afff541e7fd736cc48695ecf2442bea316120582 max Tue Aug 11 08:35:42 2026 -0700 update to the noyvertSv docs, page, based on email from author diff --git src/hg/makeDb/trackDb/human/noyvertSv.html src/hg/makeDb/trackDb/human/noyvertSv.html index 597b64f7cd4..488b8d9039e 100644 --- src/hg/makeDb/trackDb/human/noyvertSv.html +++ src/hg/makeDb/trackDb/human/noyvertSv.html @@ -1,53 +1,54 @@ <h2>Description</h2> <p> The structural variants (SVs) in this dataset were identified using Oxford Nanopore long-read whole-genome sequencing of 888 individuals from the 1000 -Genomes Project, representing five ancestry groups. The SVs were merged with +Genomes Project, representing five ancestry groups. +This dataset and the <a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna</a> track +(Schloissnig et al. 2025) are based on the same underlying Oxford Nanopore +sequencing data; the 888 samples here are a subset of the 1,019 samples in that +track and only SVs that appear in a single sample (singletons) were removed from this track, +so this callset is smaller than the Schloissnig dataset. The reason is that +this callset was created primarily for imputation: The SVs here were merged with previously identified short variants from the same individuals to generate a multi-ancestry SV imputation reference panel. This panel was used to impute SVs in approximately 500,000 UK Biobank participants and test their associations with 32 disease-relevant traits. </p> <p> The track contains all 107,445 SVs in the reference panel: 59,953 insertions, 38,459 deletions, 5,729 inversions, 2,696 breakends, and 608 duplications. +Variants seen in only a single individual (singletons) were excluded from the +panel, so every SV shown was observed in at least two individuals; the panel is +therefore not exhaustive for very rare variants. Each variant is annotated with its overall allele frequency; allele frequencies across five superpopulations (African, Admixed American, East Asian, European, and South Asian); Hardy-Weinberg equilibrium p-values; and imputation accuracy metrics from internal leave-one-out validation and UK Biobank imputation. For SVs reaching genome-wide significance, the associated traits, p-values, and INFO scores are listed on the corresponding variant details page. </p> <p> -This dataset is an independent reprocessing of the same Oxford Nanopore reads -used for the <a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna</a> track -(Schloissnig et al. 2025). The 888 samples in this dataset are a subset of the -1,019 samples included in that track, with both datasets based on the same -underlying sequencing data. -However, the data-processing and SV-calling methods differ between the two -tracks, so the individual calls are only partially concordant. This track has -about 38,000 deletions and the Vienna track about 58,000; at a 50% -reciprocal-overlap threshold roughly 12,000 are shared. That is about a third -of the deletions in this track and, conversely, about a fifth of the Vienna -deletions; requiring at least 90% mutual overlap lowers these shares to roughly -a quarter and a sixth, respectively. A similar fraction (about a quarter) of -the insertions in this track have a size-matched Vienna insertion within -100 bp. The imputation reference panel, UK Biobank imputation results, and -SV-wide association study (SV-WAS) results described here are specific to this -track. +This dataset and the <a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna</a> track +(Schloissnig et al. 2025) are based on the same underlying Oxford Nanopore +sequencing data; the 888 samples here are a subset of the 1,019 samples in that +track. The two studies applied different data-processing and SV-calling +pipelines to address distinct research objectives, so the individual calls are +only partially concordant. The imputation reference panel, UK Biobank +imputation results, and SV-wide association study (SV-WAS) results described +here are specific to this track. </p> <h2>Display Conventions and Configuration</h2> <p> Items are colored by SV type, matching the other subtracks of the container: </p> <table class="stdTbl"> <tr><th style="background-color:#C80000;width:2em"> </th> <td>Deletion (DEL)</td></tr> <tr><th style="background-color:#0000C8;width:2em"> </th> <td>Insertion (INS)</td></tr> <tr><th style="background-color:#00A000;width:2em"> </th> <td>Duplication (DUP)</td></tr> <tr><th style="background-color:#E68C00;width:2em"> </th> <td>Inversion (INV)</td></tr> @@ -133,15 +134,20 @@ <p> Thanks to Boris Noyvert and colleagues at Boehringer Ingelheim and the wider study team for generating this multi-ancestry long-read SV panel and for sharing the per-variant summary table, and to the 1000 Genomes Project and the UK Biobank participants whose data made the study possible. </p> <h2>References</h2> <p> Noyvert B, Erzurumluoglu AM, Drichel D, Omland S, Andlauer TFM <em>et al</em>. <a href="https://doi.org/10.7554/eLife.106115.1" target="_blank"> Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations</a>. <em>eLife</em>. 2025. doi:10.7554/eLife.106115.1 </p> +<p> +A continuously updated preprint version of this study is available on medRxiv: +<a href="https://doi.org/10.1101/2023.12.20.23300308" target="_blank"> +doi:10.1101/2023.12.20.23300308</a>. +</p>