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PODCAST

Base by Base

Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time. Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.

science life sciences

All Episodes

00:20:53

301: Biobank Mendelian randomization prioritizes...

Base by Base ·

2026/02/25

Ferolito BR et al., Human Genetics and Genomics Advances. 7 ( - Meta-analysis of MVP, UK Biobank and FinnGen with Mendelian randomization using eQTL/pQTL instruments implicates 6,447 genes and 69,669 causal gene-trait links. Study Highlights:The authors meta-analyzed GWAS from MVP, UK Biobank, and FinnGen across 2,003 harmonized phenotypes and used cis-eQTLs and cis-pQTLs from GTEx, eQTLGen, ARIC, Fenland, and deCODE to perform two-sample Mendelian

en-us

00:21:48

300: Population-scale WGS links MHC class II antigen...

Base by Base ·

2026/02/24

Nyeo SS et al., Nature - Population-scale WGS reanalysis quantifies persistent EBV DNA and shows MHC class II–mediated antigen presentation predicts EBV DNAemia and links to autoimmune and respiratory disease. Study Highlights:Using whole-genome sequencing from UK Biobank (n≈490,560) and All of Us (n≈245,394), the authors extracted chrEBV-mapping reads, masked low-mappability regions, and defined EBV DNAemia (>1.2 genomes per 10^4 cells) in 9.7–11.9%

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00:21:15

299: UFM1 loss and R81C mutation disrupt neuronal...

Base by Base ·

2026/02/23

Perdigão C et al., EMBO Molecular Medicine - In mouse neurons, UFM1 loss or UFM1-R81C expression reduces protein translation, triggers ER stress and PERK activation, impairing dendrite and synapse development. Study Highlights:Using murine UFM1-deficient neurons generated by conditional knockout and CRISPR/Cas9 in vivo manipulations and lentiviral rescue, the study combined FUNCAT, puromycin labeling, patch-clamp electrophysiology, RNA-seq, mass

en-us

00:20:16

298: Bi-allelic FSD1L variants in retinitis...

Base by Base ·

2026/02/22

Lin S et al., The American Journal of Human Genetics 113, 1–11 ( - Bi-allelic FSD1L variants cause retinitis pigmentosa; FSD1L localizes to the photoreceptor axoneme and a deep intronic deletion abolishes retina-enriched exon 10b inclusion. Study Highlights:In human and mouse retinal tissues and six affected individuals from four families, exome/genome sequencing identified bi-allelic ultra-rare FSD1L variants associated with retinitis pigmentosa

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00:20:38

296: snaR-A ncRNA antagonizes U2 snRNP SF3B2 to drive...

Base by Base ·

2026/02/21

Zhou S et al., Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations. Nature Communications - snaR-A noncoding RNA interacts with U2 snRNP subunit SF3B2 and nuclear speckles, increasing intron retention and promoting proliferation in human cancer-relevant cells. Study Highlights:Using human cell lines (HEK293T, A549, THP-1) and tumor chromatin data, the authors combined biotinylated

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00:21:27

297: Bi-allelic FSD1L variants disrupt mitotic...

Base by Base ·

2026/02/21

Serpieri V et al., The American Journal of Human Genetics. 113, 1–16 (March 5 - Bi-allelic FSD1L variants disrupt a microtubule-associated protein, causing hydrocephalus, corpus callosum defects and an L1 syndrome-like neurodevelopmental disorder in humans and models. Study Highlights:Exome sequencing in eleven affected individuals (including five fetuses) identified bi-allelic FSD1L variants associated with hydrocephalus and corpus callosum defects

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00:20:38

296: snaR-A ncRNA antagonizes U2 snRNP SF3B2 to drive...

Base by Base ·

2026/02/20

Zhou S et al., Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations. Nature Communications - snaR-A noncoding RNA interacts with U2 snRNP subunit SF3B2 and nuclear speckles, increasing intron retention and promoting proliferation in human cancer-relevant cells. Study Highlights:Using human cell lines (HEK293T, A549, THP-1) and tumor chromatin data, the authors combined biotinylated

en-us

00:28:25

295: CFTR deltaF508 and CF-risk variants protect...

Base by Base ·

2026/02/19

Yu M et al., Cell Genomics. 6 ( - Large-scale exome sequencing shows CFTR risk variants, including deltaF508, reduce susceptibility to inflammatory bowel disease, suggesting targeted CFTR modulation as a potential IBD therapy. Study Highlights:The authors analyzed large-scale human exome and genome sequencing data (38,558 cases and 66,945 controls in European discovery; 42,475 cases and 192,050 controls in replication across ancestries) using

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00:28:25

295: CFTR deltaF508 and CF-risk variants protect...

Base by Base ·

2026/02/19

Yu M et al., Cell Genomics. 6 ( - Large-scale exome sequencing shows CFTR risk variants, including deltaF508, reduce susceptibility to inflammatory bowel disease, suggesting targeted CFTR modulation as a potential IBD therapy. Study Highlights:The authors analyzed large-scale human exome and genome sequencing data (38,558 cases and 66,945 controls in European discovery; 42,475 cases and 192,050 controls in replication across ancestries) using

en-us

00:36:58

294: Alternative splicing, exonization and...

Base by Base ·

2026/02/18

Hunter CE et al., The EMBO Journal - Review shows how alternative splicing, via TE exonization and cis-regulatory changes and revealed by long-read RNA-seq, reshapes gene regulation and drives phenotypic evolution in mammals. Study Highlights:This review synthesizes comparative transcriptomic studies across multicellular eukaryotes with emphasis on vertebrates and mammals. It highlights methods including short- and long-read RNA-seq, single-cell

en-us

00:36:58

294: Alternative splicing, exonization and...

Base by Base ·

2026/02/18

Hunter CE et al., The EMBO Journal - Review shows how alternative splicing, via TE exonization and cis-regulatory changes and revealed by long-read RNA-seq, reshapes gene regulation and drives phenotypic evolution in mammals. Study Highlights:This review synthesizes comparative transcriptomic studies across multicellular eukaryotes with emphasis on vertebrates and mammals. It highlights methods including short- and long-read RNA-seq, single-cell

en-us

00:17:53

293: IndeLLM (ESM2) zero-shot scoring and Siamese...

Base by Base ·

2026/02/17

Gracia Carmona O et al., Patterns. 7 ( - IndeLLM uses protein language models (ESM2) to score in-frame indels and a compact Siamese transfer-learning model that achieves state-of-the-art pathogenicity prediction with MCC = 0.77. Study Highlights:Using human protein sequences and ESM2 embeddings, the authors develop IndeLLM, a zero-shot scoring function that sums overlapping-region probabilities to correct length bias in in-frame indels. They train a

en-us

00:17:53

293: IndeLLM (ESM2) zero-shot scoring and Siamese...

Base by Base ·

2026/02/17

Gracia Carmona O et al., Patterns. 7 ( - IndeLLM uses protein language models (ESM2) to score in-frame indels and a compact Siamese transfer-learning model that achieves state-of-the-art pathogenicity prediction with MCC = 0.77. Study Highlights:Using human protein sequences and ESM2 embeddings, the authors develop IndeLLM, a zero-shot scoring function that sums overlapping-region probabilities to correct length bias in in-frame indels. They train a

en-us

00:17:09

292: INS R6C signal-peptide defect reduces...

Base by Base ·

2026/02/17

Tong Y et al., EMBO Molecular Medicine - Patient data, population genetics and iPSC-derived βcell models show INS R6C impairs preproinsulin ER translocation and causes recessive insulin-deficient diabetes in homozygotes. Study Highlights:The study integrates clinical pedigrees, large-scale population screens and patient-derived iPSC βcell models, plus in vivo transplantation and transcriptomics. AlphaFold 3 structural modeling suggested weakened SRP54

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00:06:39

291: Dated gene duplications show Asgard archaeal...

Base by Base ·

2026/02/15

Kay CJ et al., Nature 650, 129–140 ( - Relaxed-clock dating of pre-LECA gene duplications in Asgard archaeal and alphaproteobacterial lineages shows a complex archaeal host with cytoskeleton, endomembrane system and nucleus before mitochondrial acquisition around 2.2 Ga. Study Highlights:The study interrogates eukaryogenesis using a time-resolved species tree and a sequential Bayesian relaxed molecular clock applied to 135 gene family trees. Analyses

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00:19:31

290: SMN1 p.Arg288AlafsTer5 exon 7 deletions evade...

Base by Base ·

2026/02/14

Wirth B et al., The American Journal of Human Genetics - Two SMN1 exon 7 4-bp deletions (p.Arg288AlafsTer5) evade standard PCR newborn screening but produce a low-abundance, thermostable SMN protein that functionally rescues smn1-deficient zebrafish and averted therapy. Study Highlights:In two clinically healthy newborns flagged as lacking SMN1 by PCR-based NBS, long-range SMN1-specific PCR, Sanger sequencing, MLPA and ddPCR identified distinct 4-bp exon

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00:16:18

289: MinION detection of chimeric reads in murine...

Base by Base ·

2026/02/13

White R et al., F1000Research - Nanopore MinION sequencing of murine Ifna, Ifnb and Actb amplicons identified post-amplification chimeric reads during library ligation, with ~1.7% of mapped reads containing chimeric elements. Study Highlights: cDNA from a Nippostrongylus brasiliensis–treated mouse amplified for Ifna family, Ifnb and Actb amplicons. Key methods: separate PCR amplicons were barcoded, ligated using two methods (quick vs overnight), sequenced

en-us

00:16:18

289: MinION detection of chimeric reads in murine...

Base by Base ·

2026/02/13

White R et al., F1000Research - Nanopore MinION sequencing of murine Ifna, Ifnb and Actb amplicons identified post-amplification chimeric reads during library ligation, with ~1.7% of mapped reads containing chimeric elements. Study Highlights: cDNA from a Nippostrongylus brasiliensis–treated mouse amplified for Ifna family, Ifnb and Actb amplicons. Key methods: separate PCR amplicons were barcoded, ligated using two methods (quick vs overnight), sequenced

en-us

00:16:55

288: Cryo-EM of rat cerebellar α1/α6 GABAA receptors...

Base by Base ·

2026/02/12

Sun C et al., PNAS - Using cryo-EM and mass spectrometry in rat cerebellum, α1- and α6-containing GABAA receptor assemblies (β‑α‑β‑α‑γ stoichiometry) and PZ-II-029 binding were defined. Study Highlights:The study used rat cerebellum tissue and combined confocal immunofluorescence, affinity purification with mass spectrometry, and high-resolution cryo-EM to characterize native α1-containing GABAA receptors. Cryo-EM classification resolved eight distinct

en-us

00:16:55

288: Cryo-EM of rat cerebellar α1/α6 GABAA receptors...

Base by Base ·

2026/02/12

Sun C et al., PNAS - Using cryo-EM and mass spectrometry in rat cerebellum, α1- and α6-containing GABAA receptor assemblies (β‑α‑β‑α‑γ stoichiometry) and PZ-II-029 binding were defined. Study Highlights:The study used rat cerebellum tissue and combined confocal immunofluorescence, affinity purification with mass spectrometry, and high-resolution cryo-EM to characterize native α1-containing GABAA receptors. Cryo-EM classification resolved eight distinct

en-us

473 results

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