{"id":2738,"date":"2024-08-27T11:26:20","date_gmt":"2024-08-27T02:26:20","guid":{"rendered":"https:\/\/www.hiro-clinic.or.jp\/nippt\/snp-likelihood-ratio-calculation\/"},"modified":"2024-10-07T17:18:26","modified_gmt":"2024-10-07T08:18:26","slug":"snp-likelihood-ratio-calculation","status":"publish","type":"post","link":"https:\/\/www.hiro-clinic.or.jp\/nippt\/snp-likelihood-ratio-calculation\/?lang=en","title":{"rendered":"How to obtain likelihood ratios using SNPs"},"content":{"rendered":"\n

To find the likelihood ratio using SNPs, the probability of genotype match is calculated, which is then used to calculate the likelihood for a specific hypothesis (e.g. the hypothesis that a person has a specific parent-child relationship).Specifically, the following steps are performed.<\/p>\n\n\n\n

SNP<\/a> data collection: collect SNP<\/a> data from the DNA of the parent-offspring candidates.
Match probability calculation: calculates the SNP<\/a> match probability between parent-offspring candidates.
Likelihood ratio calculation: computes the likelihood ratio by comparing the likelihoods of the parent-offspring and non-parent-offspring relationship hypotheses.

For example, if the probability that the SNPs match is p and the probability that they do not match is q, the likelihood ratio (LR) is expressed as p\/q. <\/p>\n\n\n\n

Specific examples are given here.<\/p>\n\n\n\n

Assumptions:
Allele of SNP<\/a> A: parent ‘AA’, child ‘AA’.
Frequency of allele A in population:<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

1. likelihood in the presence of a parent-child relationship:<\/p>\n\n\n\n

If the parent is ‘AA’, the probability that the child is also ‘AA’ is 1.<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

2. likelihood of no parent-child relationship:<\/p>\n\n\n\n

The probability that a child is ‘AA’ depends on how common allele A is in the population.<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

3. calculation of the likelihood ratio (LR):
<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

The likelihood ratio of 100 indicates that the hypothesis of a parent-child relationship is 100 times more favored than the hypothesis of no parent-child relationship.<\/p>\n\n\n\n

If multiple SNPs are used, a similar calculation is performed for each SNP<\/a> and their likelihood ratios are multiplied to obtain the final likelihood ratio.<\/p>\n","protected":false},"excerpt":{"rendered":"

To find the likelihood ratio using SNPs, the probability of genotype match is calcula…<\/p>\n","protected":false},"author":5,"featured_media":1806,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[33],"tags":[73,69,39,80,76,72],"class_list":{"0":"post-2738","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-genetic-testing-en","8":"tag-dna_profiling-en","9":"tag-dna_test-en","10":"tag-expert-en","11":"tag-forensic_science-en","12":"tag-genetic_testing-en","13":"tag-analysis-en","14":"article"},"acf":[],"_links":{"self":[{"href":"https:\/\/www.hiro-clinic.or.jp\/nippt\/wp-json\/wp\/v2\/posts\/2738","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.hiro-clinic.or.jp\/nippt\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.hiro-clinic.or.jp\/nippt\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.hiro-clinic.or.jp\/nippt\/wp-json\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"https:\/\/www.hiro-clinic.or.jp\/nippt\/wp-json\/wp\/v2\/comments?post=2738"}],"version-history":[{"count":6,"href":"https:\/\/www.hiro-clinic.or.jp\/nippt\/wp-json\/wp\/v2\/posts\/2738\/revisions"}],"predecessor-version":[{"id":5521,"href":"https:\/\/www.hiro-clinic.or.jp\/nippt\/wp-json\/wp\/v2\/posts\/2738\/revisions\/5521"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.hiro-clinic.or.jp\/nippt\/wp-json\/wp\/v2\/media\/1806"}],"wp:attachment":[{"href":"https:\/\/www.hiro-clinic.or.jp\/nippt\/wp-json\/wp\/v2\/media?parent=2738"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.hiro-clinic.or.jp\/nippt\/wp-json\/wp\/v2\/categories?post=2738"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.hiro-clinic.or.jp\/nippt\/wp-json\/wp\/v2\/tags?post=2738"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}