From ed1a515075525cadff619c4c71a464299078faba Mon Sep 17 00:00:00 2001 From: ch-kr Date: Wed, 8 Nov 2023 14:27:35 -0500 Subject: [PATCH 1/8] Updated FAF to make it clearer that this field contains information about group with highest FAF, not FAF calculated on group with highest AF --- browser/help/topics/faf.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/browser/help/topics/faf.md b/browser/help/topics/faf.md index 8da9cb251..04de508a6 100644 --- a/browser/help/topics/faf.md +++ b/browser/help/topics/faf.md @@ -7,10 +7,10 @@ This annotation can be used for filtering variants by allele frequency against a This calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals (`rmi`) groups. -On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation is computed globally and for each genetic ancestry group. Genetic ancestry group specific AFs are listed separately with 95% and 99% CIs. +On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation is computed globally and for each genetic ancestry group. Genetic ancestry group specific filtering allele frequencies (FAFs) are listed separately with 95% and 99% CIs. -### Group maximum allele frequency +### Group maximum filtering allele frequency -This annotation (abbreviated "`grpmax`") contains allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest frequency. +This annotation (abbreviated "`grpmax FAF`") contains filtering allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest FAF. Note that this field contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**. -For gnomAD v4, this excludes Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (mid), and "Remaining Individuals" (`rmi`) groups. For gnomAD v2, this excludes Ashkenazi Jewish (`asj`), European Finnish (`fin`), and "Remaining Individuals" (`rmi`) groups. +For gnomAD v4, this calculation excludes Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (mid), and "Remaining Individuals" (`rmi`) groups. For gnomAD v2, this calculation excludes Ashkenazi Jewish (`asj`), European Finnish (`fin`), and "Remaining Individuals" (`rmi`) groups. From 9341e8a1c30b750acf769eba677a6e1df38e78b8 Mon Sep 17 00:00:00 2001 From: ch-kr Date: Tue, 14 Nov 2023 10:37:16 -0500 Subject: [PATCH 2/8] add note about grpmax --- browser/help/topics/faf.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/browser/help/topics/faf.md b/browser/help/topics/faf.md index 4a070dc4d..f808a4f9b 100644 --- a/browser/help/topics/faf.md +++ b/browser/help/topics/faf.md @@ -13,6 +13,6 @@ On the browser, this annotation is directly available on the variant page. In th ### Group maximum filtering allele frequency -This annotation (abbreviated "`grpmax`") contains allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest **AF**. +This annotation (abbreviated "`grpmax`") contains allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest **AF**. Note that `grpmax` is distinct from filtering allele frequency. For gnomAD v4, this calculation excludes Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups. For gnomAD v2, this calculation excludes Ashkenazi Jewish (`asj`), European Finnish (`fin`), and "Remaining Individuals" (`rmi`) groups. From 98340ec4de681a1e46a2d136f40da22e1e6b6de6 Mon Sep 17 00:00:00 2001 From: ch-kr Date: Tue, 14 Nov 2023 10:47:14 -0500 Subject: [PATCH 3/8] remove grpmax from faf and add to topics list --- browser/help/helpPageTableOfContents.ts | 1 + browser/help/topics/faf.md | 8 +------- browser/help/topics/grpmax.md | 8 ++++++++ 3 files changed, 10 insertions(+), 7 deletions(-) create mode 100644 browser/help/topics/grpmax.md diff --git a/browser/help/helpPageTableOfContents.ts b/browser/help/helpPageTableOfContents.ts index 965d893ba..0c14ef73c 100644 --- a/browser/help/helpPageTableOfContents.ts +++ b/browser/help/helpPageTableOfContents.ts @@ -11,6 +11,7 @@ const helpPageTableOfContents: { topics: string[]; faq: FaqTopic[] } = { 'relatedness-filtering', 'vep', 'faf', + 'grpmax', 'constraint', 'pext', 'regional-constraint', diff --git a/browser/help/topics/faf.md b/browser/help/topics/faf.md index f808a4f9b..8a1c7937d 100644 --- a/browser/help/topics/faf.md +++ b/browser/help/topics/faf.md @@ -9,10 +9,4 @@ Note that this annotation contains filtering allele frequency information from t The filtering allele frequency calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups. -On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation (abbreviated "`faf`") is computed globally and for each genetic ancestry group. Filtering allele frequencies (FAFs) for each genetic ancestry group specific are listed separately with 95% and 99% CIs. - -### Group maximum filtering allele frequency - -This annotation (abbreviated "`grpmax`") contains allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest **AF**. Note that `grpmax` is distinct from filtering allele frequency. - -For gnomAD v4, this calculation excludes Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups. For gnomAD v2, this calculation excludes Ashkenazi Jewish (`asj`), European Finnish (`fin`), and "Remaining Individuals" (`rmi`) groups. +On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation (abbreviated "`faf`") is computed globally and for each genetic ancestry group. Filtering allele frequencies (FAFs) for each genetic ancestry group specific are listed separately with 95% and 99% CIs. \ No newline at end of file diff --git a/browser/help/topics/grpmax.md b/browser/help/topics/grpmax.md new file mode 100644 index 000000000..5aa749876 --- /dev/null +++ b/browser/help/topics/grpmax.md @@ -0,0 +1,8 @@ +--- +id: grpmax +title: 'Group maximum allele frequency' +--- + +This annotation (abbreviated "`grpmax`") contains allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest **AF**. Note that `grpmax` is distinct from filtering allele frequency. + +For gnomAD v4, this calculation excludes Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups. For gnomAD v2, this calculation excludes Ashkenazi Jewish (`asj`), European Finnish (`fin`), and "Remaining Individuals" (`rmi`) groups. From 72dea719e9ab8ac5271588c3e868064c72dfd338 Mon Sep 17 00:00:00 2001 From: Katherine Chao Date: Tue, 14 Nov 2023 11:19:14 -0500 Subject: [PATCH 4/8] Update browser/help/topics/faf.md Co-authored-by: klaricch --- browser/help/topics/faf.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/browser/help/topics/faf.md b/browser/help/topics/faf.md index 8a1c7937d..5fc9babac 100644 --- a/browser/help/topics/faf.md +++ b/browser/help/topics/faf.md @@ -9,4 +9,4 @@ Note that this annotation contains filtering allele frequency information from t The filtering allele frequency calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups. -On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation (abbreviated "`faf`") is computed globally and for each genetic ancestry group. Filtering allele frequencies (FAFs) for each genetic ancestry group specific are listed separately with 95% and 99% CIs. \ No newline at end of file +On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation (abbreviated "`faf`") is computed globally and for each genetic ancestry group. Filtering allele frequencies (FAFs) for each genetic ancestry group are listed separately with 95% and 99% CIs. \ No newline at end of file From 57f13170364713c2ed65900ac57d5dee9f13fd44 Mon Sep 17 00:00:00 2001 From: ch-kr Date: Tue, 14 Nov 2023 11:20:25 -0500 Subject: [PATCH 5/8] add comment about grpmax faf --- browser/help/topics/faf.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/browser/help/topics/faf.md b/browser/help/topics/faf.md index 5fc9babac..48a3fc6e2 100644 --- a/browser/help/topics/faf.md +++ b/browser/help/topics/faf.md @@ -5,7 +5,7 @@ title: 'Filtering allele frequency' This annotation can be used for filtering variants by allele frequency against a disease-specific threshold that can be set for each disease (e.g. BA1 in the 2015 ACMG/AMP guidelines). In this case the filtering allele frequency (FAF) is the maximum credible genetic ancestry group AF (e.g. the lower bound of the 95% confidence interval (CI)). If the FAF is above the disease-specific threshold, then the observed AC is not compatible with pathogenicity. See http://cardiodb.org/allelefrequencyapp/ and [Whiffin _et al._ 2017](https://www.nature.com/articles/gim201726) for additional information. -Note that this annotation contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**. +Note that this annotation contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**. This means that the annotation displayed on the variant pages is the GroupMax FAF. The filtering allele frequency calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups. From 875e4ff21137084daa1c7f5b29fd5eb579799128 Mon Sep 17 00:00:00 2001 From: ch-kr Date: Tue, 14 Nov 2023 11:22:29 -0500 Subject: [PATCH 6/8] move note about grpmax faf --- browser/help/topics/faf.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/browser/help/topics/faf.md b/browser/help/topics/faf.md index 48a3fc6e2..bd3128c3d 100644 --- a/browser/help/topics/faf.md +++ b/browser/help/topics/faf.md @@ -5,8 +5,8 @@ title: 'Filtering allele frequency' This annotation can be used for filtering variants by allele frequency against a disease-specific threshold that can be set for each disease (e.g. BA1 in the 2015 ACMG/AMP guidelines). In this case the filtering allele frequency (FAF) is the maximum credible genetic ancestry group AF (e.g. the lower bound of the 95% confidence interval (CI)). If the FAF is above the disease-specific threshold, then the observed AC is not compatible with pathogenicity. See http://cardiodb.org/allelefrequencyapp/ and [Whiffin _et al._ 2017](https://www.nature.com/articles/gim201726) for additional information. -Note that this annotation contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**. This means that the annotation displayed on the variant pages is the GroupMax FAF. +Note that this annotation contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**. The filtering allele frequency calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups. -On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation (abbreviated "`faf`") is computed globally and for each genetic ancestry group. Filtering allele frequencies (FAFs) for each genetic ancestry group are listed separately with 95% and 99% CIs. \ No newline at end of file +On the browser, the **GroupMax FAF** annotation is directly available on the variant page. In the VCF and Hail Tables, the filtering allele frequency annotation (abbreviated "`faf`") is computed globally and for each genetic ancestry group. Filtering allele frequencies (FAFs) for each genetic ancestry group are listed separately with 95% and 99% CIs. \ No newline at end of file From 33d13db8ec2301450329115bf9281ed4ea82072e Mon Sep 17 00:00:00 2001 From: ch-kr Date: Tue, 14 Nov 2023 13:31:05 -0500 Subject: [PATCH 7/8] this annotation -> GroupMax FAF --- browser/help/topics/faf.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/browser/help/topics/faf.md b/browser/help/topics/faf.md index bd3128c3d..a86003d8e 100644 --- a/browser/help/topics/faf.md +++ b/browser/help/topics/faf.md @@ -5,7 +5,7 @@ title: 'Filtering allele frequency' This annotation can be used for filtering variants by allele frequency against a disease-specific threshold that can be set for each disease (e.g. BA1 in the 2015 ACMG/AMP guidelines). In this case the filtering allele frequency (FAF) is the maximum credible genetic ancestry group AF (e.g. the lower bound of the 95% confidence interval (CI)). If the FAF is above the disease-specific threshold, then the observed AC is not compatible with pathogenicity. See http://cardiodb.org/allelefrequencyapp/ and [Whiffin _et al._ 2017](https://www.nature.com/articles/gim201726) for additional information. -Note that this annotation contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**. +Note that the GroupMax FAF contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**. The filtering allele frequency calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups. From fa4c6afd7984874844e1d556846d6faa8522593f Mon Sep 17 00:00:00 2001 From: Riley Grant Date: Wed, 15 Nov 2023 09:51:04 -0500 Subject: [PATCH 8/8] fixup: update jest snapshot --- .../help/__snapshots__/HelpPage.spec.tsx.snap | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/browser/src/help/__snapshots__/HelpPage.spec.tsx.snap b/browser/src/help/__snapshots__/HelpPage.spec.tsx.snap index 7bd54a46d..942f4b59d 100644 --- a/browser/src/help/__snapshots__/HelpPage.spec.tsx.snap +++ b/browser/src/help/__snapshots__/HelpPage.spec.tsx.snap @@ -688,6 +688,15 @@ exports[`Help Page has no unexpected changes 1`] = ` faf +
  • + + grpmax + +
    • +
  • + + grpmax + +