As a framework, we identify three ways in which build can impact results. This can be due to (1) a gene is only annotated in a given build, or a gene is annotated in both builds but (2) quantified at different levels between the builds, or (3) quantified in only one of builds. (2/8) - ThreadSky

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raungar.bsky.social • 413 days ago

As a framework, we identify three ways in which build can impact results. This can be due to (1) a gene is only annotated in a given build, or a gene is annotated in both builds but (2) quantified at different levels between the builds, or (3) quantified in only one of builds. (2/8)

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raungar.bsky.social•413 days ago

For this framework, we identify differences between the hg19 and hg38 build (hg19:hg38) and hg38 and chm13 build (hg38:chm13). Across numerous metrics, we see that the hg38:chm13 comparisons display more differences than the hg19:hg38 comparisons. (3/8)

raungar.bsky.social•413 days ago

We then investigate how build impacts detection of outliers. Most outlier status is consistent between builds, but we do see that the amount gene’s quantification changes between builds is correlated with the average z-score change. (4/8)

raungar.bsky.social•413 days ago

Finally, we look into the impact on clinically-relevant genes. We identified 341 rare disease & 68 cancer genes with changes between builds. In the top transcriptome-guided candidate lists we found annotation-specific genes and solved genes with rank differences between builds. (5/8)

raungar.bsky.social•413 days ago

We also provide a resource (Supplementary Table 1) in which you can find your favorite gene, and see if it is impacted by genome build. (6/8)

raungar.bsky.social•413 days ago

This work was done extremely closely with Pagé Goddard, with huge help from Tanner Jensen and Fabien Degalez and Stephen Montgomery, along with the a wonderful team including Devon Bonner, Kevin Smith, Jon Bernstein, & @mwheelermd.bsky.social (7/8)

raungar.bsky.social•413 days ago

Please let us know if you have any questions, feedback, or comments! (8/8)

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