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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

00:16:21

151: EQA of ctDNA Mutation Testing Across the COIN...

Base by Base ·

2025/09/28

️ Episode 151: EQA of ctDNA Mutation Testing Across the COIN Consortium In this episode of PaperCast Base by Base, we explore how 16 Dutch laboratories evaluated their real‑world workflows for circulating tumor DNA (ctDNA) mutation testing across BRAF, EGFR, and KRAS using a coordinated external quality assessment within the COIN consortium. Study Highlights:The team distributed six plasma samples—three commercial references with predefined variants and

en-us

00:17:52

150: Patrilineal segmentary systems and the...

Base by Base ·

2025/09/27

️ Episode 150: Patrilineal segmentary systems and the post‑Neolithic Y‑chromosome bottleneck In this episode of PaperCast Base by Base, we explore a Nature Communications study that proposes a peaceful, socio‑cultural explanation for the sharp decline in male effective population size observed 3,000–5,000 years ago. Instead of widespread violence, the authors show that the dynamics of patrilineal segmentary systems—where lineages split and reproductive

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00:15:04

149: Cultural Hitchhiking and the Post‑Neolithic...

Base by Base ·

2025/09/26

️ Episode 149: Cultural Hitchhiking and the Post‑Neolithic Y‑Chromosome Bottleneck In this episode of PaperCast Base by Base, we explore how patrilineal social structures and intergroup competition can reshape genetic diversity, offering a cultural explanation for the striking male‑specific bottleneck observed 5,000–7,000 years ago across the Old World. Study Highlights:The authors synthesize anthropological theory, population genomics, and mathematical

en-us

00:14:44

148: Systematic Minigene-Based Splicing Analysis and...

Base by Base ·

2025/09/25

️ Episode 148: Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants In this episode of PaperCast Base by Base, we explore a comprehensive functional assessment of splice-site variants in CHEK2 using reporter minigenes, revealing how disrupted pre-mRNA splicing contributes to hereditary breast cancer risk and how these readouts can support clinical variant classification. Study Highlights:The

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00:15:37

147: Comprehensive Annotation of Complete ABO Alleles...

Base by Base ·

2025/09/24

️ Episode 147: Comprehensive Annotation of Complete ABO Alleles and Resolution of ABO Variants In this episode of PaperCast Base by Base, we explore a groundbreaking study that introduces an improved long-read sequencing method to fully resolve ABO haplotypes, spanning from the 5′ to the 3′ untranslated regions. This work addresses a major gap in blood group genomics by delivering the most comprehensive annotation of complete ABO alleles to date. Study

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00:15:56

146: Automated and Decentralized Genomic Profiling of...

Base by Base ·

2025/09/23

️ Episode 146: Automated and Decentralized Genomic Profiling of Plasma Cell-Free DNA in Solid Tumors In this episode of PaperCast Base by Base, we explore the clinical feasibility of an automated and decentralized cfDNA sequencing system designed to identify actionable and resistance alterations in advanced solid tumors. Study Highlights:Researchers evaluated plasma cfDNA from 298 patients with advanced cancers using the Oncomine Precision Assay GX and

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00:16:59

145: A Validated Highly Sensitive Microsatellite...

Base by Base ·

2025/09/22

️ Episode 145: A Validated Highly Sensitive Microsatellite Instability Assay Identifies PMS2 Variants in CMMRD In this episode of PaperCast Base by Base, we explore a study that validates a next-generation sequencing-based highly sensitive microsatellite instability (hs-MSI) assay for the diagnosis of constitutional mismatch repair deficiency (CMMRD), a rare childhood-onset cancer predisposition syndrome. The work focuses on improving detection of PMS2

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00:17:10

144: Revised time estimation of the ancestral human...

Base by Base ·

2025/09/21

️ Episode 144: Revised time estimation of the ancestral human chromosome 2 fusion In this episode of PaperCast Base by Base, we explore a study that revisits one of the most defining events in human evolution: the fusion that gave rise to chromosome 2. This work refines previous estimates and provides a clearer timeline for when this pivotal genomic change occurred. Study Highlights:The authors developed an improved algorithm to analyze biased clustered

en-us

00:17:10

144: Revised time estimation of the ancestral human...

Base by Base ·

2025/09/21

️ Episode 144: Revised time estimation of the ancestral human chromosome 2 fusion In this episode of PaperCast Base by Base, we explore a study that revisits one of the most defining events in human evolution: the fusion that gave rise to chromosome 2. This work refines previous estimates and provides a clearer timeline for when this pivotal genomic change occurred. Study Highlights:The authors developed an improved algorithm to analyze biased clustered

en-us

00:18:56

143: The genetic history of the Southern Caucasus:...

Base by Base ·

2025/09/20

️ Episode 143: The genetic history of the Southern Caucasus: 5,000 years of continuity despite high mobility In this episode of PaperCast Base by Base, we explore a comprehensive archaeogenomic study tracing 230 ancient individuals from Georgia and Armenia over 5,000 years, from the Bronze Age to the Early Middle Ages. The research investigates how extensive mobility and cultural interactions shaped the genetic landscape of the Southern Caucasus. Study

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00:16:35

142: Specifications of the ACMG/AMP Guidelines for...

Base by Base ·

2025/09/19

️ Episode 142: Specifications of the ACMG/AMP Guidelines for PALB2 Variant Interpretation In this episode of PaperCast Base by Base, we explore how the Hereditary Breast, Ovarian, and Pancreatic Cancer Variant Curation Expert Panel (HBOP VCEP) developed gene-specific ACMG/AMP guidelines for the interpretation of PALB2 germline sequence variants, a key gene in hereditary cancer syndromes. Study Highlights:The HBOP VCEP assembled an international team of

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00:26:12

141: RetiGene, a comprehensive gene atlas for...

Base by Base ·

2025/09/18

️ Episode 141: RetiGene, a comprehensive gene atlas for inherited retinal diseases In this episode of PaperCast Base by Base, we explore RetiGene, an expert-curated resource that consolidates genetic, transcriptomic, and functional information on inherited retinal diseases (IRDs). The study highlights the urgent need for a unified gene catalog to guide diagnosis and research in one of the most genetically heterogeneous groups of human disorders. Study

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00:20:18

140: Landscapes of missense variant impact for human...

Base by Base ·

2025/09/17

️ Episode 140: Landscapes of missense variant impact for human superoxide dismutase 1 In this episode of PaperCast Base by Base, we explore a large-scale functional analysis of missense variants in SOD1, a key gene implicated in amyotrophic lateral sclerosis (ALS). The study addresses the challenge of classifying variants of uncertain significance by systematically testing their functional impact across nearly all possible amino acid substitutions.

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00:14:03

139: MosCoverY: A new method to estimate mosaic loss...

Base by Base ·

2025/09/16

️ Episode 139: MosCoverY: A new method to estimate mosaic loss of Y chromosome from sequencing coverage data In this episode of PaperCast Base by Base, we explore the development of MosCoverY, a computational method designed to detect and quantify mosaic loss of the Y chromosome (mLOY) from exome and whole-genome sequencing data. This condition, the most common somatic mutation in men, is strongly linked with aging and several diseases. Study

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00:19:43

138: Social exposome and brain health outcomes of...

Base by Base ·

2025/09/15

️ Episode 138: Social exposome and brain health outcomes of dementia across Latin America In this episode of PaperCast Base by Base, we explore how a multidimensional social exposome across the lifespan—covering education, food insecurity, financial status, assets, access to healthcare, childhood labor, subjective socioeconomic status, childhood experiences, traumatic events, and relationships—relates to brain health and dementia outcomes in Latin

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00:25:11

137: Rethinking RNA-binding proteins: Riboregulation...

Base by Base ·

2025/09/14

️ Episode 137: Rethinking RNA-binding proteins: Riboregulation challenges prevailing views In this episode of PaperCast Base by Base, we explore how a sweeping expansion of the RNA-binding proteome has reframed long‑held assumptions about RNA–protein interactions, spotlighting ‘non‑canonical’ RBPs and the emerging concept of riboregulation—RNA directly regulating protein function. Study Highlights:The authors synthesize discovery platforms that tripled

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00:25:11

137: Rethinking RNA-binding proteins: Riboregulation...

Base by Base ·

2025/09/14

️ Episode 137: Rethinking RNA-binding proteins: Riboregulation challenges prevailing views In this episode of PaperCast Base by Base, we explore how a sweeping expansion of the RNA-binding proteome has reframed long‑held assumptions about RNA–protein interactions, spotlighting ‘non‑canonical’ RBPs and the emerging concept of riboregulation—RNA directly regulating protein function. Study Highlights:The authors synthesize discovery platforms that tripled

en-us

00:14:48

136: Gene Context Drift Identifies Drug Targets to...

Base by Base ·

2025/09/13

️ Episode 136: Gene Context Drift Identifies Drug Targets to Mitigate Cancer Treatment Resistance In this episode of PaperCast Base by Base, we explore RECODR, a graph‑embedding pipeline that reads single‑cell and single‑nucleus transcriptomes as co‑expression networks to quantify “gene context drift” during therapy and expose druggable vulnerabilities that drive relapse across aggressive cancers. Study Highlights:RECODR constructs co‑expression graph

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00:14:26

135: Global impact of micronutrients in modern human...

Base by Base ·

2025/09/12

️ Episode 135: Global impact of micronutrients in modern human evolution In this episode of PaperCast Base by Base, we explore how dietary micronutrients have influenced modern human evolution. The study investigates the role of essential minerals in shaping genetic adaptation and highlights the health risks posed by imbalances in micronutrient availability worldwide. Study Highlights:Researchers analyzed 276 genes linked to 13 micronutrients across 40

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00:15:47

134: Single-Cell Maps Link Intestinal Metaplasia to...

Base by Base ·

2025/09/11

️ Episode 134: Single-Cell Maps Link Intestinal Metaplasia to Esophageal Adenocarcinoma Risk In this episode of PaperCast Base by Base, we explore how single-cell RNA sequencing of Barrett’s esophagus (BE), esophageal adenocarcinoma (EAC), and matched normal tissues reveals which cell types carry germline-linked risk and shape progression toward cancer. Study Highlights:The authors profiled epithelial, stromal, endothelial, and immune cells with 10x

en-us

456 results

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