Update Post “2023-11-gnomad-v4-0” (#193)

Author: ch-kr

content/posts/2023-11-gnomad-v4-0.md

@@ -51,7 +51,7 @@ We have removed support for subsets from the gnomAD v4 exomes for two major reas
 
 ### Updated filtering allele frequency
 
-We have released a new, combined filtering allele frequency (FAF), which integrates variant frequencies across the 734,947 exomes and 76,215 genomes. The exome FAF and genome FAF are still listed on the variant pages as well.
+We have released a new, combined filtering allele frequency (FAF), which integrates variant frequencies across the 730,947 exomes and 76,215 genomes. The exome FAF and genome FAF are still listed on the variant pages as well.
 
 ### Structural Variants
 
@@ -168,16 +168,16 @@ In gnomAD [v3.1.2](https://gnomad.broadinstitute.org/news/2021-10-gnomad-v3-1-2-
 For both of these methods, we compared samples to the defined distribution and flagged any samples for filtering if the sample's value was **4 median absolute deviations (MADs)**:
 
 * **over** or **under** the following metrics
-* * insertion : deletion ratio
-  * transition : transversion ratio
-  * singleton transition : transversion ratio
-  * * We only computed this metric for samples with:
-    * * 50 nearest neighbors:
-      * * number of singletons > median number of singletons calculated with the 50 nearest neighbors
-      * Platform stratification + genetic ancestry PC regression filtering:
-      * * residual number of singletons > median residual number of singletons for that platform
+    * insertion : deletion ratio
+    * transition : transversion ratio
+    * singleton transition : transversion ratio
+      * We only computed this metric for samples with:
+        * 50 nearest neighbors:
+            * number of singletons > median number of singletons calculated with the 50 nearest neighbors
+        * Platform stratification + genetic ancestry PC regression filtering:
+              * residual number of singletons > median residual number of singletons for that platform
 * OR **over** the median for:
-* * heterozygous : homozygous ratio
+    * heterozygous : homozygous ratio
 
 Only samples that were filtered by **both** the 50 nearest neighbors and the platform stratification + genetic ancestry PC regression filtering were removed.
 
@@ -228,3 +228,5 @@ Finally, thanks to critical guidance by members of the [gnomAD steering committe
 1. Lu, W., Gauthier, L.D., Poterba, T., Giacopuzzi, E., Goodrich, J.K., Steves, C.R., King, D., Daly, M.J., Neale, B.M. &  Karczewski, K.J. CHARR efficiently estimates contamination from DNA sequencing data. *bioRxiv* 2023.06.28.545801 (2023). <https://doi.org/10.1101/2023.06.28.545801>
 2. Koenig, Z., Yohannes, M.T., Nkambule, L.LGoodrich, J.K., Kim, H.A., Zhao, X., Wilson, M.W., Tiao, G., Hao, S.P., Sahakian, N., Chao, K.R., gnomAD Project Consortium, Talkowski, M.E., Daly, M.J., Brand, H., Karczewski, K.J., Atkinson, E.G. & Martin, A.R. A harmonized public resource of deeply sequenced diverse human genomes. *bioRxiv* 2023.01.23.525248 (2023). <https://doi.org/10.1101/2023.01.23.525248>
 3. Bergström, A., McCarthy, S. A., Hui, R., Almarri, M. A., Ayub, Q., Danecek, P., Chen, Y., Felkel, S., Hallast, P., Kamm, J., Blanché, H., Deleuze, J. F., Cann, H., Mallick, S., Reich, D., Sandhu, M. S., Skoglund, P., Scally, A., Xue, Y., Durbin, R., … Tyler-Smith, C. (2020). Insights into human genetic variation and population history from 929 diverse genomes. Science (New York, N.Y.), 367(6484), eaay5012. <https://doi.org/10.1126/science.aay5012>
+
+*Updated in August 2025 to fix typo and formatting.*