{"id":100,"date":"2015-11-06T15:56:13","date_gmt":"2015-11-06T22:56:13","guid":{"rendered":"https:\/\/www.enlis.com\/blog\/?p=100"},"modified":"2015-11-07T13:06:19","modified_gmt":"2015-11-07T20:06:19","slug":"new-vs-old-a-comparison-of-23andmes-health-reports-and-the-raw-data","status":"publish","type":"post","link":"https:\/\/www.enlis.com\/blog\/2015\/11\/06\/new-vs-old-a-comparison-of-23andmes-health-reports-and-the-raw-data\/","title":{"rendered":"New vs. Old – a comparison of 23andMe’s health reports and the raw data"},"content":{"rendered":"

We’ve already determined that 23andMe’s raw data offers the most health information<\/a>\u00c2\u00a0among consumer genomic tests.
\n<\/em><\/p>\n

We’ve fixed problems<\/a> with the SNP data, and reverse-engineered<\/a> 23andMe’s proprietary insertions and deletions — allowing us to make the most accurate and comprehensive interpretation.
\n<\/em><\/p>\n

Now lets jump in and take a look at the health information that is available from 23andMe and from the raw data.<\/em><\/p>\n

\n

 <\/p>\n

23andMe was launched with the promise of bringing personal genome information to consumers everywhere.\u00c2\u00a0 For several years, they were able to provide information on both health-related traits and ancestry.\u00c2\u00a0 Then, in 2013 the FDA stepped in to stop the delivery of results on health-related traits.\u00c2\u00a0 Starting last month, 23andMe has revamped their service, and will now be able to offer some health reports, but not as many as before.<\/p>\n

 <\/p>\n

As we developed and tested Enlis Genome Personal<\/a> – it became clear that the raw data from 23andMe contains significantly<\/strong> more health information than they are reporting in their health reports.\u00c2\u00a0 That got us interested to put some numbers on just how much information there was in the raw data.\u00c2\u00a0 First, we wanted to compare the count of diseases or health-related traits that are reported by 23andme vs. how many are found in the raw data.<\/p>\n

 <\/p>\n\n\n\n
\"23andMeNumReported2\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

The previous 23andMe health reports had 201 health-related diseases or traits, while the new reports only have 36.\u00c2\u00a0 These 36 diseases are limited to carrier status on autosomal recessive disorders.\u00c2\u00a0 An autosomal recessive disorder is one in which a person needs 2 bad copies of a gene to be affected by the disorder.\u00c2\u00a0 With only 1 bad copy, that person is considered a non-affected ‘carrier’.\u00c2\u00a0 Interestingly, 23andMe’s website<\/a> claims that:<\/p>\n

“Our tests can be used to determine carrier status in adults, but cannot determine if you have two copies of the genetic variant.”<\/p><\/blockquote>\n

Edit: This is surprising because the Illumina Infinium technology (the genotyping chip that 23andMe uses) tends to have low error rates and 23andMe has real world data on over 1 million customers now.\u00c2\u00a0\u00c2\u00a0 The FDA document<\/a> about 23andMe’s approved Bloom Syndrome carrier test says that “all homozygous variant genotype samples receive a ‘no-call’ result, since the calling software was designed not to detect homozygous variant genotypes.” It sounds to me like they designed the software to ignore and throw out homozygous data.<\/span><\/span><\/p>\n

With raw data imported into Enlis Genome Personal – there are over 2,000 diseases or health-related traits analyzed.\u00c2\u00a0 Here is a complete list<\/a> of the diseases and traits found in 23andMe’s raw data. (In this non-consolidated list, sub-types of diseases are listed separately)<\/p>\n

 <\/p>\n

 <\/p>\n

A disease or trait can be caused by different genomic variants, and each of these variants can be tested by 23andMe.\u00c2\u00a0 For instance, 23andMe reports on 28 different variants that are connected with Cystic Fibrosis.\u00c2\u00a0 So how many total health-related variants are reported by 23andMe?\u00c2\u00a0 And how many are in 23andMe’s raw data?<\/p>\n

 <\/p>\n\n\n\n
\"\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

23andme has a long way to go to get back to reporting the same number of variants they were before the FDA ban.\u00c2\u00a0 However – both the previous and new 23andMe reports pale in comparison to an analysis of the raw data.\u00c2\u00a0 23andMe’s new reports tell you about less than 1% of the health-related variants that are in their raw data.<\/p>\n

 <\/p>\n

How does this translate to the level of individual diseases? Let’s look at the count of variants for some specific diseases and inherited conditions:<\/p>\n

 <\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Disease<\/td>\nNumber of variants in previous 23andMe reports<\/span><\/td>\nNumber of variants in new 23andMe reports<\/span><\/td>\nNumber of variants tested in the raw data<\/span><\/td>\n<\/tr>\n
Beta Thalassemia<\/td>\n17<\/td>\n10<\/td>\n43<\/td>\n<\/tr>\n
BRCA1\/2 Inherited Breast Cancer<\/td>\n3<\/td>\n0<\/td>\n677<\/td>\n<\/tr>\n
Cystic Fibrosis<\/td>\n26<\/td>\n28<\/td>\n225<\/td>\n<\/tr>\n
Gaucher Disease<\/td>\n3<\/td>\n0<\/td>\n47<\/td>\n<\/tr>\n
Hypertrophic Cardiomyopathy<\/td>\n1<\/td>\n0<\/td>\n201<\/td>\n<\/tr>\n
Li-Fraumeni syndrome<\/td>\n0<\/td>\n0<\/td>\n32<\/td>\n<\/tr>\n
Lynch Syndrome<\/td>\n0<\/td>\n0<\/td>\n708<\/td>\n<\/tr>\n
Marfan Syndrome<\/td>\n0<\/td>\n0<\/td>\n100<\/td>\n<\/tr>\n
Phenylketonuria<\/td>\n27<\/td>\n0<\/td>\n95<\/td>\n<\/tr>\n
Tay-Sachs Disease<\/td>\n6<\/td>\n4<\/td>\n31<\/td>\n<\/tr>\n
Usher Syndrome<\/td>\n2<\/td>\n2<\/td>\n30<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

This is only a small sample of diseases and conditions, but you can see the enormous disparity between the number of variants reported by 23andMe and the number that is in the raw data.<\/p>\n

If you want to get the most health information out of your 23andMe data, you need to get a third-party interpretation.\u00c2\u00a0 Given our quality control and comprehensive, easy to use software, I think that our interpretation it the best.\u00c2\u00a0 Give it a try here:<\/p>\n

https:\/\/www.enlis.com\/import\/<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

We’ve already determined that 23andMe’s raw data offers the most health information\u00c2\u00a0among consumer genomic tests. We’ve fixed problems with the SNP data, and reverse-engineered 23andMe’s proprietary insertions and deletions — allowing us to make the most accurate and comprehensive interpretation. Now lets jump in and take a look at the health information that is available […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-100","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/www.enlis.com\/blog\/wp-json\/wp\/v2\/posts\/100","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.enlis.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.enlis.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.enlis.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.enlis.com\/blog\/wp-json\/wp\/v2\/comments?post=100"}],"version-history":[{"count":0,"href":"https:\/\/www.enlis.com\/blog\/wp-json\/wp\/v2\/posts\/100\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.enlis.com\/blog\/wp-json\/wp\/v2\/media?parent=100"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.enlis.com\/blog\/wp-json\/wp\/v2\/categories?post=100"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.enlis.com\/blog\/wp-json\/wp\/v2\/tags?post=100"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}