{"id":111396,"date":"2024-06-30T09:26:19","date_gmt":"2024-06-30T00:26:19","guid":{"rendered":"https:\/\/www.hiro-clinic.or.jp\/nipt\/about-snp\/"},"modified":"2026-07-12T21:06:08","modified_gmt":"2026-07-12T12:06:08","slug":"about-snp","status":"publish","type":"post","link":"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/","title":{"rendered":"What is SNP (Single Nucleotide Polymorphism)"},"content":{"rendered":"\n<div style=\"border:solid #ffe6e6 0.8rem;background-color: #fff9f9;padding:3% 5%;margin:1rem 0 3rem;\"><div id=\"ez-toc-container\" class=\"ez-toc-v2_0_88 counter-hierarchy ez-toc-counter ez-toc-grey ez-toc-container-direction\">\n<div class=\"ez-toc-title-container\">\n<p class=\"ez-toc-title\" style=\"cursor:inherit\">\u76ee\u6b21<\/p>\n<span class=\"ez-toc-title-toggle\"><a href=\"#\" class=\"ez-toc-pull-right ez-toc-btn ez-toc-btn-xs ez-toc-btn-default ez-toc-toggle\" aria-label=\"Toggle Table of Content\"><span class=\"ez-toc-js-icon-con\"><span class=\"\"><span class=\"eztoc-hide\" style=\"display:none;\">Toggle<\/span><span class=\"ez-toc-icon-toggle-span\"><svg style=\"fill: #999;color:#999\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" class=\"list-377408\" width=\"20px\" height=\"20px\" viewBox=\"0 0 24 24\" fill=\"none\"><path d=\"M6 6H4v2h2V6zm14 0H8v2h12V6zM4 11h2v2H4v-2zm16 0H8v2h12v-2zM4 16h2v2H4v-2zm16 0H8v2h12v-2z\" fill=\"currentColor\"><\/path><\/svg><svg style=\"fill: #999;color:#999\" class=\"arrow-unsorted-368013\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"10px\" height=\"10px\" viewBox=\"0 0 24 24\" version=\"1.2\" baseProfile=\"tiny\"><path d=\"M18.2 9.3l-6.2-6.3-6.2 6.3c-.2.2-.3.4-.3.7s.1.5.3.7c.2.2.4.3.7.3h11c.3 0 .5-.1.7-.3.2-.2.3-.5.3-.7s-.1-.5-.3-.7zM5.8 14.7l6.2 6.3 6.2-6.3c.2-.2.3-.5.3-.7s-.1-.5-.3-.7c-.2-.2-.4-.3-.7-.3h-11c-.3 0-.5.1-.7.3-.2.2-.3.5-.3.7s.1.5.3.7z\"\/><\/svg><\/span><\/span><\/span><\/a><\/span><\/div>\n<nav><ul class='ez-toc-list ez-toc-list-level-1 ' ><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#Article_Summary\" >Article Summary<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-2\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#What_Is_an_SNP_Single_Nucleotide_Polymorphism\" >What Is an SNP (Single Nucleotide Polymorphism)?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-3\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#Genes_DNA_Genome_and_Chromosomes_Whats_the_Difference\" >Genes, DNA, Genome, and Chromosomes: What&#8217;s the Difference?<\/a><ul class='ez-toc-list-level-3' ><li class='ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-4\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#What_Is_a_Gene\" >What Is a Gene?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-5\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#What_Is_DNA\" >What Is DNA?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-6\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#What_Is_a_Genome\" >What Is a Genome?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-7\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#What_Are_Chromosomes\" >What Are Chromosomes?<\/a><ul class='ez-toc-list-level-4' ><li class='ez-toc-heading-level-4'><a class=\"ez-toc-link ez-toc-heading-8\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#The_Human_Genome_Project\" >The Human Genome Project<\/a><\/li><\/ul><\/li><\/ul><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-9\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#What_SNPs_Give_Rise_To\" >What SNPs Give Rise To<\/a><ul class='ez-toc-list-level-4' ><li class='ez-toc-heading-level-4'><ul class='ez-toc-list-level-4' ><li class='ez-toc-heading-level-4'><a class=\"ez-toc-link ez-toc-heading-10\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#Remarkable_Advances_in_SNP_Analysis_Methods\" >Remarkable Advances in SNP Analysis Methods<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-4'><a class=\"ez-toc-link ez-toc-heading-11\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#The_Rise_of_SNP-Based_Precision_Medicine\" >The Rise of SNP-Based Precision Medicine<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-4'><a class=\"ez-toc-link ez-toc-heading-12\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#SNP_Projects_and_Personal_Data_From_National_Governments_to_Corporations\" >SNP Projects and Personal Data: From National Governments to Corporations<\/a><\/li><\/ul><\/li><\/ul><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-13\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#How_SNPs_Relate_to_NIPT\" >How SNPs Relate to NIPT<\/a><ul class='ez-toc-list-level-3' ><li class='ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-14\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#What_Is_SNP-Based_NIPT_How_It_Tells_Maternal_and_Fetal_DNA_Apart\" >What Is SNP-Based NIPT? How It Tells Maternal and Fetal DNA Apart<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-15\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#The_Limits_of_SNP-Based_NIPT_and_What_Happens_After_a_Positive_Result\" >The Limits of SNP-Based NIPT, and What Happens After a Positive Result<\/a><\/li><\/ul><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-16\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#Frequently_Asked_Questions\" >Frequently Asked Questions<\/a><ul class='ez-toc-list-level-3' ><li class='ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-17\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#Are_SNPs_and_genes_the_same_thing\" >Are SNPs and genes the same thing?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-18\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#How_common_are_SNPs\" >How common are SNPs?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-19\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#How_is_SNP-based_NIPT_different_from_standard_NIPT\" >How is SNP-based NIPT different from standard NIPT?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-20\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#Does_a_positive_SNP-based_NIPT_result_mean_a_definitive_diagnosis\" >Does a positive SNP-based NIPT result mean a definitive diagnosis?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-21\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#Are_SNPs_used_directly_to_diagnose_disease\" >Are SNPs used directly to diagnose disease?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-22\" href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/about-snp\/#What_technologies_are_used_to_analyze_SNPs\" >What technologies are used to analyze SNPs?<\/a><\/li><\/ul><\/li><\/ul><\/nav><\/div>\n<h2 style=\"margin-top:1rem;\"><span class=\"ez-toc-section\" id=\"Article_Summary\"><\/span>Article Summary<span class=\"ez-toc-section-end\"><\/span><\/h2><p>An SNP (Single Nucleotide Polymorphism) is a common type of genetic variation in which a single base in the DNA sequence differs between individuals. This article explains the basics of genes, DNA, genomes, and chromosomes, then looks at how SNP analysis is used in research and precision medicine.<\/p>\n\n<p>We also cover &#8220;SNP-based <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a>,&#8221; a prenatal testing method that applies SNP analysis to distinguish maternal DNA from placenta-derived DNA, along with what its results can and cannot tell you.<\/p><\/div>\n\n\n\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"What_Is_an_SNP_Single_Nucleotide_Polymorphism\"><\/span><strong>What Is an SNP (Single Nucleotide Polymorphism)?<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">An SNP (pronounced &#8220;snip&#8221;) stands for Single Nucleotide Polymorphism. It refers to a single base within the genomic DNA sequence \u2014 often called the blueprint of life \u2014 being replaced by a different base. Because a single base substitution can influence physical traits and susceptibility to disease, researchers are actively studying SNPs as a foundation for precision, genetics-informed medicine.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Genes_DNA_Genome_and_Chromosomes_Whats_the_Difference\"><\/span><strong>Genes, DNA, Genome, and Chromosomes: What&#8217;s the Difference?<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Genetic testing has become far more accessible in recent years, regardless of how reliable any individual test may be. Genome-edited foods, genetically modified crops, and DNA testing also come up regularly in the news. When it comes to chromosomes specifically, <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/nipt\/\">NIPT (Non-Invasive Prenatal Testing)<\/a> is well known for its ability to detect the likelihood of fetal chromosomal abnormalities from a maternal blood sample with high accuracy.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Genes, DNA, genomes, and chromosomes have all become familiar terms as a result. Even so, few people can clearly explain how a genome, DNA, and a gene actually differ, and it is common to mistakenly equate DNA with &#8220;the cause of heredity.&#8221; Understanding what each term means is the first step toward understanding SNPs.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"What_Is_a_Gene\"><\/span><strong>What Is a Gene?<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">A gene is the data that builds an organism&#8217;s body. From collagen, the elastic substance in skin, to the muscles that move the body, the hemoglobin that carries oxygen throughout the bloodstream, and even digestive enzymes and our sense of smell \u2014 our bodies are built from proteins.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Proteins are produced based on the data contained in genes, and this is what forms a living body. Humans are estimated to have around 20,000 genes.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"What_Is_DNA\"><\/span><strong>What Is DNA?<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">DNA stands for deoxyribonucleic acid. It is easiest to picture as the double-helix shape shown in explainer videos. Within that helix are four bases \u2014 adenine (A), thymine (T), guanine (G), and cytosine (C) \u2014 and the order in which they appear (the base sequence) is what carries genetic information.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">If a gene is the data, DNA is the blueprint used to build the organism. The human base sequence spans roughly 3 billion base pairs and contains the genetic information needed to produce offspring resembling their parents. The complete set of hereditary information passed down in this way is called &#8220;genomic DNA,&#8221; and it is why children tend to resemble their parents.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Based on the blueprint recorded in this DNA, the body determines where and how much of each protein structure to build. Differences in DNA base sequence are also what account for variation in facial features, body type, and constitution among individuals.<\/p>\n\n\n\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"What_Is_a_Genome\"><\/span><strong>What Is a Genome?<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">&#8220;Genome&#8221; combines &#8220;gene&#8221; with the Greek\/German-derived suffix &#8220;-ome,&#8221; meaning &#8220;all of.&#8221; It was coined in 1920 by German botanist Hans Winkler and is generally translated as &#8220;the complete set of genetic information.&#8221;<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">As the name suggests, a genome refers to &#8220;the entire set of genes an organism needs to be that organism.&#8221; A mouse&#8217;s offspring becomes a mouse, and a human&#8217;s offspring becomes a human \u2014 the genome can be thought of as the complete DNA set required for each species.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"What_Are_Chromosomes\"><\/span><strong>What Are Chromosomes?<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">A chromosome is a structure formed when strands of DNA are wound around proteins called histones. A single chromosome contains anywhere from several hundred to several thousand genes. Humans inherit one chromosome from each parent in every pair, giving a total of 46 chromosomes (23 pairs). Of these, 44 are autosomes, numbered from largest to smallest.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The remaining two are sex chromosomes, which determine biological sex. There are two types, X and Y: an XY combination results in male sex, while an XX combination results in female sex.<\/p>\n\n\n\n<h4 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"The_Human_Genome_Project\"><\/span><strong>The Human Genome Project<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">The Human Genome Project was an international effort launched to fully decode the base sequence of DNA contained in the nucleus of every human cell. Its goal was to determine the order of all 3 billion bases, where each is located, and what information each segment encodes.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The full human genome sequence was completed in 2003. Since then, this data has driven advances in genetic medicine, including research into disease causes and the development of gene-based therapeutics.<\/p>\n\n\n\n    <a href=\"\/nipt\/snp\/\" class=\"blog-card\">\n      <div class=\"blog-card-content\">\n          <div class=\"blog-card-title\">NIPT\uff08\u65b0\u578b\u51fa\u751f\u524d\u8a3a\u65ad\uff09\u3068\u306f\uff5c\u308f\u304b\u308b\u75c5\u6c17\u30fb\u7cbe\u5ea6\u30fb\u53d7\u3051\u3089\u308c\u308b\u6642\u671f <\/div>\n          <div class=\"blog-card-excerpt\">NIPT\uff08\u65b0\u578b\u51fa\u751f\u524d\u8a3a\u65ad\uff09\u306f\u3001\u598a\u5a66\u3055\u3093\u306e\u63a1\u8840\u304b\u3089\u8d64\u3061\u3083\u3093\u306e\u67d3\u8272\u4f53\u75be\u60a3\u306e\u53ef\u80fd\u6027\u3092\u8abf\u3079\u308b\u975e\u78ba\u5b9a\u7684\u691c\u67fb\u3067\u3059\u3002NIPT\u306e\u4ed5\u7d44\u307f\u3001\u308f\u304b\u308b\u75c5\u6c17\u3001\u7cbe\u5ea6\u3001\u53d7\u3051\u3089\u308c\u308b\u6642\u671f\u3001\u6ce8\u610f\u70b9\u3092\u308f\u304b\u308a\u3084\u3059\u304f\u89e3\u8aac\u3057\u307e\u3059\u3002...<\/div>\n      <\/div>\n    <\/a>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"What_SNPs_Give_Rise_To\"><\/span><strong>What SNPs Give Rise To<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">The 3-billion-base sequence of human genomic DNA is not identical from person to person. When a single base at a given position differs from the standard sequence, the resulting variation is called an SNP (Single Nucleotide Polymorphism).<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">SNPs occur roughly once every 300 to 1,500 bases in human DNA. These single-base differences \u2014 differences in genetic information, in other words \u2014 are part of what shapes individual traits such as facial features, personality tendencies, hay fever susceptibility, and alcohol tolerance.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">By definition, an SNP is a variation present in at least 1% of a population; base changes occurring in less than 1% of the population are classified instead as mutations.<\/p>\n\n\n\n<h4 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Remarkable_Advances_in_SNP_Analysis_Methods\"><\/span><strong>Remarkable Advances in SNP Analysis Methods<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">SNP analysis traditionally focused on one target SNP (or a handful) at a time, examined individually. Methods such as RFLP (amplifying the target region by PCR, then treating it with restriction enzymes) and SSCP (amplifying the target region by PCR, then running electrophoresis while preserving its three-dimensional structure) fall into this category. These methods, however, were labor-intensive and not especially accurate.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">From the 2000s onward, demand grew for higher-throughput analysis methods. Rather than examining SNPs one at a time, researchers increasingly turned to comprehensive, genome-wide SNP analysis \u2014 an approach that remains central today. DNA microarray technology marked a particularly notable leap forward: many DNA fragments (probes) are arranged in a grid on a chip, hybridized with a sample&#8217;s DNA, and read out using fluorescent signals to determine the sequence contained in the sample. For SNP analysis specifically, using probes designed around the neighboring nucleotides of each SNP made comprehensive, genome-wide screening possible.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">DNA microarray technology has since advanced further and become more accessible as costs have fallen. More recently, whole-genome sequencing using next-generation sequencers (NGS) has made it possible to detect even low-frequency SNPs, and the scope of what can be analyzed is expected to keep expanding. SNP databases built using these technologies are also becoming more comprehensive, laying the groundwork for wider use of SNP data in research and clinical medicine.<\/p>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"640\" height=\"427\" src=\"\/nipt\/wp-content\/uploads\/2024\/12\/23429581_s-1.jpg\" alt=\"\u30af\u30ea\u30fc\u30f3\u30eb\u30fc\u30e0\u306e\u4e8c\u4eba\" class=\"wp-image-86754\"\/><\/figure>\n<\/div>\n\n\n\n\n\n<h4 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"The_Rise_of_SNP-Based_Precision_Medicine\"><\/span><strong>The Rise of SNP-Based Precision Medicine<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">Genome research has continued to accelerate ever since the human genome was fully decoded in 2003. The field has shifted from identifying the causes of single-gene disorders toward comprehensive, genome-wide analysis of complex diseases and drug response \u2014 differences in how individuals respond to medication, including both efficacy and side effects \u2014 and this research continues to expand.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Disease is not caused by genetic factors alone; environmental factors are also deeply involved, so SNP analysis alone will never explain everything. Even so, it holds real promise for understanding disease mechanisms and supporting prevention.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Analyzing and accumulating SNP data makes it possible to anticipate how a patient will respond to a drug \u2014 including potential side effects \u2014 before treatment even begins. This is opening the door to &#8220;precision medicine,&#8221; in which the right drug is given at the right dose and the right time based on a person&#8217;s genetic background, and this field is expected to keep growing. Beyond precision medicine, SNP analysis is also being applied to develop drugs whose effects are less dependent on genetic background and medications with more consistent efficacy across patients.<\/p>\n\n\n\n<h4 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"SNP_Projects_and_Personal_Data_From_National_Governments_to_Corporations\"><\/span><strong>SNP Projects and Personal Data: From National Governments to Corporations<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">Governments are currently pursuing genome analysis of cancers and rare diseases as part of national research initiatives. Large corporations have also announced voluntary programs asking employees to share genomic data alongside health checkup results in support of workplace healthcare initiatives. Falling genome sequencing costs are a major factor behind this trend.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">At the same time, an individual&#8217;s genomic data is arguably the ultimate form of personal information. Under Japan&#8217;s amended Act on the Protection of Personal Information (2015), the base sequence that makes up a person&#8217;s DNA is explicitly classified as an individual identification code.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Without specialized genetics knowledge, it is generally difficult to link genomic data back to a specific individual. However, if genomic data were to leak, it could potentially be used to infer a person&#8217;s predisposition to certain hereditary conditions. That, in turn, raises real \u2014 if not absolute \u2014 concerns about discrimination in employment, marriage, or access to financial services based on someone&#8217;s genetic profile.<\/p>\n\n\n\n    <a href=\"\/nipt\/about-forensic-medicine\/\" class=\"blog-card\">\n      <div class=\"blog-card-content\">\n          <div class=\"blog-card-title\">NIPT\uff08\u65b0\u578b\u51fa\u751f\u524d\u8a3a\u65ad\uff09\u3068\u306f\uff5c\u308f\u304b\u308b\u75c5\u6c17\u30fb\u7cbe\u5ea6\u30fb\u53d7\u3051\u3089\u308c\u308b\u6642\u671f <\/div>\n          <div class=\"blog-card-excerpt\">NIPT\uff08\u65b0\u578b\u51fa\u751f\u524d\u8a3a\u65ad\uff09\u306f\u3001\u598a\u5a66\u3055\u3093\u306e\u63a1\u8840\u304b\u3089\u8d64\u3061\u3083\u3093\u306e\u67d3\u8272\u4f53\u75be\u60a3\u306e\u53ef\u80fd\u6027\u3092\u8abf\u3079\u308b\u975e\u78ba\u5b9a\u7684\u691c\u67fb\u3067\u3059\u3002NIPT\u306e\u4ed5\u7d44\u307f\u3001\u308f\u304b\u308b\u75c5\u6c17\u3001\u7cbe\u5ea6\u3001\u53d7\u3051\u3089\u308c\u308b\u6642\u671f\u3001\u6ce8\u610f\u70b9\u3092\u308f\u304b\u308a\u3084\u3059\u304f\u89e3\u8aac\u3057\u307e\u3059\u3002...<\/div>\n      <\/div>\n    <\/a>\n\n\n\n<p class=\"wp-block-paragraph\">SNP research, along with rapidly advancing genetic testing methods such as <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/nipt\/\">NIPT (Non-Invasive Prenatal Testing)<\/a>, will only keep expanding. Working through these ethical and legal questions may end up being just as transformative for medicine as the technology itself.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"How_SNPs_Relate_to_NIPT\"><\/span><strong>How SNPs Relate to NIPT<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">The SNP fundamentals covered above are actually put to direct use in one of the testing methods available under <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/nipt\/\">NIPT (Non-Invasive Prenatal Testing)<\/a>. This section explains how &#8220;SNP-based <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a>&#8221; works and what to keep in mind when interpreting your results.<\/p>\n\n\n\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"What_Is_SNP-Based_NIPT_How_It_Tells_Maternal_and_Fetal_DNA_Apart\"><\/span><strong>What Is SNP-Based NIPT? How It Tells Maternal and Fetal DNA Apart<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>SNP-based <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a> is a testing method that compares SNP patterns between DNA in the mother&#8217;s blood and DNA derived from the placenta to estimate chromosomal changes.<\/strong> <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a> includes several different testing methods, and the SNP-based approach is one of them.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">During pregnancy, a small amount of placenta-derived DNA fragments (cell-free DNA, or cfDNA) circulates in the mother&#8217;s blood alongside her own DNA. SNP-based testing distinguishes between the two by comparing how much the SNP patterns of the mother and the fetus (via the placenta) differ. One distinguishing feature of this method is that it can also determine whether a twin pregnancy is identical or fraternal. For a comparison of <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a>&#8217;s four main testing methods, see our <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/nipt-types-comparison-guide\/\">article comparing the different types of NIPT and their accuracy<\/a>.<\/p>\n\n\n\n<figure>\n<svg role=\"img\" aria-label=\"Diagram showing how SNP-based NIPT distinguishes maternal and fetal DNA. It illustrates the process of comparing SNP patterns between maternal-derived DNA and placenta-derived DNA found in a maternal blood sample, and using the differences to identify fetal-side DNA.\" viewBox=\"0 0 640 200\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n<rect x=\"0\" y=\"0\" width=\"640\" height=\"200\" fill=\"#fff9f9\"\/>\n<g font-family=\"sans-serif\" font-size=\"14\" text-anchor=\"middle\">\n<rect x=\"20\" y=\"30\" width=\"180\" height=\"140\" rx=\"12\" fill=\"#ffe6e6\" stroke=\"#e6a3a3\"\/>\n<text x=\"110\" y=\"60\" font-weight=\"bold\">Draw maternal blood<\/text>\n<text x=\"110\" y=\"100\" font-size=\"12\">Maternal DNA<\/text>\n<text x=\"110\" y=\"120\" font-size=\"12\">+ placental DNA<\/text>\n<text x=\"110\" y=\"150\" font-size=\"12\">(cfDNA)<\/text>\n<text x=\"230\" y=\"105\" font-size=\"20\">\u2192<\/text>\n<rect x=\"250\" y=\"30\" width=\"180\" height=\"140\" rx=\"12\" fill=\"#ffe6e6\" stroke=\"#e6a3a3\"\/>\n<text x=\"340\" y=\"60\" font-weight=\"bold\">Compare SNP patterns<\/text>\n<text x=\"340\" y=\"100\" font-size=\"12\">Analyze differences<\/text>\n<text x=\"340\" y=\"120\" font-size=\"12\">between mother and placenta<\/text>\n<text x=\"460\" y=\"105\" font-size=\"20\">\u2192<\/text>\n<rect x=\"480\" y=\"30\" width=\"140\" height=\"140\" rx=\"12\" fill=\"#ffe6e6\" stroke=\"#e6a3a3\"\/>\n<text x=\"550\" y=\"60\" font-weight=\"bold\">Estimate chromosome count<\/text>\n<text x=\"550\" y=\"100\" font-size=\"12\">Assess likely<\/text>\n<text x=\"550\" y=\"120\" font-size=\"12\">fetal-side result<\/text>\n<\/g>\n<\/svg>\n<\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">The proportion of fetal-derived DNA in the mother&#8217;s blood is called the &#8220;fetal fraction.&#8221; If this proportion is too low, the test can sometimes come back inconclusive. For a full walkthrough of the <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a> testing process, see our <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/en\/principles-of-nipt\/\">article explaining how NIPT works step by step<\/a>.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Research is also underway to extend SNP-based analysis toward estimating single-gene disorders. <a href=\"https:\/\/x.com\/SRH_Research\" target=\"_blank\" rel=\"noopener\">@SRH_Research<\/a>, an account on X that shares medical research updates, recently shared findings on next-generation <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a> research: an approach that analyzes DNA in maternal blood to estimate the fetal genotype, screening for single-gene disorders, structural chromosomal abnormalities, and aneuploidy all at once. SNP-based analysis techniques are gradually expanding what this kind of testing can offer in exactly this way.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"The_Limits_of_SNP-Based_NIPT_and_What_Happens_After_a_Positive_Result\"><\/span><strong>The Limits of SNP-Based NIPT, and What Happens After a Positive Result<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Regardless of testing method, every version of <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a> \u2014 including the SNP-based approach \u2014 is a non-diagnostic screening test. A positive result requires a confirmatory test such as amniocentesis.<\/strong> This holds true across all testing methods.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">In outpatient consultations, I sometimes hear patients say something like, &#8220;I heard SNP-based testing is highly accurate, so I assumed it was basically a diagnosis.&#8221; In reality, though, every version of <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a> has a positive predictive value (the probability that a condition is actually present given a positive result) that varies by condition and maternal age, so it needs to be considered separately from a definitive diagnosis.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/x.com\/fetus7\" target=\"_blank\" rel=\"noopener\">@fetus7<\/a>, an account on X focused on obstetrics-related information, made a useful point along these lines: even with SNP-based cfDNA testing, the positive predictive value for monosomy X (a numerical change in the sex chromosomes) can sometimes be lower than expected. That kind of variation in positive predictive value by chromosome type is worth keeping in mind when interpreting a result.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The <a href=\"https:\/\/jams-prenatal.jp\/testing\/nipt\/\" target=\"_blank\" rel=\"noopener\">explanatory page on NIPT<\/a> from the Japan Association of Obstetricians and Gynecologists&#8217; Prenatal Testing Certification Operating Committee explains this in similar terms. A positive result can still mean the condition is absent (a false positive), so a confirmatory test is needed either way. A negative result, on the other hand, is not typically followed up with amniocentesis for confirmation. A report from Japan&#8217;s Ministry of Health, Labour and Welfare expert panel on prenatal testing, <a href=\"https:\/\/www.mhlw.go.jp\/content\/000783387.pdf\" target=\"_blank\" rel=\"noopener\">available here<\/a>, likewise positions <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a> as a non-diagnostic test.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">If a result comes back positive, the typical next steps are as follows. First, genetic counseling helps you understand what the result actually means. From there, you and your partner can decide together, with guidance from a specialist, whether to pursue a confirmatory amniocentesis. There is no need to rush \u2014 take the time to work through each step with a specialist.<\/p>\n\n\n\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Frequently_Asked_Questions\"><\/span><strong>Frequently Asked Questions<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Are_SNPs_and_genes_the_same_thing\"><\/span>Are SNPs and genes the same thing?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">No, they are different concepts. A gene is a functional unit of DNA that serves as the body&#8217;s blueprint, while an SNP refers to a single-base difference occurring within a DNA sequence. SNPs can occur both inside genes and in regions outside of genes.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"How_common_are_SNPs\"><\/span>How common are SNPs?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">The human genome contains around 3 billion base pairs, and SNPs are estimated to occur at several million to over 10 million positions within it. They are extremely common and widely distributed across the entire genome.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"How_is_SNP-based_NIPT_different_from_standard_NIPT\"><\/span>How is SNP-based NIPT different from standard NIPT?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a> includes several different testing methods, and the SNP-based approach is one of them. It compares SNP patterns between maternal and placenta-derived DNA, and one notable feature is its ability to determine whether a twin pregnancy is identical or fraternal. You can compare it against other testing methods using each provider&#8217;s materials or our comparison article on this site.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Does_a_positive_SNP-based_NIPT_result_mean_a_definitive_diagnosis\"><\/span>Does a positive SNP-based NIPT result mean a definitive diagnosis?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">No. Every version of <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a>, including the SNP-based method, is a non-diagnostic screening test. If the result is positive, a confirmatory test such as amniocentesis is needed to establish a definitive diagnosis.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Are_SNPs_used_directly_to_diagnose_disease\"><\/span>Are SNPs used directly to diagnose disease?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Generally, no single SNP on its own can confirm the presence or absence of a disease. For most conditions, multiple SNPs combine with other factors to influence overall risk, so SNP data is mainly used for risk assessment and as a lead for further research rather than as a standalone diagnostic tool.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"What_technologies_are_used_to_analyze_SNPs\"><\/span>What technologies are used to analyze SNPs?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Common approaches include DNA sequencing, SNP arrays, and methods that combine PCR with RFLP. In recent years, the growing use of next-generation sequencers (NGS) has made it possible to analyze large numbers of SNPs in a much shorter time.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Medical supervision: Hiroshi Oka<\/strong> \u2014 Director-General, Hiro Clinic <a href=\"https:\/\/www.hiro-clinic.or.jp\/nipt\/\">NIPT<\/a> (Fukubikai Medical Corporation), and Lab Director. A graduate of Keio University School of Medicine, Dr. Oka has passed the medical licensing examinations in both Japan and the United States and holds a Ph.D. He is one of a small number of Lab Director-qualified specialists in Japan and serves as a visiting faculty member at a professional graduate school. This article was prepared with attention to Japan&#8217;s medical advertising guidelines and references public and academic sources, including BioBank Japan (Institute of Medical Science, The University of Tokyo), RIKEN, Japan&#8217;s Ministry of Health, Labour and Welfare, and the Japan Association of Obstetricians and Gynecologists&#8217; Prenatal Testing Certification Operating Committee. Figures and technology trends described here may change as research progresses, so please consult your physician for the latest information and for guidance on interpreting your individual test results.<\/p>\n\n\n<script type=\"application\/ld+json\">\n{\n  \"@context\": \"https:\/\/schema.org\",\n  \"@type\": \"FAQPage\",\n  \"mainEntity\": [\n    {\n      \"@type\": \"Question\",\n      \"name\": \"Are SNPs and genes the same thing?\",\n      \"acceptedAnswer\": {\n        \"@type\": \"Answer\",\n        \"text\": \"No, they are different concepts. A gene is a functional unit of DNA that serves as the body's blueprint, while an SNP refers to a single-base difference occurring within a DNA sequence. 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