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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

00:25:03

🎙️ Episode 28: Cell-Type-Resolved TWAS — scPrediXcan...

Base by Base ·

2025/05/22

🎙️ Episode 28: Cell-Type-Resolved TWAS — scPrediXcan Integrates Deep Learning and Single-Cell Data for Transcriptome-Wide Association Studies🧬 In this episode of Base por Base, we explore the groundbreaking framework scPrediXcan introduced by Zhou et al. (2025) in Cell Genomics. This approach combines a deep learning–based model, ctPred, with single-cell RNA-seq data to predict cell-type-specific gene expression, and then linearizes those predictions into a SNP-based model, ℓ-ctPred, for use in

en-us

00:25:04

️ 28: Cell-Type-Resolved TWAS — scPrediXcan...

Base by Base ·

2025/05/22

️ Episode 28: Cell-Type-Resolved TWAS — scPrediXcan Integrates Deep Learning and Single-Cell Data for Transcriptome-Wide Association Studies In this episode of Base por Base, we explore the groundbreaking framework scPrediXcan introduced by Zhou et al. (2025) in Cell Genomics. This approach combines a deep learning–based model, ctPred, with single-cell RNA-seq data to predict cell-type-specific gene expression, and then linearizes those predictions into a

en-us

00:16:20

️ 27: Nucleocytosolic Vehicles — A CRISPR RNP...

Base by Base ·

2025/05/21

️ Episode 27: Nucleocytosolic Vehicles — A CRISPR RNP Delivery Breakthrough In this episode of Base by Base, we delve into a novel virus-like particle (VLP) platform, ENVLPE, developed by Geilenkeuser et al. (2025) in Cell. This innovation harnesses nucleocytosolic shuttling and RNA aptamer recruitment to efficiently package and deliver fully assembled CRISPR ribonucleoproteins (RNPs), overcoming spatial and loading limitations of previous VLP approaches

en-us

00:16:19

🎙️ Episode 27: Nucleocytosolic Vehicles — A CRISPR...

Base by Base ·

2025/05/21

🎙️ Episode 27: Nucleocytosolic Vehicles — A CRISPR RNP Delivery Breakthrough🧬 In this episode of Base by Base, we delve into a novel virus-like particle (VLP) platform, ENVLPE, developed by Geilenkeuser et al. (2025) in Cell. This innovation harnesses nucleocytosolic shuttling and RNA aptamer recruitment to efficiently package and deliver fully assembled CRISPR ribonucleoproteins (RNPs), overcoming spatial and loading limitations of previous VLP approaches.🔍 Main Highlights:The ENVLPE system

en-us

00:15:49

️ 26: Reannotation in Focus — Uncovering Functional...

Base by Base ·

2025/05/20

️ Episode 26: Reannotation in Focus — Uncovering Functional Non-Coding Mutations in Melanoma In this episode of Base por Base, we delve into a breakthrough study by Pepe et al. (2025) in The American Journal of Human Genetics that challenges conventional cancer mutation annotation. The authors present an automated pipeline combining RNA-seq–based transcript quantification and Ensembl VEP reannotation to map somatic variants to the transcripts actually

en-us

00:15:48

🎙️ Episode 26: Reannotation in Focus — Uncovering...

Base by Base ·

2025/05/20

🎙️ Episode 26: Reannotation in Focus — Uncovering Functional Non-Coding Mutations in Melanoma🧬 In this episode of Base por Base, we delve into a breakthrough study by Pepe et al. (2025) in The American Journal of Human Genetics that challenges conventional cancer mutation annotation. The authors present an automated pipeline combining RNA-seq–based transcript quantification and Ensembl VEP reannotation to map somatic variants to the transcripts actually expressed in melanoma tumors. By integrating

en-us

00:16:21

️ 25: Uncovering Mitochondrial DNA Diseases — The...

Base by Base ·

2025/05/19

️ Episode 25: Uncovering Mitochondrial DNA Diseases — The Solve-RD Experience with Genotype and Phenotype Integration In this episode of Base por Base, we delve into a groundbreaking study by Ratnaike et al. (2025) published in The American Journal of Human Genetics, which presents a semi-automated workflow combining mtDNA variant filtering and MitoPhen-based HPO phenotype similarity scoring applied to exome and genome data from the Solve-RD cohort of

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00:16:20

🎙️ Episode 25: Uncovering Mitochondrial DNA Diseases...

Base by Base ·

2025/05/19

🎙️ Episode 25: Uncovering Mitochondrial DNA Diseases — The Solve-RD Experience with Genotype and Phenotype Integration🧬 In this episode of Base por Base, we delve into a groundbreaking study by Ratnaike et al. (2025) published in The American Journal of Human Genetics, which presents a semi-automated workflow combining mtDNA variant filtering and MitoPhen-based HPO phenotype similarity scoring applied to exome and genome data from the Solve-RD cohort of undiagnosed rare disease cases .🔍 Study

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00:14:52

🎙️ Episode 24: The Role of the X Chromosome in...

Base by Base ·

2025/05/18

🎙️ Episode 24: The Role of the X Chromosome in Complex Trait Genetics — Unraveling Dosage-Compensation Mechanisms🧬 In this installment of Base por Base, we delve into groundbreaking work by Fu et al. (2025) in The American Journal of Human Genetics, which systematically interrogates how the X chromosome shapes human quantitative traits. Leveraging data from over 350,000 UK Biobank participants with replication in more than 400,000 FinnGen individuals, the study quantifies the X chromosome’s

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00:14:53

️ 24: The Role of the X Chromosome in Complex Trait...

Base by Base ·

2025/05/18

️ Episode 24: The Role of the X Chromosome in Complex Trait Genetics — Unraveling Dosage-Compensation Mechanisms In this installment of Base por Base, we delve into groundbreaking work by Fu et al. (2025) in The American Journal of Human Genetics, which systematically interrogates how the X chromosome shapes human quantitative traits. Leveraging data from over 350,000 UK Biobank participants with replication in more than 400,000 FinnGen individuals, the

en-us

00:14:12

️ 23: Evaluating the Return of Additional Findings...

Base by Base ·

2025/05/17

️ Episode 23: Evaluating the Return of Additional Findings from the 100,000 Genomes Project — Participant Experiences of Secondary Genomic Findings In this episode of Base por Base, we explore a mixed-methods study by Stafford-Smith et al. (2025) published in Genetics in Medicine, which examines how participants in England’s 100,000 Genomes Project experienced the disclosure of additional (secondary) genomic findings. By combining a cross-sectional survey

en-us

00:14:11

🎙️ Episode 23: Evaluating the Return of Additional...

Base by Base ·

2025/05/17

🎙️ Episode 23: Evaluating the Return of Additional Findings from the 100,000 Genomes Project — Participant Experiences of Secondary Genomic Findings🧬 In this episode of Base por Base, we explore a mixed-methods study by Stafford-Smith et al. (2025) published in Genetics in Medicine, which examines how participants in England’s 100,000 Genomes Project experienced the disclosure of additional (secondary) genomic findings. By combining a cross-sectional survey of 147 adults who received either

en-us

00:16:24

️ 22: Immune Sensing Unveiled — Ribonuclease Control...

Base by Base ·

2025/05/16

️ Episode 22: Immune Sensing Unveiled — Ribonuclease Control of Naked Extracellular RNA In this episode of Base por Base, we explore a landmark study by Castellano et al. (2025) published in Cell Genomics that uncovers how extracellular ribonucleases regulate the immune detection and functional uptake of naked extracellular RNA (exRNA). Through strategic use of a broad-spectrum ribonuclease inhibitor, the authors demonstrate that, contrary to long-held

en-us

00:16:23

🎙️ Episode 22: Immune Sensing Unveiled — Ribonuclease...

Base by Base ·

2025/05/16

🎙️ Episode 22: Immune Sensing Unveiled — Ribonuclease Control of Naked Extracellular RNA🧬 In this episode of Base por Base, we explore a landmark study by Castellano et al. (2025) published in Cell Genomics that uncovers how extracellular ribonucleases regulate the immune detection and functional uptake of naked extracellular RNA (exRNA). Through strategic use of a broad-spectrum ribonuclease inhibitor, the authors demonstrate that, contrary to long-held assumptions, naked exRNAs can be

en-us

00:17:04

🎙️ Episode 21: High-Throughput Variant Discovery —...

Base by Base ·

2025/05/16

🎙️ Episode 21: High-Throughput Variant Discovery — Pooled Prime Editing in Human Cells🧬 In this episode of Base by Base, we explore a cutting-edge platform for scalable functional screening of human genetic variants reported by Herger et al. (2025) in Cell Genomics. The study introduces a pooled prime editing workflow in haploid HAP1 cells that optimizes pegRNA scaffold design, employs co-selection via an ATP1A1 resistance mutation, and integrates surrogate targets to enrich and filter highly

en-us

00:17:05

️ 21: High-Throughput Variant Discovery — Pooled...

Base by Base ·

2025/05/16

️ Episode 21: High-Throughput Variant Discovery — Pooled Prime Editing in Human Cells In this episode of Base by Base, we explore a cutting-edge platform for scalable functional screening of human genetic variants reported by Herger et al. (2025) in Cell Genomics. The study introduces a pooled prime editing workflow in haploid HAP1 cells that optimizes pegRNA scaffold design, employs co-selection via an ATP1A1 resistance mutation, and integrates surrogate

en-us

00:15:28

🎙️ Episode 20: Genotype-Specific Chemoprevention with...

Base by Base ·

2025/05/16

🎙️ Episode 20: Genotype-Specific Chemoprevention with Sulfadoxine-Pyrimethamine🧬 In this episode of Base by Base, we examine a comprehensive analysis by Mousa et al. (2025) in Nature Communications that quantifies how mutations in the Plasmodium falciparum dihydropteroate synthase (dhps) gene affect the duration of protection conferred by sulfadoxine-pyrimethamine (SP) chemoprevention across Africa. A Bayesian multi-strain model was applied to reinfection data from seven therapeutic efficacy

en-us

00:15:29

️ 20: Genotype-Specific Chemoprevention with...

Base by Base ·

2025/05/16

️ Episode 20: Genotype-Specific Chemoprevention with Sulfadoxine-Pyrimethamine In this episode of Base by Base, we examine a comprehensive analysis by Mousa et al. (2025) in Nature Communications that quantifies how mutations in the Plasmodium falciparum dihydropteroate synthase (dhps) gene affect the duration of protection conferred by sulfadoxine-pyrimethamine (SP) chemoprevention across Africa. A Bayesian multi-strain model was applied to reinfection

en-us

00:18:18

️ 19: Systematic Identification of Promoter and UTR...

Base by Base ·

2025/05/14

️ Episode 19: Systematic Identification of Promoter and UTR Variants in Rare Disease Diagnostics In this episode of Base by Base, we delve into Martin-Geary et al.’s (2025) innovative framework for uncovering disease-causing variants within promoters and untranslated regions (UTRs) in individuals with rare disorders. Leveraging genome sequencing data from 8,040 undiagnosed trios in the Genomics England 100,000 Genomes Project, the authors combine precise

en-us

00:18:16

🎙️ Episode 19: Systematic Identification of Promoter...

Base by Base ·

2025/05/14

🎙️ Episode 19: Systematic Identification of Promoter and UTR Variants in Rare Disease Diagnostics🧬 In this episode of Base by Base, we delve into Martin-Geary et al.’s (2025) innovative framework for uncovering disease-causing variants within promoters and untranslated regions (UTRs) in individuals with rare disorders. Leveraging genome sequencing data from 8,040 undiagnosed trios in the Genomics England 100,000 Genomes Project, the authors combine precise region definitions based on MANE

en-us

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