | ||
3. Once the last SNP (the rightmost SNP) is read the process repeats with the next chromosome | 3. Once the last SNP (the rightmost SNP) is read the process repeats with the next chromosome <br> <br> | ||
At each SNP, however, the order the allele's are nost listed in any particular order. AG, for example means the exact same thing as GA. It would be nice if the first allele was always from the father and the second always from the mother or vice versa but unfortunately it is a random mixture. When dealing with a heterozygous SNP the best way to know which allele is from which parent is to compare against other relatives. Sorting out the paternal and maternal SNPS is called phasing. In this situation, if you compared your DNA against your mom's and at the spot where you have C G, your mom has G G then you must have inherited the C from your dad and the G from your mom. If you are C G and your mom is also C G, then it is still unclear which allele came from which parent and comparing against your dad or another relative would be necessary to figure it out. Programs such as GedMatch.com offer the ability to phase your DNA by comparing it against one or both parents. Using phased kits reduces the amount of false segments identified between you and a match and is a valuable tool for people interested in small DNA segments. However, in cases where you and the parent being compared against are both heterozygous (like C G) the value becomes a no call and is discarded from the comparison. For this reason, comparing your DNA against both parents creates better results than just comparing against one. Perhaps in the spot where you and your mom are both C G, your father is C C, now it can be concluded you inherited the C from your father and the G from your mother. | At each SNP, however, the order the allele's are nost listed in any particular order. AG, for example means the exact same thing as GA. It would be nice if the first allele was always from the father and the second always from the mother or vice versa but unfortunately it is a random mixture. When dealing with a heterozygous SNP the best way to know which allele is from which parent is to compare against other relatives. Sorting out the paternal and maternal SNPS is called phasing. In this situation, if you compared your DNA against your mom's and at the spot where you have C G, your mom has G G then you must have inherited the C from your dad and the G from your mom. If you are C G and your mom is also C G, then it is still unclear which allele came from which parent and comparing against your dad or another relative would be necessary to figure it out. Programs such as GedMatch.com offer the ability to phase your DNA by comparing it against one or both parents. Using phased kits reduces the amount of false segments identified between you and a match and is a valuable tool for people interested in small DNA segments. However, in cases where you and the parent being compared against are both heterozygous (like C G) the value becomes a no call and is discarded from the comparison. For this reason, comparing your DNA against both parents creates better results than just comparing against one. Perhaps in the spot where you and your mom are both C G, your father is C C, now it can be concluded you inherited the C from your father and the G from your mother. | ||
[[Category:Genetic_Research]] | [[Category:Genetic_Research]] | ||