@sdtemple

PhD, he/him, @LosAlamosNatLab @um_midas @UWStat I am rarely on social media but will post informative threads when I publish a scientific paper.

 Los Alamos, NM; Seattle, WA
sdtemple.github.io
Joined June 2020
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Presenting our new scan that uses IBD segments to detect genetic associations with cohorts stratified by a categorical variable (i.e., case-control studies). biorxiv.org/content/10.1101/…

Multiple-testing corrections in case-control studies using identity-by-descent segments

Identity-by-descent (IBD) mapping provides complementary signals to genome-wide association studies (GWAS) when multiple causal haplotypes or variants are present, but not directly tested. However,...

biorxiv.org
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Seth D. Temple retweeted
AJHG@AJHGNewsFeb 17
🧬New from @sdtemple et al! 📄Multiple-testing corrections in case-control studies using identity-by-descent segments cell.com/ajhg/fulltext/S0002…

Multiple-testing corrections in case-control studies using identity-by-descent segments

We developed an automated, reproducible, and scalable workflow to perform scans for disproportionate identity-by-descent sharing between cases and controls, determining well-controlled significance...

cell.com
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FLARE2: local ancestry inference with poorly-matched reference panels biorxiv.org/content/10.1101/… #biorxiv_genetic

FLARE2: local ancestry inference with poorly-matched reference panels

The original FLARE method provides computationally efficient and highly accurate local ancestry inference in cases where a closely-matched reference panel is available for each ancestry. In this...

biorxiv.org
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The final thesis chapter is published OA at @AJHGNews ! In short, we determine a valid significance level for a "selection" scan and apply it to 3 ancestry groups in 2 biobanks. 🧵 for updates from the helpful peer review. sciencedirect.com/science/ar…
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While we have improved (made a more conservative threshold for the African American analysis), there are still unmodeled complexities and likely fine-scale structure that violates our assumption. Buyer beware if signal is weak (barely GW significant)!
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Overall, the method is a scalable and interpretable way to look for haplotype homozygosity in biobanks. I have spent a lot of time implementing it to make it user friendly. Running this can be important to check for confounding: see our other preprint. pubmed.ncbi.nlm.nih.gov/4067…

Multiple-testing corrections in case-control studies using identity-by-descent segments - PubMed

Identity-by-descent (IBD) mapping provides complementary signals to genome-wide association studies (GWAS) when multiple causal haplotypes or variants are present, but not directly tested. However,...

pubmed.ncbi.nlm.nih.gov
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Seth D. Temple retweeted
AJHG@AJHGNews26 Sep 2025
📣New from @sdtemple & Browning! 📄Multiple-testing corrections in selection scans using identity-by-descent segments cell.com/ajhg/fulltext/S0002…

Multiple-testing corrections in selection scans using identity-by-descent segments

By modeling correlations along the genome, we determined significance levels for a scan of excess identity-by-descent sharing that help avoid reporting false positive results. Some large signals...

cell.com
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Our paper on the limiting distribution of IBD rates (Gaussian) is now published in TPB. Really an amazing experience to work with and learn from Prof Elizabeth Thompson! doi.org/10.1016/j.tpb.2025.0…
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This is a new conceptual figure which explains how to make our proofs. I hope this idea is helpful to other population geneticists.
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The test is a two-sample modification of the one-sample selection scan from my prior work (Temple and Thompson, 2025): high IBD rates differences in cases versus controls could indicate a genetic association.
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You can also run a fast scan with randomized phenotypes to double check if selection is confounding.
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This project completes my development of our suite of methods called isweep, which can detect recent selection and case-control associations, can narrow in on the selection signal, and has fast local simulations to perform statistical inference.
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The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure academic.oup.com/nar/article…

The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence...

Abstract. RNA viruses like SARS-CoV-2 have high mutation rates, which contribute to their rapid evolution. Mutation rates depend on mutation type and can v

academic.oup.com
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